Improve argument handling and clean up unecessary files

auto_namd_python/functions.py

@@ -1,28 +0,0 @@
-import os
-import re
-import argparse
-
-# Natural sort
-def natural_key(string_):
-    return [int(s) if s.isdigit() else s for s in re.split(r'(\d+)', string_)]
-
-# Return absolute path from relative or absolute path
-def abs_path(path):
-    abs_path = os.path.abspath(path)
-    return abs_path
-
-# Input argument parser
-def parser():
-    parser = argparse.ArgumentParser()
-    parser.add_argument('--steps', type=int,
-                    help='Number of timesteps to run the simulation')
-    parser.add_argument('--jobs_path', type=str, nargs='+', action='append',
-                    help='Directory path containing the jobs to be run')
-    parser.add_argument('--namd_params', type=str,
-                    help='Optional parameters to send to namd')
-    parser.add_argument('--ffs_path', type=str,
-                    help='Location of the forcefield files')
-    parser.add_argument('--namd2_bin', type=str,
-                    help='Location of the namd2 executable')
-    args = parser.parse_args()
-    return args

auto_namd_python/job.py

@@ -1,163 +0,0 @@
-import os
-import sys
-import glob
-
-from auto_namd_python.functions import natural_key, abs_path
-
-class Job:
-    """
-    A class that represents a job/system residing in a unique directory path
-
-    Attributes:
-    self.path = absolute job directory path
-    self.name = name of the job, derived from parent directory
-    self.prefix = self.path + self.name
-    self.pdb = latest .pdb file
-    self.psf = latest .psf file
-    self.coor = latest .coor file
-    self.stage = current simulation stage
-    self.step = current simulation steps
-
-    Calling prepare_sim() assigns the additional instance variables:
-
-    self.steps = number of steps to run the simulation
-    self.ffs = a list of forcefield files for the simulation
-    self.next_stage = next simulation stage to be run
-    self.next_step = final simulation steps after simulation cycle
-    self.conf, self.out = the configuration file and the simulation output filenames
-    """
-
-    def __init__(self, path):
-        self.set_empty_vars()
-        self.path = path
-        self.name = self.get_job_name()
-        self.prefix = os.path.join(self.path, self.name)
-        self.pdb, self.psf = self.get_pdb_and_psf()
-        self.stage, self.step, self.coor = self.get_stage()
-
-
-    def set_empty_vars(self):
-        self.pdb, self.psf = '', ''
-        self.steps = ''
-        self.ffs_path, self.ffs = '', ''
-        self.next_stage, self.next_step = '', ''
-        self.conf, self.out = '', ''
-
-
-    def get_job_name(self):
-        '''Get job name from path'''
-        name = os.path.basename(self.path)
-        return name
-
-
-    def get_pdb_and_psf(self):
-        pdb = glob.glob(f'{self.prefix}*_solv_ion.pdb')
-        psf = glob.glob(f'{self.prefix}*_solv_ion.psf')
-        if len(pdb) == 1 and len(psf) == 1:
-            return pdb[0], psf[0]
-        pdb = glob.glob(f'{self.prefix}.pdb')
-        psf = glob.glob(f'{self.prefix}.psf')
-        if len(pdb) == 1 and len(psf) == 1:
-            return pdb[0], psf[0]
-        else:
-            print('No PDB or PSF files found, exiting...')
-            sys.exit(1)
-
-
-    def get_stage(self):
-        coors_path = self.prefix + '*.coor'
-        coors = glob.glob(coors_path)
-        coors.sort(key=natural_key)
-        if len(coors) >= 1:
-            coor = coors[-1]
-            stage = coor.split('_')[-2].split('.')[0]
-            step = int(coor.split('_')[-1].split('.')[0])
-        else:
-            coor = ''
-            stage = ''
-            step = 0
-        return stage, int(step), coor
-
-
-    def prepare_sim(self, ffs_path, steps):
-        self.steps = steps
-        self.ffs_path = abs_path(ffs_path)
-        self.ffs = self.get_ffs()
-        self.next_stage, self.next_step = self.get_next_stage()
-        self.conf, self.out = self.conf_out_file()
-
-
-    def get_next_stage(self):
-        if self.stage == '4-sim':
-            next_stage = '4-sim'
-            next_step = self.step + self.steps
-        elif self.stage == '3-heat':
-            next_stage = '4-sim'
-            next_step = steps
-        elif self.stage == '2-min':
-            next_stage = '3-heat'
-            next_step = 0
-        elif self.stage == '1-min':
-            next_stage = '2-min'
-            next_step = 0
-        elif self.stage == '':
-            next_stage = '1-min'
-            next_step = 0
-        return next_stage, int(next_step)
-
-
-    def get_ffs(self):
-        ffs = glob.glob(os.path.join(self.ffs_path, '*'))
-        return ffs
-
-
-    def conf_out_file(self):
-        if self.next_stage == '4-sim':
-            conf = f'{self.prefix}_{self.next_stage}' \
-                        f'_{str(self.next_step)}.conf'
-            out = f'{self.prefix}_{self.next_stage}' \
-                       f'_{str(self.next_step)}.out'
-        else:
-            conf = f'{self.prefix}_{self.next_stage}.conf'
-            out = f'{self.prefix}_{self.next_stage}.out'
-
-        return conf, out
-
-
-    def info(self):
-        print(f'Job Path: {self.path}\n'
-              f'Name: {self.name}\n'
-              f'Working PDB: {self.pdb}\n'
-              f'Working PSF: {self.psf}\n'
-              f'Previous Step: {self.stage}\n'
-              f'Previous Step Number: {str(self.step)}\n'
-              f'Next Stage: {self.next_stage}\n'
-              f'Next Step Number: {str(self.next_step)}\n'
-              f'FF Path: {self.ffs_path}\n'
-              f'FFs: {self.ffs}\n'
-              )
-
-
-
-def get_jobs_from_path(jobs_path):
-    jobs_path += '/**/*.pdb'
-    job_dirs = glob.glob(jobs_path, recursive=True)
-    job_dirs_l = []
-    for job_dir in job_dirs:
-        job_dirs_l.append(os.path.dirname(job_dir))
-    if len(job_dirs_l) < 1:
-        print('No valid jobs found in jobs path!')
-        sys.exit(1)
-    return job_dirs_l
-
-
-def get_next_job(jobs):
-    jobs.sort(key=lambda x: (x.stage, x.step))
-    return jobs[0]
-
-
-def create_job_instances(job_paths):
-    job_instances = []
-    for job_path in job_paths:
-        job_instances.append(Job(job_path))
-    return job_instances

auto_namd_python/simulate.py

@@ -1,285 +0,0 @@
-import subprocess as sp
-import vmd
-
-class Simulate:
-
-    def __init__(self, job, namdbin, params):
-        self.prepare(job)
-        self.run_namd(job, namdbin, params)
-
-    def prepare(self, job):
-        if job.next_stage == '1-min':
-            self.min1(job)
-        if job.next_stage == '2-min':
-            self.min2(job)
-        if job.next_stage == '3-heat':
-            self.heat(job)
-        if job.next_stage == '4-sim':
-            self.sim(job)
-
-    def run_namd(self, job, namdbin, params):
-        cmd = f'{namdbin} {params} {job.conf} > {job.out}'
-        print(f'Running: {cmd}')
-        p1 = sp.run(cmd, shell=True)
-
-    def monitor_namd(self):
-        pass
-
-    def min1(self, job):
-        steps = 15000
-        with open(job.conf, 'w') as conf:
-            conf.write('# Input\n')
-            conf.write(f'structure {job.psf}\n')
-            conf.write(f'coordinates {job.pdb}\n')
-            conf.write('paraTypeCharmm on\n')
-            for ff in job.ffs:
-              conf.write(f'parameters {ff}\n')
-            conf.write('\n')
-            conf.write('# Temperature\n')
-            conf.write('temperature 0\n')
-            conf.write('\n')
-            conf.write('# Force-Field Parameters\n')
-            conf.write('exclude scaled1-4\n')
-            conf.write('1-4scaling 1.0\n')
-            conf.write('cutoff 12.\n')
-            conf.write('switching on\n')
-            conf.write('switchdist 10.\n')
-            conf.write('pairlistdist 14\n')
-            conf.write('\n')
-            conf.write('# Integrator Parameters\n')
-            conf.write('timestep 1.0  ;# 1fs/step\n')
-            conf.write('nonbondedFreq 1\n')
-            conf.write('fullElectFrequency 2\n')
-            conf.write('stepspercycle 10\n')
-            conf.write('\n')
-            conf.write('# Output\n')
-            conf.write(f'outputName {job.name}_{job.next_stage}_{steps}\n')
-            conf.write('outputEnergies 100\n')
-            conf.write('outputPressure 100\n')
-            conf.write('\n')
-            conf.write('# Run\n')
-            conf.write(f'minimize {steps}')
-
-    def min2(self, job):
-        solv_ion(job)
-        cbvx, cbvy, cbvz, corx, cory, corz = calc_pcell(job)
-        steps = 15000
-        with open(job.conf, 'w') as conf:
-            conf.write('# Input\n')
-            conf.write(f'structure {job.psf}\n')
-            conf.write(f'coordinates {job.pdb}\n')
-            conf.write('paraTypeCharmm on\n')
-            for ff in job.ffs:
-              conf.write(f'parameters {ff}\n')
-            conf.write('\n')
-            conf.write('# Temperature\n')
-            conf.write('temperature 0\n')
-            conf.write('\n')
-            conf.write('# Periodic Boundary Conditions\n')
-            conf.write('wrapWater on\n')
-            conf.write('wrapAll on\n')
-            conf.write(f'cellOrigin\t{corx}\t{cory}\t{corz}\n')
-            conf.write(f'cellBasisVector1\t{cbvx}\t0.0\t0.0\n')
-            conf.write(f'cellBasisVector2\t0.0\t{cbvy}\t0.0\n')
-            conf.write(f'cellBasisVector3\t0.0\t0.0\t{cbvz}\n')
-            conf.write('\n')
-            conf.write('# Force-Field Parameters\n')
-            conf.write('exclude scaled1-4\n')
-            conf.write('1-4scaling 1.0\n')
-            conf.write('cutoff 12.\n')
-            conf.write('switching on\n')
-            conf.write('switchdist 10.\n')
-            conf.write('pairlistdist 14\n')
-            conf.write('\n')
-            conf.write('# Integrator Parameters\n')
-            conf.write('timestep 1.0  ;# 1fs/step\n')
-            conf.write('nonbondedFreq 1\n')
-            conf.write('fullElectFrequency 2\n')
-            conf.write('stepspercycle 10\n')
-            conf.write('\n')
-            conf.write('# Output\n')
-            conf.write(f'outputName {job.name}_{job.next_stage}_{steps}\n')
-            conf.write('outputEnergies 100\n')
-            conf.write('outputPressure 100\n')
-            conf.write('\n')
-            conf.write('# Run\n')
-            conf.write(f'minimize {steps}')
-
-    def heat(self, job):
-        temp_reinit_steps = 100
-        steps = 10000
-        final_steps = 30 * temp_reinit_steps + steps
-        cbvx, cbvy, cbvz, corx, cory, corz = calc_pcell(job)
-        with open(job.conf, 'w') as conf:
-            conf.write('# Input\n')
-            conf.write(f'structure {job.psf}\n')
-            conf.write(f'coordinates {job.pdb}\n')
-            conf.write(f'bincoordinates {job.coor}\n')
-            conf.write('paraTypeCharmm on\n')
-            for ff in job.ffs:
-              conf.write(f'parameters {ff}\n')
-            conf.write('\n')
-            conf.write('# Temperature\n')
-            conf.write('temperature 0\n')
-            conf.write('\n')
-            conf.write('# Periodic Boundary Conditions\n')
-            conf.write('wrapWater on\n')
-            conf.write('wrapAll on\n')
-            conf.write(f'cellOrigin\t{corx}\t{cory}\t{corz}\n')
-            conf.write(f'cellBasisVector1\t{cbvx}\t0.0\t0.0\n')
-            conf.write(f'cellBasisVector2\t0.0\t{cbvy}\t0.0\n')
-            conf.write(f'cellBasisVector3\t0.0\t0.0\t{cbvz}\n')
-            conf.write('# Force-Field Parameters\n')
-            conf.write('exclude scaled1-4\n')
-            conf.write('1-4scaling 1.0\n')
-            conf.write('cutoff 12.\n')
-            conf.write('switching on\n')
-            conf.write('switchdist 10.\n')
-            conf.write('pairlistdist 14\n')
-            conf.write('\n')
-            conf.write('# Full Electrostatics\n')
-            conf.write('PME on\n')
-            conf.write('PMEGridSpacing 1.0\n')
-            conf.write('\n')
-            conf.write('# Integrator Parameters\n')
-            conf.write('timestep 1.0 ;# 1fs/step\n')
-            conf.write('nonbondedFreq 1\n')
-            conf.write('fullElectFrequency 2\n')
-            conf.write('stepspercycle 10\n')
-            conf.write('\n')
-            conf.write('# Output\n')
-            conf.write(f'outputName {job.name}_{job.next_stage}_{final_steps}\n')
-            conf.write('outputEnergies 100\n')
-            conf.write('outputPressure 100\n')
-            conf.write('dcdfreq 1000\n')
-            conf.write('\n')
-            conf.write('# Constant Temperature Control\n')
-            conf.write('langevin on ;# do langevin dynamics\n')
-            conf.write('langevinDamping 0.5 ;# damping coefficient (gamma) of 0.5/ps\n')
-            conf.write('langevinTemp 310\n')
-            conf.write('langevinHydrogen yes ;# couple langevin bath to hydrogens\n')
-            conf.write('\n')
-            conf.write('# Constant Pressure Control\n')
-            conf.write('useGroupPressure no ;# needed for 2fs steps\n')
-            conf.write('useFlexibleCell yes ;# no for water box, yes for membrane\n')
-            conf.write('useConstantRatio yes ;# no for water box, yes for membrane\n')
-            conf.write('langevinPiston on\n')
-            conf.write('langevinPistonTarget 1.01325 ;#  in bar -> 1 atm\n')
-            conf.write('langevinPistonPeriod 100.\n')
-            conf.write('langevinPistonDecay 50.\n')
-            conf.write('langevinPistonTemp 310\n')
-            conf.write('\n')
-            conf.write('# Run equilibration\n')
-            conf.write(f'set freq {temp_reinit_steps}\n')
-            conf.write('for {set i 10} {$i <= 310} {incr i 10} {\n')
-            conf.write('reinitvels $i\n')
-            conf.write('langevinTemp $i\n')
-            conf.write('run $freq\n')
-            conf.write('}\n')
-            conf.write('# Run stabilization\n')
-            conf.write(f'run {steps}')
-
-
-    def sim(self, job):
-        cbvx, cbvy, cbvz, corx, cory, corz = calc_pcell(job)
-        with open(job.conf, 'w') as conf:
-            conf.write('# Input\n')
-            conf.write(f'structure {job.psf}\n')
-            conf.write(f'coordinates {job.pdb}\n')
-            conf.write(f'bincoordinates {job.coor}\n')
-            conf.write('paraTypeCharmm on\n')
-            for ff in job.ffs:
-              conf.write(f'parameters {ff}\n')
-            conf.write('\n')
-            conf.write('# Temperature\n')
-            conf.write('temperature 0\n')
-            conf.write('\n')
-            conf.write('# Periodic Boundary Conditions\n')
-            conf.write('wrapWater on\n')
-            conf.write('wrapAll on\n')
-            conf.write(f'cellOrigin\t{corx}\t{cory}\t{corz}\n')
-            conf.write(f'cellBasisVector1\t{cbvx}\t0.0\t0.0\n')
-            conf.write(f'cellBasisVector2\t0.0\t{cbvy}\t0.0\n')
-            conf.write(f'cellBasisVector3\t0.0\t0.0\t{cbvz}\n')
-            conf.write('# Force-Field Parameters\n')
-            conf.write('exclude scaled1-4\n')
-            conf.write('1-4scaling 1.0\n')
-            conf.write('cutoff 12.\n')
-            conf.write('switching on\n')
-            conf.write('switchdist 10.\n')
-            conf.write('pairlistdist 14\n')
-            conf.write('\n')
-            conf.write('# Full Electrostatics\n')
-            conf.write('PME on\n')
-            conf.write('PMEGridSpacing 1.0\n')
-            conf.write('\n')
-            conf.write('# Integrator Parameters\n')
-            conf.write('timestep 2.0 ;# 2fs/step\n')
-            conf.write('rigidBonds all ;# needed for 2fs steps\n')
-            conf.write('nonbondedFreq 1\n')
-            conf.write('fullElectFrequency 2\n')
-            conf.write('stepspercycle 10\n')
-            conf.write('\n')
-            conf.write('# Output\n')
-            conf.write(f'outputName {job.name}_{job.next_stage}_{job.next_step}\n')
-            conf.write('outputEnergies 10000\n')
-            conf.write('outputPressure 10000\n')
-            conf.write('dcdfreq 10000\n')
-            conf.write('\n')
-            conf.write('# Constant Temperature Control\n')
-            conf.write('langevin on ;# do langevin dynamics\n')
-            conf.write('langevinDamping 0.5 ;# damping coefficient (gamma) of 0.5/ps\n')
-            conf.write('langevinTemp 310\n')
-            conf.write('langevinHydrogen no ;# couple langevin bath to hydrogens\n')
-            conf.write('\n')
-            conf.write('# Constant Pressure Control\n')
-            conf.write('useGroupPressure yes ;# needed for 2fs steps\n')
-            conf.write('useFlexibleCell yes ;# no for water box, yes for membrane\n')
-            conf.write('useConstantRatio yes ;# no for water box, yes for membrane\n')
-            conf.write('langevinPiston on\n')
-            conf.write('langevinPistonTarget 1.01325 ;#  in bar -> 1 atm\n')
-            conf.write('langevinPistonPeriod 100.\n')
-            conf.write('langevinPistonDecay 50.\n')
-            conf.write('langevinPistonTemp 310\n')
-            conf.write('\n')
-            conf.write('# Run\n')
-            conf.write(f'run {job.steps}')
-
-
-def del_all_mols():
-    for mol in vmd.molecule.listall():
-        vmd.molecule.delete(mol)
-
-
-def solv_ion(job):
-    pdb_f = f'{job.prefix}_{job.stage}.pdb'
-    psf_f = f'{job.prefix}.psf'
-    solv_f = f'{job.prefix}_{job.stage}_solv'
-    solv_ion_f = f'{job.prefix}_{job.stage}_solv_ion'
-    molid = vmd.molecule.load('psf', psf_f, 'namdbin', job.coor)
-    vmd.molecule.write(molid, 'pdb', pdb_f)
-    vmd.evaltcl('package require solvate')
-    vmd.evaltcl(f'solvate {job.psf} {pdb_f} -o {solv_f} '
-            f'-s WT -x 13 -y 13 -z 13 +x 13 +y 13 +z 13 -b 2.4')
-    vmd.evaltcl('package require autoionize')
-    vmd.evaltcl(f'autoionize -psf {solv_f}.psf -pdb {solv_f}.pdb -o {solv_ion_f} '
-            f'-sc 0.15')
-    del_all_mols()
-
-
-def calc_pcell(job):
-    if job.next_stage == '2-min' or job.next_stage == '3-min':
-        molid = vmd.molecule.load('psf', job.psf, 'pdb', job.pdb)
-    else:
-        molid = vmd.molecule.load('psf', job.psf, 'namdbin', job.coor)
-    all = vmd.atomsel("all", molid=molid)
-    minmax = all.minmax()
-    center = all.center()
-    cbvx = minmax[1][0] - minmax[0][0]
-    cbvy = minmax[1][1] - minmax[0][1]
-    cbvz = minmax[1][2] - minmax[0][2]
-    corx = center[0]
-    cory = center[1]
-    corz = center[2]
-    del_all_mols()
-    return cbvx, cbvy, cbvz, corx, cory, corz

run.py

@@ -1,40 +0,0 @@
-#!/usr/bin/env python3
-
-import glob
-import os
-
-from auto_namd_python.job import get_next_job, get_jobs_from_path, create_job_instances
-from auto_namd_python.simulate import Simulate
-from auto_namd_python.functions import abs_path, parser
-
-
-def main(jobs_path, ffs_path, steps, namdbin, params):
-
-    jobs_path = abs_path(jobs_path)
-    job_dirs_l = get_jobs_from_path(jobs_path)
-    jobs = create_job_instances(job_dirs_l)
-    job = get_next_job(jobs)
-    job.prepare_sim(ffs_path, steps)
-    job.info()
-    Simulate(job, namdbin, params)
-
-
-if __name__ == '__main__':
-
-    args = parser()
-
-    if args.jobs_path is not None and os.path.isdir(args.jobs_path):
-        jobs_path = args.jobs_path
-    else:
-        jobs_path = '/home/bryan/MD/CFTR/4-jobs'
-
-    if args.namd_params is not None:
-        params = args.namd_params
-    else:
-        params = '+p7'
-
-    main(jobs_path=jobs_path,
-         ffs_path='/home/bryan/MD/CFTR/0-forcefields',
-         steps=1000000,
-         namdbin='/home/bryan/bin/namd2',
-         params=params)

run_analysis.py

@@ -0,0 +1,16 @@
+#!/usr/bin/env python3
+
+from auto_namd.functions import analysis_parser
+from auto_namd.job import get_next_job, get_jobs_from_path, create_job_instances
+
+
+def main(jobs_path, ffs_path, steps, namdbin, params):
+
+    jobs_path = abs_path(jobs_path)
+    job_dirs_l = get_jobs_from_path(jobs_path)
+    jobs = create_job_instances(job_dirs_l)
+
+
+
+if __name__ == '__main__':
+    main()

run_simulation.py

@@ -0,0 +1,27 @@
+#!/usr/bin/env python3
+
+from auto_namd.functions import *
+from auto_namd.job import get_next_job
+
+
+def main(**kwargs):
+
+    while True:
+        job = get_next_job(kwargs['jobs_path'])
+        job.simulate(kwargs['ffs_path'], kwargs['steps'], kwargs['namdbin'], kwargs['params'])
+
+
+if __name__ == '__main__':
+
+    # Defaults
+    args = {
+        'jobs_path': ['/home/bryan/MD/CFTR/4-jobs', 'Number of timesteps to run'],
+        'ffs_path': ['/home/bryan/MD/CFTR/0-forcefields', 'Location of the forcefield files'],
+        'steps': [1000000, 'Number of timesteps to run the simulation'],
+        'namdbin': ['namd2', 'Location of the namd2 executable'],
+        'params': [f'+p{os.cpu_count() - 1}', 'Optional namd parameters']
+    }
+
+    # Override defaults with user input
+    args = sim_parser(args)
+    main(**args)

tests/0-forcefields/par_all36_lipid.prm

@@ -0,0 +1,532 @@
+*  \\\\\\\ CHARMM36 All-Hydrogen Lipid Parameter File ///////
+*  All comments and questions should be submitted to the
+*  parameter forum at the CHARMM website: www.charmm.org
+*
+
+!references
+!
+!Jeffery B. Klauda, Richard M. Venable, J. Alfredo Freites, Joseph
+!W. O'Connor, Douglas J. Tobias, Carlos Mondragon-Ramirez, Igor
+!Vorobyov, Alexander D. MacKerell, Jr. and Richard W. Pastor "Update of
+!the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six
+!Lipid Types" J. Phys. Chem. B 2010, 114, 7830-7843
+!
+! PUFA Modifications
+!Jeffery B. Klauda, Viviana Monje, Taehoon Kim, and Wonpil Im. "Improving
+!the CHARMM Force Field for Polyunsaturated Fatty Acid Chains" J. Phys. Chem. B.
+!2012 ASAP http://dx.doi.org/10.1021/jp304056p
+
+ATOMS
+MASS  -1  HL         1.00800 ! polar H (equivalent to protein H)
+MASS  -1  HCL        1.00800 ! charged H for PE (equivalent to protein HC)
+MASS  -1  HOL        1.00800 ! Nucleic acid phosphate hydroxyl proton
+MASS  -1  HAL1       1.00800 ! alphatic proton
+MASS  -1  HAL2       1.00800 ! alphatic proton
+MASS  -1  HAL3       1.00800 ! alphatic proton
+MASS  -1  HEL1       1.00800 ! for alkene; RHC=CR
+MASS  -1  HEL2       1.00800 ! for alkene; H2C=CR
+MASS  -1  HBL        1.00800 ! POPS SER backbone H
+MASS  -1  CL        12.01100 ! carbonyl C (acetic acid/methyl acetate)
+MASS  -1  CTL1      12.01100 ! sp3 carbon with 1 H  (-CH1-)
+MASS  -1  CTL2      12.01100 ! carbon of methylene group (-CH2-)
+MASS  -1  CTL3      12.01100 ! carbon of methyl group (-CH3)
+MASS  -1  CTL5      12.01100 ! carbon of methyl group (-CH3) for tetramethylammonium
+MASS  -1  CEL1      12.01100 ! for alkene; RHC=CR
+MASS  -1  CEL2      12.01100 ! for alkene; H2C=CR
+MASS  -1  CCL       12.01100 ! for POPS
+MASS  -1  NTL       14.00700 ! ammonium nitrogen
+MASS  -1  NH3L      14.00700 ! nitrogen phosphatidylethanolamine
+MASS  -1  OBL       15.99940 ! acetic acid carboxyl oxygen (e. to protein OB)
+MASS  -1  OCL       15.99940 ! acetate oxygen
+MASS  -1  OSL       15.99940 ! ester oxygen
+MASS  -1  O2L       15.99940 ! Nucleic acid =O in phosphate or sulfate
+MASS  -1  OHL       15.99940 ! Nucleic acid phosphate hydroxyl oxygen
+MASS  -1  OSLP      15.99940 ! Phosphate oxygen, to avoid conflict with methylacetate type O
+MASS  -1  PL        30.97400 ! phosphorus
+MASS  -1  SL        32.06000 ! Sulfate sulfur
+MASS  -1  CRL1      12.01100 ! sp3 carbon with 1 H on a ring  (-CH1-) for sterols
+MASS  -1  CRL2      12.01100 ! carbon of methylene group on a ring (-CH2-) for sterols
+
+BONDS
+!
+!V(bond) = Kb(b - b0)**2
+!
+!Kb: kcal/mole/A**2
+!b0: A
+!
+!atom type Kb          b0
+!
+CTL3  CL    200.0       1.522   ! methyl acetate
+CTL2  CL    200.0       1.522   ! methyl acetate
+CTL1  CL    200.0       1.522   ! methyl acetate
+CTL1  CCL   200.0       1.522   ! for POPS
+OBL   CL    750.0       1.220   ! methyl acetate
+OCL   CL    525.0       1.260   ! acetate, protein
+OCL   CCL   525.0       1.260   ! for POPS
+OSL   CL    150.0       1.334   ! methyl acetate
+OSLP  CL    150.0       1.334   ! methyl acetate
+OHL   CL    230.0       1.40    ! methyl acetate
+HOL   OHL   545.0       0.960   ! acetic acid
+CTL1  HAL1  309.00      1.111   ! alkanes, 3/92
+CTL1  HBL   330.00      1.080   ! for POPS
+CTL2  HAL2  309.00      1.111   ! alkanes, 4/98
+CTL3  HAL3  322.00      1.111   ! alkanes, 4/98
+CTL3  OSL   340.0       1.43    ! phosphate
+CTL2  OSL   340.0       1.43    ! phosphate
+CTL1  OSL   340.0       1.43    ! phosphate
+CTL3  OSLP  340.0       1.43    !
+CTL2  OSLP  340.0       1.43    !
+CTL1  OSLP  340.0       1.43    !
+OSL   PL    270.0       1.60    ! phosphate
+OSLP  PL    270.0       1.60    !
+O2L   PL    580.0       1.48    ! phosphate
+OHL   PL    237.0       1.59    ! phosphate
+NH3L  HCL   410.0       1.04    ! ethanolamine
+NH3L  CTL1  200.0       1.48    ! for POPS
+NH3L  CTL2  261.0       1.51    ! ethanolamine
+NTL   CTL2  215.00      1.51    ! tetramethylammonium
+NTL   CTL5  215.00      1.51    ! tetramethylammonium
+CTL5  HL    300.00      1.08    ! tetramethylammonium
+CTL2  HL    300.00      1.08    ! tetramethylammonium
+CTL1  CTL1  222.500     1.500   ! alkanes, 3/92
+CTL1  CTL2  222.500     1.538   ! alkanes, 3/92
+CTL1  CTL3  222.500     1.538   ! alkanes, 3/92
+CTL2  CTL2  222.500     1.530   ! alkanes, 3/92
+CTL2  CTL3  222.500     1.528   ! alkanes, 3/92
+CTL3  CTL3  222.500     1.530   ! alkanes, 3/92
+OHL   CTL1  428.0       1.420   !  glycerol
+OHL   CTL2  428.0       1.420   !  glycerol
+OHL   CTL3  428.0       1.420   !  glycerol
+SL    O2L   540.0       1.448   ! methylsulfate
+SL    OSL   250.0       1.575   ! methylsulfate
+CEL2  CEL2  510.000     1.330   ! ethene yin,adm jr., 12/95
+HEL2  CEL2  365.000     1.100   ! propene; from ethene, yin,adm jr., 12/95
+CEL1  CTL3  383.000     1.504   ! butene, yin,adm jr., 12/95
+CEL1  CEL2  500.000     1.342   ! propene, yin,adm jr., 12/95
+HEL1  CEL1  360.500     1.100   ! propene, yin,adm jr., 12/95
+CEL1  CTL2  365.000     1.502   ! butene; from propene, yin,adm jr., 12/95
+CEL1  CEL1  440.000     1.340   ! butene, yin,adm jr., 12/95
+
+ANGLES
+!
+!V(angle) = Ktheta(Theta - Theta0)**2
+!
+!V(Urey-Bradley) = Kub(S - S0)**2
+!
+!Ktheta: kcal/mole/rad**2
+!Theta0: degrees
+!Kub: kcal/mole/A**2 (Urey-Bradley)
+!S0: A
+!
+!atom types     Ktheta    Theta0   Kub     S0
+!
+!
+OBL  CL   CTL3    70.0     125.0     20.0   2.442  ! methyl acetate
+OBL  CL   CTL2    70.0     125.0     20.0   2.442  ! methyl acetate
+OBL  CL   CTL1    70.0     125.0     20.0   2.442  ! methyl acetate
+OSL  CL   OBL     90.0     125.9    160.0   2.2576 ! acetic acid
+CL   OSL  CTL1    40.0     109.6     30.0   2.2651 ! methyl acetate
+CL   OSL  CTL2    40.0     109.6     30.0   2.2651 ! methyl acetate
+CL   OSL  CTL3    40.0     109.6     30.0   2.2651 ! methyl acetate
+HAL2 CTL2 CL      33.00    109.50   30.00   2.163  ! methyl acetate
+HAL3 CTL3 CL      33.00    109.50   30.00   2.163  ! methyl acetate
+CTL2 CTL2 CL      52.0     108.00   ! alkane
+CTL2 CTL1 CCL     52.0     108.00   ! for POPS
+CTL3 CTL2 CL      52.0     108.00   ! alkane
+OSL  CL   CTL3    55.0     109.0    20.00   2.3260 ! methyl acetate
+OSL  CL   CTL2    55.0     109.0    20.00   2.3260 ! methyl acetate
+OSL  CL   CTL1    55.0     109.0    20.00   2.3260 ! methyl acetate
+OHL  CL   OBL     50.0     123.0    210.0   2.2620 ! acetic acid
+OCL  CL   CTL2    40.0     118.0     50.0   2.3880 ! acetate
+OCL  CL   CTL3    40.0     118.0     50.0   2.3880 ! acetate
+OCL  CL   OCL    100.0     124.0     70.0   2.2250 ! acetate
+OCL  CCL  OCL    100.0     124.0     70.0   2.2250 ! for POPS
+OCL  CCL  CTL1    40.0     118.0     50.0   2.3880 ! for POPS
+OHL  CL   CTL3    55.0     110.50   ! acetic acid
+OHL  CL   CTL2    55.0     110.50   ! acetic acid
+HOL  OHL  CL     55.0      115.0    ! acetic acid
+OSL  CTL1 CTL1   75.700    110.10   ! acetic acid, PIP
+OSL  CTL1 CTL2   75.700    110.10   ! acetic acid
+OSL  CTL1 CTL3   75.700    110.10   ! acetic acid
+OSL  CTL2 CTL1   75.700    110.10   ! acetic acid
+OSL  CTL2 CTL2   75.700    110.10   ! acetic acid
+OSL  CTL2 CTL3   75.700    110.10   ! acetic acid
+OSLP CTL1 CTL1   75.700    110.10   ! acetic acid, PIP
+OSLP CTL1 CTL2   75.700    110.10   ! acetic acid
+OSLP CTL1 CTL3   75.700    110.10   ! acetic acid
+OSLP CTL2 CTL1   75.700    110.10   ! acetic acid
+OSLP CTL2 CTL2   75.700    110.10   ! acetic acid
+OSLP CTL2 CTL3   75.700    110.10   ! acetic acid
+HAL2 CTL2 HAL2   35.500    109.00    5.40   1.80200 ! alkane, 3/92
+HAL3 CTL3 HAL3   35.500    108.40    5.40   1.80200 ! alkane, 3/92
+HAL1 CTL1 OSL    60.0      109.5    ! phosphate
+HAL2 CTL2 OSL    60.0      109.5    ! phosphate
+HAL3 CTL3 OSL    60.0      109.5    ! phosphate
+HAL1 CTL1 OSLP   60.0      109.5    ! phosphate
+HAL2 CTL2 OSLP   60.0      109.5    ! phosphate
+HAL3 CTL3 OSLP   60.0      109.5    ! phosphate
+CTL1 OSL  PL     20.0      120.0    35.0    2.33   ! phosphate, PIP
+CTL2 OSL  PL     20.0      120.0    35.0    2.33   ! phosphate
+CTL3 OSL  PL     20.0      120.0    35.0    2.33   ! phosphate
+CTL1 OSLP PL     20.0      120.0    35.0    2.33   ! phosphate, PIP
+CTL2 OSLP PL     20.0      120.0    35.0    2.33   ! phosphate
+CTL3 OSLP PL     20.0      120.0    35.0    2.33   ! phosphate
+HOL  OHL  PL     30.0      115.0    40.0    2.30   ! phosphate
+OSL  PL   OSL    80.0      104.3    ! phosphate
+OSL  PL   O2L    98.9      111.6    ! phosphate
+OSL  PL   OHL    48.1      108.0    ! phosphate
+OSLP PL   OSLP   80.0      104.3    ! phosphate
+OSLP PL   O2L    98.9      111.6    ! phosphate
+OSLP PL   OHL    48.1      108.0    ! phosphate
+O2L  PL   O2L   120.0      120.0    ! phosphate
+O2L  PL   OHL    98.9      108.23   ! phosphate
+NTL  CTL2 HL     40.0      109.5    27.     2.13   ! tetramethylammonium
+NTL  CTL5 HL     40.0      109.5    27.     2.13   ! tetramethylammonium
+HL   CTL2 HL     24.0      109.50   28.     1.767  ! tetramethylammonium
+HL   CTL5 HL     24.0      109.50   28.     1.767  ! tetramethylammonium
+CTL2 NTL  CTL2   60.0      109.5    26.     2.466  ! tetraethylammonium, from CTL5 NTL  CTL2
+CTL5 NTL  CTL2   60.0      109.5    26.     2.466  ! tetramethylammonium
+CTL5 NTL  CTL5   60.0      109.5    26.     2.466  ! tetramethylammonium
+HL   CTL2 CTL2   33.430    110.10   22.53   2.179  ! alkane
+HL   CTL2 CTL3   33.430    110.10   22.53   2.179  ! alkane
+HAL1 CTL1 CTL1   34.500    110.10   22.53   2.179  ! alkane, 3/92
+HAL1 CTL1 CTL2   34.500    110.10   22.53   2.179  ! alkane, 3/92
+HAL1 CTL1 CTL3   34.500    110.10   22.53   2.179  ! alkane, 3/92
+HAL2 CTL2 CTL1   26.500    110.10   22.53   2.179  ! alkane, 4/98
+HAL2 CTL2 CTL2   26.500    110.10   22.53   2.179  ! alkane, 4/98
+HAL2 CTL2 CTL3   34.600    110.10   22.53   2.179  ! alkane, 4/98
+HAL3 CTL3 CTL1   33.430    110.10   22.53   2.179  ! alkane, 4/98
+HAL3 CTL3 CTL2   34.600    110.10   22.53   2.179  ! alkane, 4/98
+HAL3 CTL3 CTL3   37.500    110.10   22.53   2.179  ! alkane, 4/98
+HBL  CTL1 CCL    50.000    109.50   ! for POPS
+HBL  CTL1 CTL2   35.000    111.00   ! for POPS
+NTL  CTL2 CTL2   67.7      115.00   ! tetramethylammonium
+NTL  CTL2 CTL3   67.7      115.00   ! tetramethylammonium
+HCL  NH3L CTL2   33.0      109.50    4.00   2.056  ! ethanolamine
+HCL  NH3L CTL1   30.0      109.50   20.00   2.074  ! for POPS
+HCL  NH3L HCL    41.0      109.50   ! ethanolamine
+NH3L CTL2 CTL2   67.7      110.00   ! ethanolamine
+NH3L CTL2 HAL2   45.0      107.50   35.00   2.0836 ! ethanolamine
+CTL1 CTL1 CTL1   53.350    111.00    8.00   2.561  ! alkane, 3/92
+NH3L CTL1 CCL    43.7      110.00   ! for POPS
+NH3L CTL1 CTL2   67.7      110.00   ! for POPS
+NH3L CTL1 HBL    51.5      107.50   ! for POPS
+CTL1 CTL1 CTL2   58.350    113.50   11.16   2.561  ! glycerol
+CTL1 CTL1 CTL3   53.350    108.50    8.00   2.561  ! alkane, 3/92
+CTL1 CTL2 CTL1   58.350    113.50   11.16   2.561  ! glycerol
+CTL1 CTL2 CTL2   58.350    113.50   11.16   2.561  ! glycerol
+CTL1 CTL2 CTL3   58.350    113.50   11.16   2.561  ! glycerol
+CTL2 CTL1 CTL2   58.350    113.50   11.16   2.561  ! glycerol
+CTL2 CTL1 CTL3   58.350    113.50   11.16   2.561  ! glycerol
+CTL2 CTL2 CTL2   58.350    113.60   11.16   2.561  ! alkane, 3/92
+CTL2 CTL2 CTL3   58.000    115.00    8.00   2.561  ! alkane, 3/92
+CTL3 CTL1 CTL3   58.350    113.50   11.16   2.561  ! glycerol
+HOL  OHL  CTL1   57.500    106.00   ! glycerol
+HOL  OHL  CTL2   57.500    106.00   ! glycerol
+HOL  OHL  CTL3   57.500    106.00   ! glycerol
+OHL  CTL1 CTL1   75.700    110.10   ! glycerol, PIP
+OHL  CTL1 CTL2   75.700    110.10   ! glycerol
+OHL  CTL2 CTL1   75.700    110.10   ! glycerol
+OHL  CTL2 CTL2   75.700    110.10   ! glycerol
+OHL  CTL2 CTL3   75.700    110.10   ! glycerol
+OHL  CTL1 HAL1   45.900    108.89   ! glycerol
+OHL  CTL2 HAL2   45.900    108.89   ! glycerol
+OHL  CTL3 HAL3   45.900    108.89   ! glycerol
+O2L  SL   O2L   130.0      109.47  35.0    2.45 ! methylsulfate
+O2L  SL   OSL    85.0       98.0                ! methylsulfate
+CTL2 OSL  SL     15.0      109.0   27.00   1.90 ! methylsulfate
+CTL3 OSL  SL     15.0      109.0   27.00   1.90 ! methylsulfate
+CEL1 CEL1 CTL2   48.00     123.50   ! from 2-butene, yin,adm jr., 12/95
+CEL1 CEL1 CTL3   48.00     123.50   ! 2-butene, yin,adm jr., 12/95
+CEL2 CEL1 CTL2   48.00     126.00   ! 1-butene; from propene, yin,adm jr., 12/95
+CEL2 CEL1 CTL3   47.00     125.20   ! propene, yin,adm jr., 12/95
+HEL1 CEL1 CEL1   52.00     119.50   ! 2-butene, yin,adm jr., 12/95
+HEL1 CEL1 CEL2   42.00     118.00   ! propene, yin,adm jr., 12/95
+HEL1 CEL1 CTL2   40.00     116.00   ! 1-butene; from propene, yin,adm jr., 12/95
+HEL1 CEL1 CTL3   22.00     117.00   ! propene, yin,adm jr., 12/95
+HEL2 CEL2 CEL1   45.00     120.50   ! propene, yin,adm jr., 12/95
+HEL2 CEL2 CEL2   55.50     120.50   ! ethene, yin,adm jr., 12/95
+HEL2 CEL2 HEL2   19.00     119.00   ! propene, yin,adm jr., 12/95
+CEL1 CTL2 CTL2   32.00     112.20   ! 1-butene; from propene, yin,adm jr., 12/95
+CEL1 CTL2 CTL3   32.00     112.20   ! 1-butene; from propene, yin,adm jr., 12/95
+HAL2 CTL2 CEL1   45.00     111.50   ! 1-butene; from propene, yin,adm jr., 12/95
+HAL3 CTL3 CEL1   42.00     111.50   ! 2-butene, yin,adm jr., 12/95
+CEL1 CTL2 CEL1   30.0      114.0    ! 1,4-dipentene, adm jr., 2/00
+ 
+DIHEDRALS
+!
+!V(dihedral) = Kchi(1 + cos(n(chi) - delta))
+!
+!Kchi: kcal/mole
+!n: multiplicity
+!delta: degrees
+!
+!atom types             Kchi    n   delta
+!
+X    CTL1 OHL  X        0.14    3     0.00 ! glycerol
+X    CTL2 OHL  X        0.14    3     0.00 ! glycerol
+X    CTL3 OHL  X        0.14    3     0.00 ! glycerol
+OCL  CCL  CTL1 NH3L     3.20    2   180.00 ! for POPS
+OBL  CL   CTL2 HAL2     0.00    6   180.00 ! acetic acid
+OBL  CL   CTL3 HAL3     0.00    6   180.00 ! acetic acid
+OSL  CL   CTL2 HAL2     0.00    6   180.00 ! acetic acid
+OSL  CL   CTL3 HAL3     0.00    6   180.00 ! acetic acid
+OSLP CL   CTL2 HAL2     0.00    6   180.00 ! acetic acid
+OSLP CL   CTL3 HAL3     0.00    6   180.00 ! acetic acid
+OBL  CL   OSL  CTL1     0.965   1   180.00 ! methyl acetate
+OBL  CL   OSL  CTL1     3.85    2   180.00 ! methyl acetate
+OBL  CL   OSL  CTL2     0.965   1   180.00 ! methyl acetate
+OBL  CL   OSL  CTL2     3.85    2   180.00 ! methyl acetate
+OBL  CL   OSL  CTL3     0.965   1   180.00 ! methyl acetate
+OBL  CL   OSL  CTL3     3.85    2   180.00 ! methyl acetate
+X    CL   OSL  X        2.05    2   180.00 ! methyl acetate
+X    CTL2 CL   X        0.05    6   180.00 ! methyl acetate
+X    CTL3 CL   X        0.05    6   180.00 ! methyl acetate
+X    CL   OHL  X        2.05    2   180.00 ! acetic acid
+X    CTL1 CCL  X        0.05    6   180.00 ! for POPS
+HAL2 CTL2 CL   OHL      0.00    6   180.00
+HAL3 CTL3 CL   OHL      0.00    6   180.00
+PL   OSLP CTL2 CTL1     0.407   2     0.00 ! Phos-gly, 8/05
+PL   OSLP CTL2 CTL1     0.241   1   180.00 ! Phos-gly, 8/05
+PL   OSLP CTL2 CTL2     0.407   2     0.00 ! Phos-gly, 8/05
+PL   OSLP CTL2 CTL2     0.241   1   180.00 ! Phos-gly, 8/05
+OSL  PL   OSL  CTL1     1.20    1   180.00 ! phosphate, new NA, 4/98, adm jr., PIP
+OSL  PL   OSL  CTL1     0.10    2   180.00 ! phosphate, new NA, 4/98, adm jr., PIP
+OSL  PL   OSL  CTL1     0.10    3   180.00 ! phosphate, new NA, 4/98, adm jr., PIP
+OSLP PL   OSLP CTL1     1.20    1   180.00 ! phosphate, new NA, 4/98, adm jr., PIP
+OSLP PL   OSLP CTL1     0.10    2   180.00 ! phosphate, new NA, 4/98, adm jr., PIP
+OSLP PL   OSLP CTL1     0.10    3   180.00 ! phosphate, new NA, 4/98, adm jr., PIP
+OSLP PL   OSLP CTL2     1.20    1   180.00 ! phosphate, new NA, 4/98, adm jr.
+OSLP PL   OSLP CTL2     0.10    2   180.00 ! phosphate, new NA, 4/98, adm jr.
+OSLP PL   OSLP CTL2     0.10    3   180.00 ! phosphate, new NA, 4/98, adm jr.
+O2L  PL   OSLP CTL2     0.10    3     0.00 ! phosphate, new NA, 4/98, adm jr.
+O2L  PL   OSL  CTL2     0.10    3     0.00 ! phosphate, new NA, 4/98, adm jr.
+OSLP PL   OSLP CTL3     1.20    1   180.00 ! phosphate, new NA, 4/98, adm jr.
+OSLP PL   OSLP CTL3     0.10    2   180.00 ! phosphate, new NA, 4/98, adm jr.
+OSLP PL   OSLP CTL3     0.10    3   180.00 ! phosphate, new NA, 4/98, adm jr.
+O2L  PL   OSLP CTL1     0.10    3     0.00 ! phosphate, new NA, 4/98, adm jr., PIP
+O2L  PL   OSL  CTL1     0.10    3     0.00 ! phosphate, new NA, 4/98, adm jr., PIP
+O2L  PL   OSLP CTL3     0.10    3     0.00 ! phosphate, new NA, 4/98, adm jr.
+O2L  PL   OSL  CTL3     0.10    3     0.00 ! phosphate, new NA, 4/98, adm jr.
+OHL  PL   OSL  CTL1     0.95    2     0.00 ! terminal phosphate, PIP
+OHL  PL   OSL  CTL1     0.50    3     0.00 ! terminal phosphate, PIP
+OHL  PL   OSL  CTL2     0.95    2     0.00 ! terminal phosphate
+OHL  PL   OSL  CTL2     0.50    3     0.00 ! terminal phosphate
+OHL  PL   OSL  CTL3     0.95    2     0.00 ! terminal phosphate
+OHL  PL   OSL  CTL3     0.50    3     0.00 ! terminal phosphate
+OHL  PL   OSLP CTL2     0.95    2     0.00 ! terminal phosphate
+OHL  PL   OSLP CTL2     0.50    3     0.00 ! terminal phosphate
+OHL  PL   OSLP CTL3     0.95    2     0.00 ! terminal phosphate
+OHL  PL   OSLP CTL3     0.50    3     0.00 ! terminal phosphate
+X    OHL  PL   X        0.30    3     0.00 ! terminal phosphate
+X    CTL1 OSL  X        0.00    3     0.00 ! phosphate, new NA, 4/98, adm jr.
+X    CTL2 OSL  X        0.00    3     0.00 ! phosphate, new NA, 4/98, adm jr.
+X    CTL3 OSL  X        0.00    3     0.00 ! phosphate, new NA, 4/98, adm jr.
+X    CTL1 OSLP X        0.00    3     0.00 ! phosphate, new NA, 4/98, adm jr.
+X    CTL2 OSLP X        0.00    3     0.00 ! phosphate, new NA, 4/98, adm jr.
+X    CTL3 OSLP X        0.00    3     0.00 ! phosphate, new NA, 4/98, adm jr.
+CTL1 CTL2 CL   OSL     -0.15    1   180.00 ! methyl propionate, 12/92
+CTL1 CTL2 CL   OSL      0.53    2   180.00 ! methyl propionate, 12/92
+CTL2 CTL2 CL   OSL      0.000   6     0.00 ! glycerol & propl ester, 6/07
+CTL2 CTL2 CL   OSL      0.030   3   180.00 ! glycerol & propl ester, 6/07
+CTL2 CTL2 CL   OSL      0.432   2   180.00 ! glycerol & propl ester, 6/07
+CTL2 CTL2 CL   OSL      0.332   1     0.00 ! glycerol & propl ester, 6/07
+CTL3 CTL2 CL   OSL      0.000   6     0.00 ! glycerol & propl ester, 6/07
+CTL3 CTL2 CL   OSL      0.030   3   180.00 ! glycerol & propl ester, 6/07
+CTL3 CTL2 CL   OSL      0.432   2   180.00 ! glycerol & propl ester, 6/07
+CTL3 CTL2 CL   OSL      0.332   1     0.00 ! glycerol & propl ester, 6/07
+CTL3 CTL2 CTL2 CL       0.000   5   180.00 ! propyl ester, 6/07
+CTL3 CTL2 CTL2 CL       0.317   3   180.00 ! propyl ester, 6/07
+CTL3 CTL2 CTL2 CL       0.557   2     0.00 ! propyl ester, 6/07
+CTL3 CTL2 CTL2 CL       0.753   1     0.00 ! propyl ester, 6/07
+CTL2 CTL2 CTL2 CL       0.000   5   180.00 ! propyl ester, 6/07
+CTL2 CTL2 CTL2 CL       0.317   3   180.00 ! propyl ester, 6/07
+CTL2 CTL2 CTL2 CL       0.557   2     0.00 ! propyl ester, 6/07
+CTL2 CTL2 CTL2 CL       0.753   1     0.00 ! propyl ester, 6/07
+OSL  CTL2 CTL1 OSL     -0.429   4    60.00 ! glycerol, 8/08
+OSL  CTL2 CTL1 OSL      0.614   3     0.00 ! glycerol, 8/08 
+OSL  CTL2 CTL1 OSL     -0.115   2    60.00 ! glycerol, 8/08 
+OSL  CTL2 CTL1 OSL      0.703   1   180.00 ! glycerol, 8/08 
+OSLP CTL2 CTL1 OSL      0.000   4     0.00 ! Fit to QM, theta2, 07/08 jbk
+OSLP CTL2 CTL1 OSL      0.607   3   180.00 ! Fit to QM, theta2, 07/08 jbk
+OSLP CTL2 CTL1 OSL      0.254   2    60.00 ! Fit to QM, theta2, 07/08 jbk
+OSLP CTL2 CTL1 OSL      2.016   1   180.00 ! Fit to QM, theta2, 07/08 jbk
+OSLP CTL2 CTL2 OSL      0.000   4     0.00 ! Fit to QM, theta2, 07/08 jbk
+OSLP CTL2 CTL2 OSL      0.607   3   180.00 ! Fit to QM, theta2, 07/08 jbk
+OSLP CTL2 CTL2 OSL      0.254   2    60.00 ! Fit to QM, theta2, 07/08 jbk
+OSLP CTL2 CTL2 OSL      2.016   1   180.00 ! Fit to QM, theta2, 07/08 jbk
+CTL3 CTL1 CTL2 OSL      0.000   3     0.00 ! glycerol, theta3
+CTL2 CTL1 CTL2 OSL      0.000   3     0.00 ! glycerol, theta3
+CTL3 CTL2 CTL2 OSL      0.000   3     0.00 ! glycerol, theta3
+CTL2 CTL2 CTL2 OSL      0.000   3     0.00 ! glycerol, theta3
+CL   OSL  CTL1 CTL2     0.000   4     0.00 ! glycerol, beta1 6/07
+CL   OSL  CTL1 CTL2     0.150   3   180.00 ! glycerol, beta1 6/07
+CL   OSL  CTL1 CTL2     1.453   2   180.00 ! glycerol, beta1 6/07
+CL   OSL  CTL1 CTL2     0.837   1   180.00 ! glycerol, beta1 6/07
+CL   OSL  CTL1 CTL3     0.000   4     0.00 ! glycerol, beta1 6/07
+CL   OSL  CTL1 CTL3     0.150   3   180.00 ! glycerol, beta1 6/07
+CL   OSL  CTL1 CTL3     1.453   2   180.00 ! glycerol, beta1 6/07
+CL   OSL  CTL1 CTL3     0.837   1   180.00 ! glycerol, beta1 6/07
+CL   OSL  CTL2 CTL1     0.267   3   180.00 ! glycerol, gamma1 6/07 
+CL   OSL  CTL2 CTL1     0.173   2     0.00 ! glycerol, gamma1 6/07 
+CL   OSL  CTL2 CTL1     0.781   1   180.00 ! glycerol, gamma1 6/07
+X    CTL2 NTL  X        0.26    3     0.00 ! tetramethylammonium
+X    CTL5 NTL  X        0.23    3     0.00 ! tetramethylammonium
+X    CTL1 NH3L X        0.10    3     0.00 ! for POPS
+X    CTL2 NH3L X        0.10    3     0.00 ! ethanolamine
+NH3L CTL2 CTL2 OHL      0.7     1   180.00 ! ethanolamine
+NH3L CTL2 CTL2 OSLP     0.7     1   180.00 ! ethanolamine
+NTL  CTL2 CTL2 OHL      4.3     1   180.00 ! choline, 12/92
+NTL  CTL2 CTL2 OHL     -0.4     3   180.00 ! choline, 12/92
+NTL  CTL2 CTL2 OSLP     3.3     1   180.00 ! choline, 12/92
+NTL  CTL2 CTL2 OSLP    -0.4     3   180.00 ! choline, 12/92
+X    CTL1 CTL1 X        0.200   3     0.00 ! alkane, 3/92
+X    CTL1 CTL2 X        0.200   3     0.00 ! alkane, 3/92
+X    CTL1 CTL3 X        0.200   3     0.00 ! alkane, 3/92
+X    CTL2 CTL2 X        0.1900  3     0.00 ! alkane, 4/98, yin and mackerell
+X    CTL2 CTL3 X        0.1600  3     0.00 ! alkane, 4/98, yin and mackerell
+X    CTL3 CTL3 X        0.1525  3     0.00 ! alkane, 4/98, yin and mackerell
+!alkane CCCC dihedrals based on pentane, heptane and hexane vdz/vqz/ccsd(t) QM data
+CTL3 CTL2 CTL2 CTL3     0.060   2     0.00 ! alkane, 7/08, jbk
+CTL3 CTL2 CTL2 CTL3     0.035   5     0.00 ! alkane, 7/08, jbk
+CTL2 CTL2 CTL2 CTL3     0.162   2     0.00 ! alkane, 7/08, jbk
+CTL2 CTL2 CTL2 CTL3     0.047   3   180.00 ! alkane, 7/08, jbk
+CTL2 CTL2 CTL2 CTL3     0.105   4     0.00 ! alkane, 7/08, jbk
+CTL2 CTL2 CTL2 CTL3     0.177   5     0.00 ! alkane, 7/08, jbk
+CTL2 CTL2 CTL2 CTL2     0.101   2     0.00 ! alkane, 7/08, jbk
+CTL2 CTL2 CTL2 CTL2     0.142   3   180.00 ! alkane, 7/08, jbk
+CTL2 CTL2 CTL2 CTL2     0.074   4     0.00 ! alkane, 7/08, jbk
+CTL2 CTL2 CTL2 CTL2     0.097   5     0.00 ! alkane, 7/08, jbk
+HAL3 CTL3 OSL  SL       0.00    3     0.00 ! methylsulfate
+CTL2 OSL  SL   O2L      0.00    3     0.00 ! methylsulfate
+CTL3 OSL  SL   O2L      0.00    3     0.00 ! methylsulfate
+HEL1 CEL1 CEL1 HEL1     1.0000  2   180.00 ! 2-butene, adm jr., 8/98 update
+CTL3 CEL1 CEL1 HEL1     1.0000  2   180.00 ! 2-butene, adm jr., 8/98 update
+X    CEL1 CEL1 X        0.4500  1   180.00 ! 2-butene, adm jr., 4/04
+X    CEL1 CEL1 X        8.5000  2   180.00 !
+X    CEL2 CEL2 X        4.9000  2   180.00 ! ethene, yin,adm jr., 12/95
+CTL2 CEL1 CEL2 HEL2     5.2000  2   180.00 ! propene, yin,adm jr., 12/95
+CTL3 CEL1 CEL2 HEL2     5.2000  2   180.00 ! propene, yin,adm jr., 12/95
+HEL1 CEL1 CEL2 HEL2     5.2000  2   180.00 ! propene, yin,adm jr., 12/95
+!alkene update, 2004,2009
+CEL1 CEL1 CTL2 HAL2     0.3000  3   180.00 !2-butene, adm jr., 4/04
+CEL1 CEL1 CTL3 HAL3     0.3000  3   180.00 !2-butene, adm jr., 4/04
+!CEL1 CEL1 CTL2 CTL3     0.9000  1   180.00 !2-pentene and 3-heptene
+!CEL1 CEL1 CTL2 CTL3     0.2000  2   180.00 !2-pentene and 3-heptene
+CEL1 CEL1 CTL2 CTL3     0.9100  1    180.0 !2-hexene, adm jr., 11/09, end fix jbk
+CEL1 CEL1 CTL2 CTL3     0.1800  2    180.0 !2-hexene, adm jr., 11/09
+CEL1 CEL1 CTL2 CTL3     0.1700  3    180.0 !2-hexene, adm jr., 11/09
+CEL1 CEL1 CTL2 CTL2     0.9100  1    180.0 !2-hexene, adm jr., 11/09
+CEL1 CEL1 CTL2 CTL2     0.1800  2    180.0 !2-hexene, adm jr., 11/09
+CEL1 CEL1 CTL2 CTL2     0.1700  3    180.0 !2-hexene, adm jr., 11/09
+CEL1 CTL2 CTL2 CL       0.1400  1    180.0 !2-hexene, adm jr., 11/09, add jbk for DHA
+CEL1 CTL2 CTL2 CL       0.1700  2      0.0 !2-hexene, adm jr., 11/09, add jbk for DHA
+CEL1 CTL2 CTL2 CL       0.0500  3    180.0 !2-hexene, adm jr., 11/09, add jbk for DHA
+CEL1 CTL2 CTL2 CTL2     0.1400  1    180.0 !2-hexene, adm jr., 11/09
+CEL1 CTL2 CTL2 CTL2     0.1700  2      0.0 !2-hexene, adm jr., 11/09
+CEL1 CTL2 CTL2 CTL2     0.0500  3    180.0 !2-hexene, adm jr., 11/09
+CEL1 CTL2 CTL2 CTL3     0.1400  1    180.0 !2-hexene, adm jr., 11/09
+CEL1 CTL2 CTL2 CTL3     0.1700  2      0.0 !2-hexene, adm jr., 11/09
+CEL1 CTL2 CTL2 CTL3     0.0500  3    180.0 !2-hexene, adm jr., 11/09
+CEL2 CEL1 CTL2 CTL2     0.5000  1   180.00 ! 1-butene, adm jr., 2/00 update
+CEL2 CEL1 CTL2 CTL2     1.3000  3   180.00 ! 1-butene, adm jr., 2/00 update
+CEL2 CEL1 CTL2 CTL3     0.5000  1   180.00 ! 1-butene, adm jr., 2/00 update
+CEL2 CEL1 CTL2 CTL3     1.3000  3   180.00 ! 1-butene, adm jr., 2/00 update
+CEL2 CEL1 CTL2 HAL2     0.1200  3     0.00 ! 1-butene, yin,adm jr., 12/95
+CEL2 CEL1 CTL3 HAL3     0.0500  3   180.00 ! propene, yin,adm jr., 12/95
+HEL1 CEL1 CTL2 CTL2     0.1200  3     0.00 ! butene, yin,adm jr., 12/95
+HEL1 CEL1 CTL2 CTL3     0.1200  3     0.00 ! butene, yin,adm jr., 12/95
+HEL1 CEL1 CTL2 HAL2     0.0000  3     0.00 ! butene, adm jr., 2/00 update
+HEL1 CEL1 CTL3 HAL3     0.0000  3     0.00 ! butene, adm jr., 2/00 update
+! 1,4-dipentene, adm jr., 2/00
+CEL2 CEL1 CTL2 CEL1     1.200   1   180.00 !1,4-dipentene
+CEL2 CEL1 CTL2 CEL1     0.400   2   180.00 !1,4-dipentene
+CEL2 CEL1 CTL2 CEL1     1.300   3   180.00 !1,4-dipentene
+CEL1 CTL2 CEL1 HEL1     0.000   2     0.00 !1,4-dipentene
+CEL1 CTL2 CEL1 HEL1     0.000   3     0.00 !1,4-dipentene
+! 2,5-diheptene, jbk., 9/2010
+! for CIS double bonds in polyunsaturated lipids (default)
+CEL1 CEL1 CTL2 CEL1     0.850   1   180.00 !2,5-diheptane
+CEL1 CEL1 CTL2 CEL1     0.300   2   180.00 !2,5-diheptane
+CEL1 CEL1 CTL2 CEL1     0.260   3     0.00 !2,5-diheptane
+CEL1 CEL1 CTL2 CEL1     0.096   4     0.00 !2,5-diheptane
+! for TRANS double bonds in polyunsaturated lipids
+! uncomment following 4 lines and comment previous 4 lines to use
+!CEL1 CEL1 CTL2 CEL1     1.200   1   180.00 !2,5-diheptane
+!CEL1 CEL1 CTL2 CEL1     0.200   2   180.00 !2,5-diheptane
+!CEL1 CEL1 CTL2 CEL1     1.200   3   180.00 !2,5-diheptane
+!CEL1 CEL1 CTL2 CEL1     0.100   4   180.00 !2,5-diheptane
+
+!
+IMPROPER
+!
+!V(improper) = Kpsi(psi - psi0)**2
+!
+!Kpsi: kcal/mole/rad**2
+!psi0: degrees
+!note that the second column of numbers (0) is ignored
+!
+!atom types           Kpsi                   psi0
+!
+OBL  X    X    CL         100.00    0     0.00 ! acetic acid
+HEL2 HEL2 CEL2 CEL2         3.00    0     0.00 ! ethene, yin,adm jr., 12/95
+OCL  X    X    CL          96.00    0     0.00 ! acetate
+OCL  X    X    CCL         96.00    0     0.00 ! for POPS
+
+
+NONBONDED nbxmod  5 atom cdiel fshift vatom vdistance vfswitch -
+cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5
+!
+!V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6]
+!
+!epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j)
+!Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j
+!
+!atom  ignored    epsilon      Rmin/2   ignored   eps,1-4       Rmin/2,1-4
+!
+HOL      0.0       -0.046     0.2245
+HAL1     0.0       -0.022     1.3200 ! alkane, 3/92
+HAL2     0.0       -0.028     1.3400 ! alkane, yin and mackerell, 4/98
+HAL3     0.0       -0.024     1.3400 ! alkane, yin and mackerell, 4/98
+HBL      0.0       -0.022     1.3200 ! for POPS
+HCL      0.0       -0.046     0.2245 ! ethanolamine
+HL       0.0       -0.046     0.7    ! polar H on NC4+
+HEL1     0.0       -0.031     1.25   ! alkene, yin,adm jr., 12/95
+HEL2     0.0       -0.026     1.26   ! alkene, yin,adm jr., 12/95
+!
+CL       0.0       -0.0700    2.00   ! methyl acetate update             
+CCL      0.0       -0.0700    2.00   ! for POPS
+CTL1     0.0       -0.0200    2.275 0.0 -0.01 1.9 ! alkane, 3/92
+CTL2     0.0       -0.0560    2.010 0.0 -0.01 1.9 ! alkane, 4/98, yin, adm jr.
+CTL3     0.0       -0.0780    2.040 0.0 -0.01 1.9 ! alkane, 4/98, yin, adm jr.
+CTL5     0.0       -0.0800    2.06  0.0 -0.01 1.9 ! old CTL3
+                                                  ! maintained for tetramethylammonium
+CEL1     0.0       -0.068     2.09   ! alkene, yin,adm jr., 12/95
+CEL2     0.0       -0.064     2.08   ! alkene, yin,adm jr., 12/95
+CRL1     0.0       -0.0360    2.010 0.0 -0.01 1.9 ! CGAFF, jbk add for cholesterol
+CRL2     0.0       -0.0600    2.020 0.0 -0.01 1.9 ! CPEN, cyclopentane, 8/06 viv (jbk add)
+
+!
+OBL      0.0       -0.12      1.70  0.0 -0.12 1.4
+OCL      0.0       -0.12      1.70
+O2L      0.0       -0.12      1.70
+OHL      0.0       -0.1521    1.77
+OSL      0.0       -0.1000    1.6500 !viv dec06 ether parameter
+OSLP     0.0       -0.1000    1.6500 !viv dec06 ether parameter
+!
+NH3L     0.0       -0.20      1.85  ! ethanolamine
+NTL      0.0       -0.20      1.85  ! as all other nitogens
+!
+SL       0.0       -0.47      2.1   ! methylsulfate
+PL       0.0       -0.585     2.15  ! ADM Jr.
+
+NBFIX
+!               Emin        Rmin
+!            (kcal/mol)     (A)
+!
+
+HBOND CUTHB 0.5  ! If you want to do hbond analysis (only), then use
+                 ! READ PARAM APPEND CARD
+                 ! to append hbond parameters from the file: par_hbond.inp
+
+END

tests/0-forcefields/par_all36_na.prm

@@ -0,0 +1,1253 @@
+* \\\\ CHARMM36 All-Hydrogen Nucleic Acid Parameter File ////
+*         Alexander D. MacKerell Jr. and coworkers
+*                        April 2011
+* All comments to the CHARMM web site: www.charmm.org parameter
+*                     set discussion forum
+*
+
+!2010/2011 additions
+! ejd, 2010 RNA update
+! adm, 2011 DNA update
+!  For DNA update, new atom type required for P of DNA. This required
+!  replication of a number of parameters and the creation of new
+!  patches, DEOX and DEO5, to convert RNA to DNA, such that previous
+!  CHARMM scripts to generate DNA will no longer work.  Note that the
+!  atom type change to P3 ONLY applies to the phosphodester linkage in
+!  DNA and NOT to terminal phosphates, DMP etc.
+!
+!
+!references
+!
+!NUCLEIC ACIDS
+!
+!Hart, K., Foloppe, N., Baker, C.M., Denning, E.J., Nilsson, L. and
+!MacKerell Jr., A.D. “Optimization of the CHARMM additive force field
+!for DNA: Improved treatment of the BI/BII conformational
+!equilibrium,” Journal of Chemical Theory and Computation, 8:348–362,
+!2012, http://dx.doi.org/10.1021/ct200723y
+!
+!Denning, E.J., Priyakumar, U.D., Nilsson, L., and MacKerell Jr., A.D.,
+!“Impact of 2’-hydroxyl sampling on the conformational properties of
+!RNA: Update of the CHARMM all-atom additive force field for RNA,”
+!JCC, In Press, 2011, NIHMSID #272247
+
+!Foloppe, N. and MacKerell, Jr., A.D. "All-Atom Empirical Force Field for
+!Nucleic Acids: 1) Parameter Optimization Based on Small Molecule and
+!Condensed Phase Macromolecular Target Data. JCC, 2000, 21: 86-104.
+!
+!MacKerell, Jr., A.D. and Banavali, N. "All-Atom Empirical Force Field for
+!Nucleic Acids: 2) Application to Molecular Dynamics Simulations of DNA
+!and RNA in Solution. JCC, 2000, 21: 105-120.
+!
+
+ATOMS
+MASS  -1  HN1        1.00800 ! Nucleic acid amine proton
+MASS  -1  HN2        1.00800 ! Nucleic acid ring nitrogen proton
+MASS  -1  HN3        1.00800 ! Nucleic acid aromatic carbon proton
+MASS  -1  HN4        1.00800 ! Nucleic acid phosphate hydroxyl proton
+MASS  -1  HN5        1.00800 ! Nucleic acid ribose hydroxyl proton
+MASS  -1  HN6        1.00800 ! Nucleic acid ribose aliphatic proton
+MASS  -1  HN7        1.00800 ! Nucleic acid proton (equivalent to protein HA)
+MASS  -1  HN8        1.00800 ! Bound to CN8 in nucleic acids/model compounds
+MASS  -1  HN9        1.00800 ! Bound to CN9 in nucleic acids/model compounds
+MASS  -1  CN1       12.01100 ! Nucleic acid carbonyl carbon
+MASS  -1  CN1T      12.01100 ! Nucleic acid carbonyl carbon (T/U C2)
+MASS  -1  CN2       12.01100 ! Nucleic acid aromatic carbon to amide
+MASS  -1  CN3       12.01100 ! Nucleic acid aromatic carbon 
+MASS  -1  CN3T      12.01100 ! Nucleic acid aromatic carbon, Thy C5
+MASS  -1  CN4       12.01100 ! Nucleic acid purine C8 and ADE C2  
+MASS  -1  CN5       12.01100 ! Nucleic acid purine C4 and C5
+MASS  -1  CN5G      12.01100 ! Nucleic acid guanine C5
+MASS  -1  CN7       12.01100 ! Nucleic acid carbon (equivalent to protein CT1)
+MASS  -1  CN7B      12.01100 ! Nucleic acid aliphatic carbon for C1'
+MASS  -1  CN8       12.01100 ! Nucleic acid carbon (equivalent to protein CT2)
+MASS  -1  CN8B      12.01100 ! Nucleic acid carbon (equivalent to protein CT2)
+MASS  -1  CN9       12.01100 ! Nucleic acid carbon (equivalent to protein CT3)
+MASS  -1  NN1       14.00700 ! Nucleic acid amide nitrogen
+MASS  -1  NN2       14.00700 ! Nucleic acid protonated ring nitrogen
+MASS  -1  NN2B      14.00700 ! From NN2, for N9 in GUA different from ADE
+MASS  -1  NN2U      14.00700 ! Nucleic acid protonated ring nitrogen, ura N3
+MASS  -1  NN2G      14.00700 ! Nucleic acid protonated ring nitrogen, gua N1
+MASS  -1  NN3       14.00700 ! Nucleic acid unprotonated ring nitrogen 
+MASS  -1  NN3A      14.00700 ! Nucleic acid unprotonated ring nitrogen, ade N1 and N3
+MASS  -1  NN3G      14.00700 ! Nucleic acid unprotonated ring nitrogen, gua N3
+MASS  -1  NN4       14.00700 ! Nucleic acid purine N7
+MASS  -1  NN6       14.00700 ! Nucleic acid sp3 amine nitrogen (equiv to protein nh3)
+MASS  -1  ON1       15.99940 ! Nucleic acid carbonyl oxygen
+MASS  -1  ON1C      15.99940 ! Nucleic acid carbonyl oxygen, cyt O2
+MASS  -1  ON2       15.99940 ! Nucleic acid phosphate ester oxygen
+MASS  -1  ON3       15.99940 ! Nucleic acid =O in phosphate 
+MASS  -1  ON4       15.99940 ! Nucleic acid phosphate hydroxyl oxygen
+MASS  -1  ON5       15.99940 ! Nucleic acid ribose hydroxyl oxygen
+MASS  -1  ON6       15.99940 ! Nucleic acid deoxyribose ring oxygen
+MASS  -1  ON6B      15.99940 ! Nucleic acid ribose ring oxygen
+MASS  -1  P         30.97400 ! phosphorus
+MASS  -1  P2        30.97400 ! phosphorus, adm, 2011 DNA update
+
+BONDS
+!
+!V(bond) = Kb(b - b0)**2
+!
+!Kb: kcal/mole/A**2
+!b0: A
+!
+!atom type Kb          b0
+!
+!2-(aminobutyl)-1,3-propandiol terms
+CN8  NN6    200.000     1.480   ! methylammonium
+NN6  HN1    403.000     1.040   ! methylammonium
+!abasic deoxynucleoside
+ON6  CN8B   260.0       1.420   ! susil
+CN8  CN8B   222.50      1.528   ! Alkanes, sacred
+! 
+CN1  CN3    302.0       1.409   !U, adm jr. 11/97
+CN1  CN3T   302.0       1.403   !T, adm jr. 11/97
+CN1  CN5G   302.0       1.360   !G, adm jr. 11/97
+CN1  NN2    380.0       1.367   !C, adm jr. 11/97
+CN1T NN2B   302.0       1.348   !U,T adm jr. 11/97
+CN1  NN2G   340.0       1.396   !G, adm jr. 11/97
+CN1  NN2U   340.0       1.389   !U,T adm jr. 11/97
+CN1T NN2U   340.0       1.383   !U,T adm jr. 11/97
+CN1  NN3    350.0       1.335   !C, adm jr. 11/97
+CN1T ON1    860.0       1.230   !nad/ppi, jjp1/adm jr. 7/95
+CN1  ON1    660.0       1.234   !U,A,G par_a4 adm jr. 10/2/91
+CN1  ON1C   620.0       1.245   !C, adm jr. 10/2/91
+CN2  CN3    320.0       1.406   !C, adm jr. 11/97
+CN2  CN5    360.0       1.358   !A, adm jr. 11/97
+CN2  NN1    360.0       1.366   !C,A,G JWK, adm jr. 10/2/91
+CN2  NN2G   400.0       1.392   !G  
+CN2  NN3    450.0       1.343   !C  
+CN2  NN3A   400.0       1.342   !A, adm jr. 11/97
+CN2  NN3G   320.0       1.326   !G, adm jr. 11/97
+CN3  CN3    500.0       1.326   !C,U adm jr. 11/97
+CN3  CN3T   560.0       1.320   !T, adm jr. 11/97
+CN3T CN9    230.0       1.478   !T, adm jr. 11/97
+CN3  HN3    350.0       1.09    !C,U, JWK
+CN3T HN3    350.0       1.09    !T, JWK
+CN3  NN2    302.0       1.343   !C, adm jr. 11/97
+CN3  NN2B   320.0       1.343   !U,T adm jr. 11/97
+CN4  HN3    380.0       1.09    !G,A, JWK par_a7 9/30/91
+CN4  NN2    320.0       1.374   !A, adm jr. 11/97
+CN4  NN2B   300.0       1.378   !G, adm jr. 11/97
+CN4  NN3A   420.0       1.322   !A, adm jr. 11/97
+CN4  NN4    400.0       1.305   !G,A, adm jr. 11/97
+CN5  CN5    310.0       1.361   !A, adm jr. 11/97
+CN5  CN5G   320.0       1.350   !G, adm jr. 11/97
+CN5  NN2    300.0       1.375   !A, adm jr. 11/97
+CN5  NN2B   302.0       1.375   !G, adm jr. 11/97
+CN5  NN3A   350.0       1.312   !A, JWK par_a8 9/30/91
+CN5  NN3G   350.0       1.315   !G, adm jr. 11/97
+CN5  NN4    310.0       1.355   !A, adm jr. 11/97
+CN5G NN4    310.0       1.365   !G, adm jr. 11/97
+CN8  CN8    222.50      1.528   !Alkanes, sacred
+CN8  CN9    222.50      1.528   !Alkanes, sacred
+CN8  NN2    400.0       1.460   !9-E-GUA, ADM JR.
+CN8  ON5    428.0       1.42    !RIBOSE, MeOH
+CN9  HN9    322.0       1.111   !alkanes
+CN9  ON2    340.0       1.43    !DMP, ADM Jr.
+HN1  NN1    488.0       1.00    !A,C,G, JWK, adm jr. 7/24/91
+HN2  NN2    474.0       1.01    !C,U, JWK
+HN2  NN2B   474.0       1.01    !G, adm jr. 11/97
+HN2  NN2G   471.0       1.01    !G, JWK, par_a12 9/30/91
+HN2  NN2U   474.0       1.01    !U, JWK, adm jr. 7/24/91
+HN4  ON4    545.0       0.960   !MP_1, ADM Jr.
+ON2  P      270.0       1.60    !DMP, ADM Jr. 
+ON2  P2     270.0       1.60    !DMP, ADM Jr., adm, 2011 DNA update
+ON3  P      580.0       1.48    !DMP, ADM Jr.
+ON3  P2     580.0       1.48    !DMP, ADM Jr., adm, 2011 DNA update
+ON4  P      237.0       1.58    !MP_1, ADM Jr.
+ON4  P2     237.0       1.58    !MP_1, ADM Jr., adm, 2011 DNA update
+!NN5  HN1    460.0       1.01    !sugar model, adm jr.
+!@@@@@@@@@ Begining of endocyclic bonds for deoxy-ribose @@@@@@@@@
+CN7B ON6    260.0       1.420   ! From exp  
+CN7B CN8    200.0       1.518   ! From exp 
+CN7  ON6    240.0       1.446   ! Fom exp.
+CN7  CN7    222.5       1.529  	! From exp 
+CN7  CN8    222.5       1.516  	! From exp. 
+CN7  CN9    222.5       1.516  	! for 5MET, From alkanes
+CN7  HN7    309.0       1.111   !Alkanes, sacred
+CN8  HN8    309.0       1.111   !Alkanes, sacred
+CN7B HN7    309.0       1.111   ! From CN8  HN7 (NF)
+!@@@@@@@@@ End of endocyclic bonds for deoxy-ribose @@@@@@@@@
+!@@@@@@@@@ Begining of endocyclic bonds for ribose @@@@@@@@@
+CN7B ON6B   260.0       1.420   ! From CN7B ON6
+CN7  ON6B   240.0       1.480   ! From CN7  ON6
+CN7B CN7B   200.0       1.450   ! 
+CN7  CN7B   222.5       1.460   ! Specific to RNA 
+!@@@@@@@@@ End of endocyclic bonds for ribose @@@@@@@@@
+
+!@@@@@@@@@ Begining of exocyclic bonds for deoxy-ribose @@@@@@@@@
+CN7  CN8B   222.5       1.512   ! From exp. 
+CN8B ON2    320.0       1.44    ! From exp
+!CN8B ON5    250.0       1.44    ! From CN8B ON2
+CN8B ON5    428.0       1.42    !From CN8 ON2, adm jr., 8/30/98
+CN7  ON2    310.0       1.433   ! From exp
+CN7B ON2    310.0       1.433   ! From exp, for NADPH and bkbmod
+!CN7  ON5    250.0       1.420   ! ALLOW   ALI ALC ARO
+CN7  ON5    428.0       1.42    !From CN8 ON2, adm jr., 8/30/98
+! C1'-N9 (purines)/C1'-N1 (pyrimidines)
+CN9  NN2    400.0       1.456   !9-M-A/C, adm jr.
+CN8  NN2B   400.0       1.458   !9-M-G/T/U, adm jr.
+CN9  NN2B   400.0       1.458   !9-M-G/T/U, adm jr.
+CN7B NN2    220.0       1.456   !A/C
+CN7B NN2B   220.0       1.458   !G/T/U
+! C5'-H in model compounds and DNA
+CN8B  HN8    309.0       1.111  !Alkanes, sacred
+ON5   HN5    545.0       0.960  !RIBOSE, MeOH
+!@@@@@@@@@ End of exocyclic bonds for deoxy-ribose @@@@@@@@@
+
+!@@@@@@@@@ Begining of exocyclic bonds for ribose @@@@@@@@@
+!CN7B ON5    250.0       1.400   ! From CN7  ON5
+CN7B ON5    428.0       1.400   ! check adm jr., 
+!FC should be 428.000 based on Meoh
+!@@@@@@@@@ End of exocyclic bonds for ribose @@@@@@@@@
+
+!@@@@@@@@@ Begining of bonds for nucleotide analogue @@@@@@@@@
+CN8  ON2    340.0       1.44    !
+!@@@@@@@@@ End of bonds for nucleotide analogue @@@@@@@@@
+
+ANGLES
+!
+!V(angle) = Ktheta(Theta - Theta0)**2
+!
+!V(Urey-Bradley) = Kub(S - S0)**2
+!
+!Ktheta: kcal/mole/rad**2
+!Theta0: degrees
+!Kub: kcal/mole/A**2 (Urey-Bradley)
+!S0: A
+!
+!atom types     Ktheta    Theta0   Kub     S0
+!
+! angle parameters have been rearranged based on model 
+! compounds and functional groups.  Additional angle 
+! parameters follow sorted based on the central atom
+!
+!2-(aminobutyl)-1,3-propandiol terms
+CN7  CN8  CN8      58.35    113.60   11.16   2.561 !alkane
+CN8  CN7  CN8      58.35    113.60   11.16   2.561 !alkane
+CN8  CN8  CN8      58.35    113.60   11.16   2.561 !alkane
+HN1  NN6  CN8      30.00    109.50   20.00   2.074 !methylammonium
+NN6  CN8  HN8      45.00    107.50   35.00   2.101 !methylammonium
+CN7  CN8  ON2     115.00    109.70  !DNA exocyclic angles
+NN6  CN8  CN8      67.70    110.00  !methylammonium
+HN1  NN6  HN1      44.00    109.50  !methylammonium
+!abasic propyl linkage
+ON2  CN8  CN8     115.0     109.7   !DNA exocyclic angles
+!abasic deoxynucleoside
+CN7  ON6  CN8B    110.0     109.0
+ON6  CN8B CN8      90.0     106.0
+CN8B CN8  CN7      80.0     106.0
+ON6  CN8B HN8      45.2     107.24 !
+HN8  CN8B CN8      34.53    110.10  22.53   2.179 ! alkane
+HN8  CN8  CN8B     34.53    110.10  22.53   2.179 ! alkane
+
+! pyrmidines
+!@@@@@@@@ Adenine
+! ade 6-mem ring
+CN2  NN3A CN4     90.0     117.8  !6R) adm jr. 11/97
+NN3A CN4  NN3A    60.0     133.0  !6R)
+CN4  NN3A CN5     90.0     110.1  !6R)
+CN5  CN5  NN3A    60.0     127.4  !6R) bridgeC4
+CN2  CN5  CN5     60.0     121.0  !6R) bridgeC5
+CN5  CN2  NN3A    60.0     110.7  !6R)
+CN5  CN5  NN2    100.0     105.7  !5R) bridgeC4
+CN5  CN5  NN4    100.0     110.0  !5R) bridgeC5
+CN4  NN4  CN5    120.0     104.6  !5R)
+NN2  CN4  NN4    100.0     113.4  !5R)
+CN4  NN2  CN5    100.0     106.3  !5R)
+NN2  CN5  NN3A   100.0     126.9  !bridgeC4
+CN2  CN5  NN4    100.0     129.0  !bridgeC5
+HN3  CN4  NN3A    38.0     113.5  !h2
+NN3A CN2  NN1     50.0     130.7  !n6
+CN5  CN2  NN1     50.0     118.6  !
+CN2  NN1  HN1     40.0     121.5  !h61,h62, C,A,G
+HN1  NN1  HN1     31.0     117.0  !C,A,G
+NN4  CN4  HN3     39.0     124.8  !h8, G,A
+NN2  CN4  HN3     39.0     121.8  !
+CN5  NN2  HN2     30.0     129.4  !h9
+CN4  NN2  HN2     30.0     125.0  !
+!@@@@@@@@ Guanine
+! gua 6-mem ring
+CN1  NN2G CN2     70.0     131.1  !6R)G, adm jr. 11/97
+NN2G CN2  NN3G    70.0     122.2  !6R)
+CN2  NN3G CN5     90.0     109.4  !6R)
+CN5G CN5  NN3G    70.0     129.9  !6R) bridgeC4
+CN1  CN5G CN5     70.0     119.6  !6R) bridgeC5
+CN5G CN1  NN2G    70.0     107.8  !6R)
+CN5G CN5  NN2B   100.0     104.6  !5R) bridgeC4
+CN5  CN5G NN4    100.0     111.4  !5R) bridgeC5
+CN4  NN4  CN5G   120.0     103.8  !5R)
+NN2B CN4  NN4    100.0     113.0  !5R)
+CN4  NN2B CN5    100.0     107.2  !5R)
+NN2B CN5  NN3G   140.0     125.5  ! bridgeC4
+CN1  CN5G NN4    125.0     129.0  ! bridgeC5
+CN1  NN2G HN2     45.0     113.3  ! h1
+CN2  NN2G HN2     45.0     115.6  !
+NN1  CN2  NN2G    95.0     115.4  ! n2 
+NN1  CN2  NN3G    95.0     122.4  !
+NN2G CN1  ON1     50.0     127.5  ! o6
+CN5G CN1  ON1     50.0     124.7  !
+HN3  CN4  NN2B    40.0     122.2  ! h8 (NN4 CN4 HN3 124.8)
+CN4  NN2B HN2     30.0     124.6  ! h9
+CN5  NN2B HN2     30.0     129.3  !
+!@@@@@@@@ Cytosine
+! cyt 6-mem ring
+CN1  NN2  CN3     50.0     124.1  !C, adm jr. 11/97
+NN2  CN1  NN3     50.0     116.8  !C
+CN1  NN3  CN2     85.0     119.1  !C
+CN3  CN2  NN3     85.0     119.3  !C
+CN2  CN3  CN3     85.0     117.8  !C
+CN3  CN3  NN2     85.0     122.9  !C
+CN1  NN2  HN2     37.0     121.2  !C, h1
+CN3  NN2  HN2     37.0     114.7  !C
+NN2  CN1  ON1C   130.0     119.4  !C, o2
+NN3  CN1  ON1C   130.0     123.8  !C
+NN3  CN2  NN1     81.0     122.3  !C, n4
+CN3  CN2  NN1     81.0     118.4  !C
+CN2  CN3  HN3     38.0     120.1  !C h5
+CN3  CN3  HN3     38.0     122.1  !C,U
+HN3  CN3  NN2     44.0     115.0  !C, h6
+!@@@@@@@@ Uracil
+! ura 6-mem ring
+CN1T NN2B CN3     70.0     122.0  !U, adm jr. 11/97
+NN2B CN1T NN2U    50.0     114.0  !U
+CN1T NN2U CN1     50.0     130.2  !U
+NN2U CN1  CN3     70.0     112.6  !U
+CN1  CN3  CN3    100.0     117.6  !U
+CN3  CN3  NN2B   100.0     123.6  !U
+CN1T NN2B HN2     40.5     122.0  !U, h1
+CN3  NN2B HN2     32.0     116.0  !U
+NN2B CN1T ON1    100.0     121.6  !U, o2
+NN2U CN1T ON1    100.0     124.4  !U
+CN1T NN2U HN2     40.5     114.4  !U, h3
+CN1  NN2U HN2     40.5     115.4  !U
+NN2U CN1  ON1    100.0     121.9  !U, o4
+CN3  CN1  ON1    100.0     125.5  !U, 
+CN1  CN3  HN3     30.0     120.3  !U, h5
+HN3  CN3  NN2B    30.0     114.3  !U, h6
+! thymine 6-mem ring (unique from ura)
+CN3T CN1 NN2U     70.0     113.5  !T, adm jr. 11/97
+CN1  CN3T CN3    120.0     116.7  !T
+CN3T CN3  NN2B   120.0     123.6  !125.3  !T
+CN3T CN1  ON1    100.0     124.6  !T, o4
+CN1  CN3T CN9     38.0     118.7  !T, c5 methyl
+CN3  CN3T CN9     38.0     124.6  !T
+CN3T CN3  HN3     30.0     122.1  !T, h6
+! base to methyl connection 
+CN1T NN2B CN9     70.0     116.0  !1-M-T/U, adm jr. 
+CN3  NN2B CN9     70.0     122.0  !1-M-T/U, adm jr. 7/24/91
+CN1  NN2  CN9     70.0     115.4  !1-M-C, adm jr. 
+CN3  NN2  CN9     70.0     120.5  !1-M-C, adm jr. 7/24/91
+CN5  NN2  CN9     70.0     125.9  !9-M-A, adm jr.
+CN4  NN2  CN9     70.0     127.8  !9-M-A, adm jr.
+CN5  NN2B CN9     70.0     125.9  !9-M-G, adm jr.
+CN4  NN2B CN9     70.0     126.9  !9-M-G, adm jr.
+CN5  NN2B CN8     70.0     125.9  !9-E-G, adm jr.
+CN4  NN2B CN8     70.0     126.9  !9-E-G, adm jr.
+NN2B CN8  CN9     70.0     113.7  !9-E-G, adm jr.
+!===== For glycosydic linkage, base to c1'
+CN1T NN2B CN7B    45.0     118.4  !U/T, FC from A
+CN3  NN2B CN7B    45.0     119.6  !U/T
+CN1  NN2  CN7B    45.0     120.0  !C, FC from A
+CN3  NN2  CN7B    45.0     115.9  !C
+CN5  NN2  CN7B    45.0     126.1  !A
+CN4  NN2  CN7B    45.0     127.6  !A
+CN5  NN2B CN7B    45.0     126.5  !G
+CN4  NN2B CN7B    45.0     126.3  !G
+ON6  CN7B NN2    110.0     108.0  !C/A DNA
+ON6B CN7B NN2    110.0     112.0  !C/A RNA
+CN8  CN7B NN2    110.0     113.7  !C/A
+CN7B CN7B NN2    110.0     111.0  !C/A, RNA
+ON6  CN7B NN2B   110.0     108.0  !T/U/G (DNA) FC from A
+ON6B CN7B NN2B   110.0     112.0  !T/U/G (RNA) FC from A
+CN8  CN7B NN2B   110.0     113.7  !T/U/G 
+CN7B CN7B NN2B   110.0     111.0  !T/U/G, RNA 
+HN7  CN7B NN2     43.0     111.0  !
+HN7  CN7B NN2B    43.0     111.0  !From HN7  CN7B NN2
+!===== End of glycosydic linkage
+! remaining terms ordered based on central atom
+CN9  CN8  HN8     34.6     110.10  22.53 2.179 ! Alkanes, sacred
+CN9  CN7  HN7     34.6     110.10  22.53 2.179 ! Alkanes, sacred
+HN8  CN8  NN2     33.43    110.1  !FOR 9-M-ADE(THY), ADM
+HN8  CN8  ON5     45.9     108.89 !RIBOSE, Adm Jr. MeOH
+CN3  CN9  HN9     33.43    110.10  22.53 2.179 ! Alkanes, sacred
+CN3T CN9  HN9     33.43    110.10  22.53 2.179 ! Alkanes, sacred
+CN8  CN9  HN9     34.60    110.10  22.53 2.179 ! Alkanes, sacred
+HN9  CN9  CN7     33.43    110.1   22.53 2.179 ! Alkanes, sacred
+HN9  CN9  NN2     33.43    110.1  !FOR 9-M-A(T), adm jr.
+HN9  CN9  NN2B    33.43    110.1  !FOR 9-M-G(C), adm jr.
+HN8  CN8  NN2B    33.43    110.1  !FOR 9-E-G, adm jr.
+HN9  CN9  ON2     60.0     109.5  !DMP, ADM Jr.
+!HN1  NN5  HN1     39.0     106.0  ! sugar model, adm jr.
+CN9  ON2  P       20.0     120.0  35.   2.33 !DMP, ADM Jr.
+HN4  ON4  P       30.0     115.0  40.0  2.35 !MP_1, ADM Jr. 
+HN4  ON4  P2      30.0     115.0  40.0  2.35 !MP_1, ADM Jr. , adm, 2011 DNA update
+HN5  ON5  CN8     57.5     106.0  !RIBOSE, Adm Jr. MeOH
+HN5  ON5  CN9     57.5     106.0  !RIBOSE, Adm Jr. MeOH
+ON2  P    ON2     80.0     104.3  !DMP, ADM Jr.
+ON2  P2   ON2     80.0     104.3  !DMP, ADM Jr., adm, 2011 DNA update
+ON2  P    ON4     48.1     108.0  !MP_1, ADM Jr.
+ON2  P2   ON4     48.1     108.0  !MP_1, ADM Jr., adm, 2011 DNA update
+ON3  P    ON4     98.9     108.23 !MP_1, ADM Jr.
+ON3  P2   ON4     98.9     108.23 !MP_1, ADM Jr., adm, 2011 DNA update
+ON4  P    ON4     98.9     104.0  !MP_0, ADM Jr.
+ON4  P2   ON4     98.9     104.0  !MP_0, ADM Jr., adm, 2011 DNA update
+CN7  CN8  ON5     75.7     110.10 !RIBOSE, adm jr. MeOH
+HN9  CN9  HN9     35.500   108.40  5.40 1.802 !alkane update, adm jr. 3/2/92
+!@@@@@@@@@ Beginning of endocyclic valence angles for regular DNA @@@@@@@
+CN7  ON6  CN7B    110.0    108.0   ! NF, 11/97, C4'O4'C1'
+ON6  CN7B CN8      90.0    102.0   ! NF, 11/97, C4'O4'C1' 
+CN7B CN8  CN7      80.00   100.0   ! NF, 11/97, C1'C2'C3'
+CN8  CN7  CN7      60.00   102.0   8.0   2.561  !NF, 11/97, C2'C3'C4'
+CN9  CN7  CN7      60.00   102.0   8.0   2.561  !for 5MET, adm jr.
+CN7  CN7  ON6     100.0    104.0   ! NF, 11/97, C3'C4'O4'
+HN7  CN7  ON6      45.2    107.24  ! 
+HN7  CN7B ON6      45.2    107.24  ! 
+HN7  CN7  CN7      40.0    108.00  !
+CN7B CN8  HN8      33.4    110.10  22.53   2.179 ! following terms directly
+CN8  CN7B HN7      33.4    110.10  22.53   2.179 ! from alkanes
+HN7  CN7  CN8      34.5    110.1   22.53   2.179 ! 
+HN8  CN8  CN7      34.53   110.10  22.53   2.179 ! 
+HN8  CN8  CN8      34.53   110.10  22.53   2.179 ! 
+HN8  CN8  HN8      35.5    109.00   5.40   1.802 ! 
+HN7  CN7  HN7      35.5    109.00   5.40   1.802 !
+!@@@@@@@@@ End of endocyclic valence angles for regular DNA @@@@@@@
+
+!@@@@@@@@@ Beginning of endocyclic valence angles for regular RNA @@@@@@@
+CN7  ON6B CN7B    110.0    115.0   ! From CN7  ON6  CN7B
+CN7  CN7  ON6B    100.0    110.0   ! From CN7  CN7  ON6
+ON6B CN7B CN7B     90.0    106.0   ! 030998 
+CN7B CN7B CN7     110.0     96.0   ! 
+CN7B CN7  CN7      60.0    100.0    8.00   2.561  !NF, 11/97, C2'C3'C4'
+HN7  CN7  ON6B     45.2    107.24  !
+HN7  CN7B ON6B     45.2    107.24  !
+CN7B CN7B HN7      33.4    110.10  22.53   2.179 ! following terms directly
+HN7  CN7B HN7      35.5    109.00   5.40   1.802 !
+!@@@@@@@@@ End of endocyclic valence angles for regular RNA @@@@@@@
+
+!@@@@@@@@@ Beginning of exocyclic valence angles for regular DNA @@@@@@@
+ON6  CN7  CN8B     90.0    108.2  !NF, 11/97, O4'C4'C5'
+ON6  CN7  CN9      90.0    108.2  !for 5MET, adm jr.
+CN7  CN7  CN8B     45.0    110.0  !NF, 11/97, C3'C4'C5'
+CN8  CN7  CN8B    58.35    113.60 11.16 2.561 ! from alkane, 25P1
+CN7  CN8B ON2      70.0    108.4  !NF, 11/97, C4'C5'O5'
+CN7  CN7  ON2     115.0    109.7  !NF, 11/97, C4'C3'O3'
+CN7B CN7B ON2     115.0    109.7  !NF, 11/97, C4'C3'O3' for NADPH and bkbmod
+CN8  CN7  ON2     115.0    109.7  !NF, 11/97, C2'C3'O3'
+CN8B ON2  P        20.0    120.0   35.00   2.33 !NF, 11/97, C5'O5'P
+CN8B ON2  P2       20.0    120.0   35.00   2.33 !NF, 11/97, C5'O5'P, adm, 2011 DNA update
+CN7  ON2  P        20.0    120.0   35.00   2.33 !NF, 11/97, C3'O3'P
+CN7  ON2  P2       20.0    120.0   35.00   2.33 !NF, 11/97, C3'O3'P, adm, 2011 DNA update
+CN7B ON2  P        20.0    120.0   35.00   2.33 !NF, 11/97, C3'O3'P, for NADPH and bkbmod
+CN7B ON2  P2       20.0    120.0   35.00   2.33 !NF, 11/97, C3'O3'P, for NADPH and bkbmod, adm, 2011 DNA update
+! sugar
+HN7  CN7  CN8B     34.5    110.1   22.53   2.179 ! From HN7  CN7  CN8
+HN8  CN8B ON2      60.0    109.5  ! From HN7  CN8  ON2
+HN5  ON5  CN8B     57.5    106.0  ! From HN5  ON5  CN8
+HN8  CN8B HN8      35.5    109.0    5.40   1.802  ! Alkanes, sacred
+HN8  CN8B CN7      34.53   110.1   22.53   2.179  ! Alkanes, sacred
+HN7  CN7  ON2      60.0    109.5  !DMP, adm jr. from HN7  CN8  ON2
+HN7  CN7B ON2      60.0    109.5  !DMP, adm jr. from HN7  CN8  ON2, for NADPH and bkbmod
+!===== For 5ter patch:
+CN7  CN8B ON5      75.7    110.10 ! From CN7  CN8B  ON5
+CN8B CN7  ON5      90.0    108.2  ! phosphoramidate, carbocyclic
+HN8  CN8B ON5      45.9    108.89 ! From HN7  CN8  ON5
+!===== For 3ter patch:
+ON5  CN7  CN8      75.7    110.0  ! from CHARMM22
+ON5  CN7  CN7      75.7    110.1  ! 
+HN7  CN7  ON5      60.0    109.5  ! 
+HN5  ON5  CN7      57.5    109.0  ! 
+!@@@@@@@@@ End of exocyclic valence angles for regular DNA @@@@@@@
+
+!@@@@@@@@@ Beginning of exocyclic valence angles for regular RNA @@@@@@@
+!O4'-C4'-C5'
+ON6B CN7  CN8B     90.0    108.2  ! 
+ON6B CN7  CN9      90.0    108.2  ! for 5MET patch, adm jr.
+!O3'-C3'-C2'
+ON2  CN7  CN7B     90.0    110.0  !
+ON5  CN7  CN7B     90.0    110.0  ! From ON5  CN7  CN8
+!O2'-C2'-C1'
+ON5  CN7B CN7B     80.0    108.4  ! 
+!O2'-C2'-C3'
+ON5  CN7B CN7      90.0    108.0  ! 
+HN7  CN7B ON5      60.0    109.5  !
+HN5  ON5  CN7B     57.5    109.0  !
+HN7  CN7B CN7      34.53   110.10  22.53   2.179
+HN7  CN7  CN7B     34.53   110.10  22.53   2.179
+
+!@@@@@@@@@ End of exocyclic valence angles for regular RNA @@@@@@@
+
+!@@@@@@@@@ Beginning of angles for the nucleotide analogue @@@@@@@
+CN8  ON2  P        20.0    120.0  35.   2.33 !DMP, adm jr.
+CN8  ON2  P2       20.0    120.0  35.   2.33 !DMP, adm jr., adm 2011 DNA update
+!@@@@@@@@@ End of angles for the nucleotide analogue @@@@@@@
+ON2  P    ON3      98.9    111.6  !DMP, adm jr.
+ON2  P2   ON3      98.9    111.6  !DMP, adm jr., adm, 2011 DNA update
+ON3  P    ON3     120.0    120.0  !DMP, adm jr.
+ON3  P2   ON3     120.0    120.0  !DMP, adm jr., adm, 2011 DNA update
+HN8  CN8  ON2      60.0    109.5  !DMP, adm jr.
+ON5  P    ON3      98.9    111.6  ! From ON2 P ON3
+!------------------------ added for araim ----------------------
+ON6  CN7B CN7     120.0     106.25   ! 
+CN7B CN7  CN8      58.35    113.6   11.16 2.561 ! 
+
+DIHEDRALS
+!
+!V(dihedral) = Kchi(1 + cos(n(chi) - delta))
+!
+!Kchi: kcal/mole
+!n: multiplicity
+!delta: degrees
+!
+!atom types             Kchi    n   delta
+!2-(aminobutyl)-1,3-propandiol terms
+X    CN8  ON2  X       -0.10    3     0.0 ! phosphate ester
+X    CN7  CN8  X        0.20    3     0.0 ! alkane
+X    CN8  NN6  X        0.10    3     0.0 ! methylammonium
+!abasic nucleoside terms - susil
+CN7  ON6  CN8B HN8      0.195   1     0.0
+ON6  CN8B CN8  HN8      0.195   1     0.0
+HN7  CN7  ON6  CN8B     0.195   3     0.0
+CN8B CN8  CN7  HN7      0.195   3     0.0
+HN8  CN8B CN8  HN8      0.195   3     0.0
+HN8  CN8B CN8  CN7      0.195   3     0.0
+!  c5'-c4'-o4'-c1', exo
+CN8B CN7  ON6  CN8B     0.5     5     0.0 ! min at 150 310 max at 25 200
+CN8B CN7  ON6  CN8B     0.1     3   180.0
+CN8B CN7  ON6  CN8B     0.5     1     0.0
+!  c1'-c2'-c3'-o3', exo
+CN8B CN8  CN7  ON5      0.4     5     0.0
+CN8B CN8  CN7  ON5      0.4     3     0.0
+CN8B CN8  CN7  ON5      0.7     2     0.0 !elevates energy at 0 (c3'endo), adm
+CN8B CN8  CN7  ON5      0.5     1   180.0 !elevates energy at 0 (c3'endo), adm
+CN8B CN8  CN7  ON2      0.4     5     0.0 !terms for oligonuclotide
+CN8B CN8  CN7  ON2      0.4     3     0.0
+CN8B CN8  CN7  ON2      0.7     2     0.0
+CN8B CN8  CN7  ON2      0.5     1   180.0
+!  c4'-o4'-c1'-c2', tau0
+CN7  ON6  CN8B CN8      0.6     6   180.0
+CN7  ON6  CN8B CN8      0.6     3     0.0
+!  o4'-c1'-c2'-c3', tau1
+ON6  CN8B CN8  CN7      0.7     5   180.0 !lowers 90, shifts c2endo minimum towards 200
+ON6  CN8B CN8  CN7      0.4     4     0.0 !lowers 90, shifts c2endo minimum towards 200
+ON6  CN8B CN8  CN7      0.4     3   180.0 !lowers 90, shifts c2endo minimum towards 200
+!  c4'-c3'-c2'-c1', tau2
+CN7  CN7  CN8  CN8B     0.5     4     0.0
+CN7  CN7  CN8  CN8B     0.1     3     0.0 !lowers energy in 150 to 250 range
+!  c1'-o4'-c4'-c3', tau4
+CN8B ON6  CN7  CN7      0.5     3     0.0 !effects surface in 200-360 region
+
+! PHOSPHATE
+ON2  P2   ON2  CN7      0.90    1   180.0  ! adm, 2011 DNA update new param, zeta, kat2 set
+ON2  P2   ON2  CN7      0.40    2   180.0  ! adm, 2011 DNA update new param, zeta, kat2 set
+ON2  P2   ON2  CN7      0.20    3   180.0  ! adm, 2011 DNA update new param, zeta, kat2 set
+ON2  P    ON2  CN7      1.20    1   180.0  !10/97, DMP, adm jr., RNA
+ON2  P    ON2  CN7      0.10    2   180.0  !10/97, DMP, adm jr., RNA
+ON2  P    ON2  CN7      0.10    3   180.0  !10/97, DMP, adm jr., RNA
+ON2  P    ON2  CN7      0.00    6     0.0  !10/97, DMP, adm jr., RNA
+ON2  P    ON2  CN8      1.20    1   180.0  !10/97, DMP, adm jr.
+ON2  P    ON2  CN8      0.10    2   180.0  !10/97, DMP, adm jr.
+ON2  P    ON2  CN8      0.10    3   180.0  !10/97, DMP, adm jr.
+ON2  P    ON2  CN8      0.00    6     0.0  !10/97, DMP, adm jr.
+ON2  P2   ON2  CN8      1.20    1   180.0  !10/97, DMP, adm jr., adm	2011 DNA update
+ON2  P2   ON2  CN8      0.10    2   180.0  !10/97, DMP, adm jr., adm	2011 DNA update
+ON2  P2   ON2  CN8      0.10    3   180.0  !10/97, DMP, adm jr., adm	2011 DNA update
+ON2  P2   ON2  CN8      0.00    6     0.0  !10/97, DMP, adm jr., adm	2011 DNA update
+! Added when C5' defined as CN8B (NF 041497):
+ON2  P2   ON2  CN8B     1.20    1   180.0  !10/97, DMP, adm jr., adm, 2011 DNA update
+ON2  P2   ON2  CN8B     0.10    2   180.0  !10/97, DMP, adm jr., adm, 2011 DNA update
+ON2  P2   ON2  CN8B     0.10    3   180.0  !10/97, DMP, adm jr., adm, 2011 DNA update
+ON2  P2   ON2  CN8B     0.00    6     0.0  !10/97, DMP, adm jr., adm, 2011 DNA update
+ON2  P    ON2  CN8B     1.20    1   180.0  !10/97, DMP, adm jr., RNA
+ON2  P    ON2  CN8B     0.10    2   180.0  !10/97, DMP, adm jr., RNA
+ON2  P    ON2  CN8B     0.10    3   180.0  !10/97, DMP, adm jr., RNA
+ON2  P    ON2  CN8B     0.00    6     0.0  !10/97, DMP, adm jr., RNA
+ON2  P    ON2  CN9      1.20    1   180.0  !dmp
+ON2  P    ON2  CN9      0.10    2   180.0  !dmp
+ON2  P    ON2  CN9      0.10    3   180.0  !dmp
+ON2  P    ON2  CN9      0.00    6     0.0  !dmp
+ON2  P2   ON2  CN9      1.20    1   180.0  !dmp, adm, 2011 DNA update
+ON2  P2   ON2  CN9      0.10    2   180.0  !dmp, adm, 2011 DNA update
+ON2  P2   ON2  CN9      0.10    3   180.0  !dmp, adm, 2011 DNA update
+ON2  P2   ON2  CN9      0.00    6     0.0  !dmp, adm, 2011 DNA update
+!
+ON3  P    ON2  CN7      0.10    3     0.0  !dmp,eps, O1P-P-O3'-C3'
+ON3  P2   ON2  CN7      0.10    3     0.0  !dmp,eps, O1P-P-O3'-C3', adm, 2011 DNA update
+ON3  P    ON2  CN7B     0.10    3     0.0  !for NADPH and bkbmod
+ON3  P    ON2  CN8      0.10    3     0.0  !dmp
+ON3  P2   ON2  CN8      0.10    3     0.0  !dmp, adm	2011 DNA update
+ON3  P    ON2  CN8B     0.10    3     0.0  !dmp,bet, O1P-P-O5'-C5'
+ON3  P2   ON2  CN8B     0.10    3     0.0  !dmp,bet, O1P-P-O5'-C5', adm, 2011 DNA update
+ON3  P    ON2  CN9      0.10    3     0.0  !dmp
+ON3  P2   ON2  CN9      0.10    3     0.0  !dmp, adm, 2011 DNA update
+! terminal phosphate terms, adm jr.
+ON4  P    ON2  CN7      0.95    2     0.0  !MP_1, adm jr.
+ON4  P    ON2  CN7      0.50    3     0.0  !MP_1, adm jr.
+ON4  P2   ON2  CN7      0.95    2     0.0  !MP_1, adm jr., adm, 2011 DNA update
+ON4  P2   ON2  CN7      0.50    3     0.0  !MP_1, adm jr., adm, 2011 DNA update
+ON4  P    ON2  CN8      0.95    2     0.0  !MP_1, adm jr.
+ON4  P    ON2  CN8      0.50    3     0.0  !MP_1, adm jr.
+ON4  P    ON2  CN8B     0.95    2     0.0  !MP_1, adm jr.
+ON4  P    ON2  CN8B     0.50    3     0.0  !MP_1, adm jr.
+ON4  P2   ON2  CN8B     0.95    2     0.0  !MP_1, adm jr., adm, 2011 DNA update
+ON4  P2   ON2  CN8B     0.50    3     0.0  !MP_1, adm jr., adm, 2011 DNA update
+ON4  P    ON2  CN9      0.95    2     0.0  !MP_1, adm jr.
+ON4  P    ON2  CN9      0.50    3     0.0  !MP_1, adm jr.
+ON4  P2   ON2  CN9      0.95    2     0.0  !MP_1, adm jr., adm, 2011 DNA update
+ON4  P2   ON2  CN9      0.50    3     0.0  !MP_1, adm jr., adm, 2011 DNA update
+X    ON4  P    X        0.30    3     0.0  !MP_1, adm jr.
+X    ON4  P2   X        0.30    3     0.0  !MP_1, adm jr., adm, 2011 DNA update
+! When O5' is ON2 (phosphodiester linkage):
+P    ON2  CN7  HN7      0.000   3     0.0  !dmp,eps, H-C3'-O3'-P
+P2   ON2  CN7  HN7      0.000   3     0.0  !dmp,eps, H-C3'-O3'-P, adm, 2011 DNA update
+P    ON2  CN7B HN7      0.000   3     0.0  !for NADPH and bkbmod
+P    ON2  CN8B HN8      0.000   3     0.0  !dmp,beta, H-C5'-O5'-P
+P2   ON2  CN8B HN8      0.000   3     0.0  !dmp,beta, H-C5'-O5'-P, adm, 2011 DNA update
+P    ON2  CN8  HN8      0.000   3     0.0  !dmp
+P    ON2  CN9  HN9      0.000   3     0.0  !dmp
+P2   ON2  CN9  HN9      0.000   3     0.0  !dmp, adm, 2011 DNA update
+! butane gauche terms
+cn9  cn8  cn8  cn9      0.15    1     0.0
+cn9  cn8  cn8  cn8      0.15    1     0.0
+! BASES                     
+! Uracil 
+NN2B CN1T NN2U CN1      1.5     2   180.0  ! adm jr. 11/97
+CN1T NN2U CN1  CN3      1.5     2   180.0  ! adm jr. 11/97
+NN2U CN1  CN3  CN3      1.5     2   180.0  ! adm jr. 11/97
+CN1  CN3  CN3  NN2B     6.0     2   180.0  ! adm jr. 11/97 
+CN3  CN3  NN2B CN1T     1.5     2   180.0  ! adm jr. 11/97
+CN3  NN2B CN1T NN2U     1.5     2   180.0  ! adm jr. 11/97
+HN3  CN3  CN3  HN3      3.0     2   180.0  ! adm jr. 11/97
+HN3  CN3  CN1  ON1      6.0     2   180.0  ! adm jr. 11/97
+ON1  CN1T NN2B HN2      0.0     2   180.0  ! adm jr. 11/97
+ON1  CN1  NN2U HN2      0.0     2   180.0  ! adm jr. 11/97
+ON1  CN1T NN2U HN2      0.0     2   180.0  ! adm jr. 11/97
+HN2  NN2B CN3  HN3      1.5     2   180.0  ! adm jr. 11/97
+NN2B CN1T NN2U HN2      3.8     2   180.0  ! adm jr. 11/97
+CN3  CN1  NN2U HN2      3.8     2   180.0  ! adm jr. 11/97
+CN3  CN3  NN2B HN2      1.6     2   180.0  ! adm jr. 11/97
+NN2U CN1T NN2B HN2      1.6     2   180.0  ! adm jr. 11/97
+!Thymine
+CN1T NN2B CN3  CN3T     1.8     2   180.0  ! adm jr. 11/97
+NN2U CN1  CN3T CN3      1.8     2   180.0  ! adm jr. 11/97
+CN1  CN3T CN3  NN2B     3.0     2   180.0  ! adm jr. 11/97
+NN2B CN1  CN3T CN9      5.6     2   180.0  ! adm jr. 11/97
+NN2B CN3  CN3T CN9      5.6     2   180.0  ! adm jr. 11/97
+CN1  CN3T CN9  HN9      0.46    3     0.0  ! adm jr. 11/97
+CN3  CN3T CN9  HN9      0.46    3     0.0  ! adm jr. 11/97
+CN3T CN1  NN2U HN2      4.8     2   180.0  ! adm jr. 11/97
+! Cytosine 
+CN3  NN2  CN1  NN3      0.6     2   180.0  ! adm jr. 11/97
+NN2  CN1  NN3  CN2      0.6     2   180.0  ! adm jr. 11/97
+CN1  NN3  CN2  CN3      6.0     2   180.0  ! adm jr. 11/97
+NN3  CN2  CN3  CN3      0.6     2   180.0  ! adm jr. 11/97
+CN2  CN3  CN3  NN2      6.0     2   180.0  ! adm jr. 11/97
+CN3  CN3  NN2  CN1      0.6     2   180.0  ! adm jr. 11/97
+NN3  CN2  NN1  HN1      1.0     2   180.0  ! adm jr. 11/97
+CN3  CN2  NN1  HN1      1.0     2   180.0  ! adm jr. 11/97
+NN1  CN2  NN3  CN1      2.0     2   180.0  ! adm jr. 11/97
+NN1  CN2  CN3  CN3      2.0     2   180.0  ! adm jr. 11/97
+NN1  CN2  CN3  HN3      2.0     2   180.0  ! adm jr. 11/97
+ON1C CN1  NN2  HN2      3.0     2   180.0  ! adm jr. 11/97
+ON1C CN1  NN3  CN2      1.6     2   180.0  ! adm jr. 11/97
+ON1C CN1  NN2  CN3      1.6     2   180.0  ! adm jr. 11/97
+NN3  CN2  CN3  HN3      3.4     2   180.0  ! adm jr. 11/97
+NN2  CN3  CN3  HN3      3.4     2   180.0  ! adm jr. 11/97
+CN2  CN3  CN3  HN3      4.6     2   180.0  ! adm jr. 11/97
+CN1  NN2  CN3  HN3      4.6     2   180.0  ! adm jr. 11/97
+X    CN2  NN3  X        2.0     2   180.0  ! adm jr. 11/97
+! Adenine  
+CN2  NN3A CN4  NN3A     1.8     2   180.0  ! adm jr. 11/97, 6-mem
+NN3A CN4  NN3A CN5      2.0     2   180.0  ! 
+CN4  NN3A CN5  CN5      1.8     2   180.0  ! 
+NN3A CN5  CN5  CN2      2.0     2   180.0  ! treated 2x
+CN5  CN5  CN2  NN3A     1.8     2   180.0  ! 
+CN5  CN2  NN3A CN4     10.0     2   180.0  ! 
+CN5  CN5  NN4  CN4      6.0     2   180.0  ! 5-mem
+CN5  NN4  CN4  NN2     14.0     2   180.0  ! 
+NN4  CN4  NN2  CN5      6.0     2   180.0  ! 
+CN4  NN2  CN5  CN5      6.0     2   180.0  !
+NN2  CN5  CN5  NN4     14.0     2   180.0  ! treated 2x
+CN2  NN3A CN4  HN3      8.5     2   180.0  ! H2
+CN5  NN3A CN4  HN3      8.5     2   180.0  ! H2
+CN5  NN4  CN4  HN3      5.2     2   180.0  ! H8
+CN5  NN2  CN4  HN3      5.2     2   180.0  ! H8
+CN5  CN5  NN2  HN2      1.2     2   180.0  ! H9
+NN4  CN4  NN2  HN2      1.2     2   180.0  ! H9
+HN2  NN2  CN4  HN3      0.0     2   180.0  ! H8-C-N-H9
+CN4  NN3A CN2  NN1      4.0     2   180.0  ! N6
+CN5  CN5  CN2  NN1      4.0     2   180.0  ! N6
+NN4  CN5  CN2  NN1      0.0     2   180.0  ! N6
+CN5  CN2  NN1  HN1      0.5     2   180.0  ! 6-NH2
+NN3A CN2  NN1  HN1      0.5     2   180.0  ! 
+! Butterfly motion
+NN3A CN5  CN5  NN4      7.0     2   180.0  !A, adm jr. 11/97
+CN2  CN5  CN5  NN2      7.0     2   180.0  !A
+NN3A CN2  CN5  NN4      2.0     2   180.0  !A
+CN2  CN5  NN4  CN4      2.0     2   180.0  !A
+CN4  NN3A CN5  NN2      2.0     2   180.0  !A
+NN3A CN5  NN2  CN4      2.0     2   180.0  !A
+! Guanine 
+CN1  NN2G CN2  NN3G     0.2     2   180.0  !adm jr. 11/97, 6-mem
+NN2G CN2  NN3G CN5      2.0     2   180.0  !
+CN2  NN3G CN5  CN5G     0.2     2   180.0  !
+NN3G CN5  CN5G CN1      2.0     2   180.0  !
+CN5  CN5G CN1  NN2G     0.2     2   180.0  !
+CN5G CN1  NN2G CN2      0.2     2   180.0  !
+CN5  CN5G NN4  CN4      6.0     2   180.0  !5-mem
+CN5G NN4  CN4  NN2B    16.0     2   180.0  !
+NN4  CN4  NN2B CN5      6.0     2   180.0  !
+CN4  NN2B CN5  CN5G     6.0     2   180.0  !
+NN2B CN5  CN5G NN4     10.0     2   180.0  !
+! substitutents
+ON1  CN1  CN5G CN5     14.0     2   180.0  !G, O6
+ON1  CN1  CN5G NN4      0.0     2   180.0  !
+ON1  CN1  NN2G CN2     14.0     2   180.0  !
+ON1  CN1  NN2G HN2      0.0     2   180.0  !
+NN1  CN2  NN2G CN1      4.0     2   180.0  !G, N2
+NN1  CN2  NN3G CN5      4.0     2   180.0  !
+NN1  CN2  NN2G HN2      0.0     2   180.0  !
+NN2G CN2  NN1  HN1      1.2     2   180.0  !
+NN3G CN2  NN1  HN1      1.2     2   180.0  !
+HN2  NN2G CN1  CN5G     3.6     2   180.0  !G, H1
+HN2  NN2G CN2  NN3G     3.6     2   180.0  !
+HN3  CN4  NN4  CN5G     5.6     2   180.0  !G, H8
+HN3  CN4  NN2B CN5      5.6     2   180.0  !
+HN3  CN4  NN2B HN2      0.0     2   180.0  !
+HN2  NN2B CN5  CN5G     1.2     2   180.0  !G, H9
+HN2  NN2B CN5  NN3G     1.2     2   180.0  !
+HN2  NN2B CN4  NN4      1.2     2   180.0  !
+! Butterfly motion
+NN3G CN5  CN5G NN4     10.0     2   180.0  !adm jr. 11/97
+CN1  CN5G CN5  NN2     10.0     2   180.0  !
+NN2G CN1  CN5G NN4      2.0     2   180.0  !
+CN1  CN5G NN4  CN4      2.0     2   180.0  !
+CN2  NN3G CN5  NN2B     2.0     2   180.0  !
+NN3G CN5  NN2B CN4      2.0     2   180.0  !
+! Wild cards for uracil, thymine and cytosine
+X    CN1  NN3  X        1.0     2   180.0  ! c22
+X    CN1  NN2  X        0.9     2   180.0  ! c22
+X    CN1T NN2B X        0.9     2   180.0  ! From X CN1 NN2 X, for thymines 
+X    CN1  NN2G X        0.9     2   180.0  ! c22
+X    CN1  NN2U X        0.9     2   180.0  ! c22
+X    CN1T NN2U X        0.9     2   180.0  ! c22
+X    CN3  NN2  X        1.0     2   180.0  ! c22
+X    CN3  NN2B X        1.0     2   180.0  ! From X CN3 NN2 X, for thymines
+X    CN3  CN3  X        1.0     2   180.0  ! c22
+X    CN3  CN3T X        1.0     2   180.0  !T, adm jr. 11/97
+X    CN1  CN3  X        1.0     2   180.0  ! c22
+X    CN1  CN3T X        1.0     2   180.0  !T, adm jr. 11/97
+X    CN2  CN3  X        0.8     2   180.0  ! c22
+! Wild cards for adenine and guanine
+X    CN1  CN5G X        1.0     2   180.0  ! adm jr. 11/97
+X    CN2  NN2G X        1.0     2   180.0  ! 
+X    CN2  CN5  X        1.0     2   180.0  ! 
+X    CN4  NN2  X        1.5     2   180.0  ! 
+X    CN4  NN2B X        1.5     2   180.0  ! From X CN4 NN2 X
+X    CN4  NN3A X        3.5     2   180.0  ! 
+X    CN4  NN4  X        2.0     2   180.0  ! A,G
+X    CN5  CN5  X        0.0     2   180.0  !
+X    CN5G CN5  X        0.0     2   180.0  ! adm jr. 11/97
+X    CN5  NN2  X        1.5     2   180.0  !
+X    CN5  NN2B X        1.5     2   180.0  ! From X CN5 NN2 X
+X    CN5  NN3A X        1.0     2   180.0  !
+X    CN5  NN3G X        1.0     2   180.0  ! adm jr. 11/97
+X    CN5  NN4  X        1.0     2   180.0  !
+X    CN5G NN4  X        1.0     2   180.0  ! adm jr. 11/97
+X    CN2  NN3A X        1.0     2   180.0  !
+X    CN2  NN3G X        1.0     2   180.0  ! adm jr. 11/97
+! MISC.          
+CN1  NN2  CN9  HN9      0.19    3     0.0 ! 1-M-C
+CN3  NN2  CN9  HN9      0.00    3     0.0 ! 1-M-C
+CN4  NN2  CN9  HN9      0.00    3     0.0 ! 9-M-A
+CN5  NN2  CN9  HN9      0.19    3     0.0 ! 9-M-A
+CN1  NN2B CN9  HN9      0.19    3     0.0 ! 1-M-U
+CN1T NN2B CN9  HN9      0.19    3     0.0 ! 1-M-T
+CN3  NN2B CN9  HN9      0.00    3     0.0 ! 1-M-T/U
+CN4  NN2B CN9  HN9      0.00    3     0.0 ! 9-M-G
+CN5  NN2B CN9  HN9      0.19    3     0.0 ! 9-M-G
+CN4  NN2B CN8  HN8      0.00    3     0.0 ! 9-E-G
+CN5  NN2B CN8  HN8      0.19    3     0.0 ! 9-E-G
+CN4  NN2B CN8  CN9      0.00    3     0.0 ! 9-E-G
+CN5  NN2B CN8  CN9      0.19    3     0.0 ! 9-E-G
+X    CN8  CN8  X        0.15    3     0.0 ! Alkanes (0.2 to 0.15)
+X    CN8  CN9  X        0.15    3     0.0 ! Alkanes (0.2 to 0.15)
+!for nadp/nadph, adm jr.
+HN7  CN7B CN7B ON2       0.195   3         0.0 !for NADPH and bkbmod
+ON2  CN7B CN7B NN2       0.0     3         0.0 !for NADPH and bkbmod
+
+! sugar, replace with ribose terms 021998
+CN7  CN7B ON6  CN7       0.6     6       180.0 
+CN7B CN7  CN7  CN7       0.4     6         0.0 ! good for amplitudes
+CN7B CN7  CN7  CN9       0.4     6         0.0 ! good for amplitudes, 5MET
+CN7  CN7  CN7  ON6       0.6     6         0.0
+CN7  CN7  CN7B ON6       0.6     6         0.0
+ON2  CN7  CN7  CN7       0.8     6         0.0 !
+ON2  CN7  CN7  CN7       0.4     5         0.0 ! Moves the barrier right
+ON2  CN7  CN7  CN7       2.0     3       180.0 !
+! for ndph
+ON2  CN7B CN7  CN7       0.8     6         0.0 !
+ON2  CN7B CN7  CN7       0.4     5         0.0 ! Moves the barrier right
+ON2  CN7B CN7  CN7       2.0     3       180.0 !
+!
+ON5  CN7  CN7  CN7       0.8     6         0.0 !
+ON5  CN7  CN7  CN7       0.4     5         0.0 ! Moves the barrier right
+ON5  CN7  CN7  CN7       2.0     3       180.0 !
+ON5  CN7  CN7  ON5       0.0     3         0.0 ! 
+ON5  CN7  CN7  ON2       0.0     3         0.0 ! 
+ON2  CN7  CN7B ON6       0.5     6         0.0 !good for amplitudes
+ON2  CN7  CN7B ON6       0.3     5         0.0 !impact on amplitudes
+ON2  CN7  CN7B ON6       0.6     4       180.0 !increases c2'endo
+ON2  CN7  CN7B ON6       0.2     3         0.0 !
+CN7  CN7  CN7  CN8B      0.5     4       180.0 !del lowers 180 deg.
+
+!%%%%%%% new terms for dna and the deoxyribose-based model compounds %%%%%%
+! The following is for: THF3P (model for espilon), THFM3P (model for puckering),
+! THF5P (model for gamma and beta), THFCH3IM (model for chi), nucleotide analogue
+!@@@@@@ Begining of chi
+!============= added for torsion about chi in adenine ============
+!For link from sugar to base:
+CN7B NN2  CN4  HN3       0.3     2       180.0 ! NF
+CN7B NN2  CN5  CN5      11.0     2       180.0 ! adm jr.
+CN7B NN2  CN4  NN4      11.0     2       180.0 ! adm jr.
+CN7B NN2  CN4  NN3A     11.0     2       180.0 ! adm jr.
+!For chi itself:
+	!DNA:
+ON6  CN7B NN2  CN5       1.1     1       180.0 !
+ON6  CN7B NN2  CN4       1.1     1         0.0 ! NF 
+        !RNA:
+ON6B CN7B NN2  CN5       1.1     1       180.0 !
+ON6B CN7B NN2  CN4       1.1     1         0.0 !
+	!DNA:
+CN8  CN7B NN2  CN5       0.3     3         0.0 ! NF
+CN8  CN7B NN2  CN4       0.0     3       180.0 ! NF
+	!RNA:
+CN7B CN7B NN2  CN5       0.3     3         0.0 ! NF
+CN7B CN7B NN2  CN4       0.0     3       180.0 ! NF
+
+HN7  CN7B NN2  CN5       0.0     3         0.0 ! NF
+HN7  CN7B NN2  CN4       0.195   3         0.0 ! NF
+!@@@@@@ End of chi in adenines 
+
+!============== terms for torsion about chi in cytosines ===========
+CN7B NN2  CN3  HN3       0.3     2       180.0 ! NF
+CN7B NN2  CN1  ON1C     11.0     2       180.0 ! adm jr. from A
+CN7B NN2  CN1  NN3      11.0     2       180.0 ! adm jr. 
+CN7B NN2  CN3  CN3      11.0     2       180.0 ! adm jr.
+	!DNA:
+ON6  CN7B NN2  CN1       0.0     3         0.0 ! 
+ON6  CN7B NN2  CN3       1.0     1         0.0 ! NF 
+        !RNA:
+ON6B CN7B NN2  CN1       0.0     3         0.0 !
+ON6B CN7B NN2  CN3       1.0     1         0.0 !
+        !DNA:
+CN8  CN7B NN2  CN1       1.0     3         0.0 ! 
+CN8  CN7B NN2  CN3       0.0     3       180.0 ! NF 030697
+        !RNA:
+CN7B CN7B NN2  CN1       1.0     3         0.0 !
+CN7B CN7B NN2  CN3       0.0     3       180.0 !
+
+HN7  CN7B NN2  CN1       0.0     3         0.0 ! NF
+HN7  CN7B NN2  CN3       0.195   3         0.0 ! NF
+!@@@@@@ End of chi in cytosines 
+
+!=========== terms for torsion about chi in uracils/thymines ===========
+CN7B NN2B CN3  HN3       0.3     2       180.0 ! NF
+CN7B NN2B CN1T ON1      11.0     2       180.0 ! adm jr. from A
+CN7B NN2B CN1T NN2U     11.0     2       180.0 ! adm jr.
+CN7B NN2B CN3  CN3T     11.0     2       180.0 ! adm jr.
+	!DNA:
+ON6  CN7B NN2B CN1       0.0     3         0.0 ! 
+ON6  CN7B NN2B CN1T      0.7     3         0.0 ! 
+ON6  CN7B NN2B CN1T      0.8     1       180.0 ! 
+ON6  CN7B NN2B CN3       0.9     1         0.0 ! NF 
+        !RNA:
+ON6B CN7B NN2B CN1       0.0     3         0.0 !
+ON6B CN7B NN2B CN1T      0.7     3         0.0 !
+ON6B CN7B NN2B CN1T      0.8     1       180.0 !
+ON6B CN7B NN2B CN3       0.9     1         0.0 !
+        !DNA:
+CN8  CN7B NN2B CN1T      0.2     3       180.0 ! 
+CN8  CN7B NN2B CN3       0.0     3       180.0 ! NF
+        !RNA:
+CN7B CN7B NN2B CN1T      0.2     3       180.0 !
+CN7B CN7B NN2B CN3       0.0     3       180.0 !
+
+HN7  CN7B NN2B CN1T      0.0     3         0.0 ! NF
+HN7  CN7B NN2B CN3       0.195   3         0.0 ! NF
+!@@@@@@ End of chi in thymines 
+
+!============= added for torsion about chi in guanine ============
+CN7B NN2B CN4  HN3       0.3     2       180.0 ! NF
+CN7B NN2B CN4  NN4      11.0     2       180.0 ! adm jr.
+CN7B NN2B CN5  CN5G     11.0     2       180.0 ! adm jr. from U
+CN7B NN2B CN5  NN3G     11.0     2       180.0 ! adm jr.
+	!DNA:
+ON6  CN7B NN2B CN5       0.2     3         0.0 !
+ON6  CN7B NN2B CN5       1.1     1       180.0 !
+ON6  CN7B NN2B CN4       1.4     1         0.0 ! NF 
+        !RNA:
+ON6B CN7B NN2B CN5       0.2     3         0.0 !
+ON6B CN7B NN2B CN5       1.1     1       180.0 !
+ON6B CN7B NN2B CN4       1.4     1         0.0 !
+        !DNA:
+CN8  CN7B NN2B CN5       0.0     3         0.0 ! NF
+CN8  CN7B NN2B CN4       0.0     3       180.0 ! NF 030697
+        !RNA:
+CN7B CN7B NN2B CN5       0.0     3         0.0 ! NF
+CN7B CN7B NN2B CN4       0.0     3       180.0 !
+
+HN7  CN7B NN2B CN5       0.0     3         0.0 ! NF
+HN7  CN7B NN2B CN4       0.195   3         0.0 ! NF
+!@@@@@@ End of chi in guanines 
+!@@@@@@ link (not chi) between base and sugar for both purines and pyrimidines:
+	!DNA:
+CN7  ON6  CN7B NN2       0.0     3         0.0
+CN7  ON6  CN7B NN2B      0.0     3         0.0
+	!RNA:
+CN7  ON6B CN7B NN2       0.0     3         0.0
+CN7  ON6B CN7B NN2B      0.0     3         0.0
+        !DNA:
+CN7  CN8  CN7B NN2       0.0     3         0.0
+CN7  CN8  CN7B NN2B      0.0     3         0.0
+HN8  CN8  CN7B NN2       0.0     3         0.0
+HN8  CN8  CN7B NN2B      0.0     3         0.0
+        !RNA:
+CN7  CN7B CN7B NN2       0.0     3         0.0
+CN7  CN7B CN7B NN2B      0.0     3         0.0
+	!RNA
+HN7  CN7B CN7B NN2       0.0     3         0.0
+HN7  CN7B CN7B NN2B      0.0     3         0.0
+
+!@@@@@@ Begining of torsions involving exocyclic sugar atoms:
+!======= CN7  CN8B  ON2  P = C4'-C5'-O5'-P 
+CN7  CN8B ON2  P        0.2     1       120.0 !bet C4'-C5'-O5'-P, adm jr.
+CN7  CN8B ON2  P2       0.2     1       120.0 !bet C4'-C5'-O5'-P, adm jr., adm, 2011 DNA update
+! the following differ significantly from the alcohols
+! in the protein (based on ethanol), they also differ from other
+! NA C-C-OH-H parameters (see below)
+! The two following terms have been replaced by their ethanol 
+! counterpart (NF, 083098)
+CN7  CN8B ON5  HN5      1.3300  1         0.00
+CN7  CN8B ON5  HN5      0.1800  2         0.00
+CN7  CN8B ON5  HN5      0.3200  3         0.00
+!======= HN8  CN8B  ON2 P = H-C5'-O5'-P )beta
+HN8  CN8B ON5  HN5      0.0     3         0.0 !bet
+!======== CN7 CN7 CN8B ON2 = C3'-C4'-C5'-O5'
+! When O5' is ON2 (phosphodiester linkage):
+CN7  CN7  CN8B ON2      0.20    4       180.0 !gam adm jr.
+CN7  CN7  CN8B ON2      0.80    3       180.0 !gam C3'-C4'-C5'-O5'
+CN7  CN7  CN8B ON2      0.40    2         0.0 !gam
+CN7  CN7  CN8B ON2      2.50    1       180.0 !gam
+!
+CN8  CN7  CN8B ON2      0.2     3       180.0 ! from gam, carbocyclic and 25P1
+! When O5' is ON5 (5TER patch):
+CN7  CN7  CN8B ON5      0.20    4       180.0 !gam adm jr.
+CN7  CN7  CN8B ON5      0.80    3       180.0 !gam C3'-C4'-C5'-O5'
+CN7  CN7  CN8B ON5      0.40    2         0.0 !gam
+CN7  CN7  CN8B ON5      2.50    1       180.0 !gam
+!======== ON6 CN7 CN8B ON2 = O4'-C4'-C5'-O5'
+! When O5' is ON2 (3'-5' phosphodiester linkage)
+ON6  CN7  CN8B ON2      3.4     1       180.0 !gam O4'-C4'-C5'-O5',influences +60
+ON6B CN7  CN8B ON2      3.4     1       180.0 !gam, RNA
+! When O5' is ON5 (5TER patch):
+ON6  CN7  CN8B ON5      3.4     1       180.0 !gam
+ON6B CN7  CN8B ON5      3.4     1       180.0 !gam, RNA
+!======== HN8  CN8B  CN7  CN7 = H-C5'-C4'-H
+HN8  CN8B CN7  CN7      0.195   3         0.0 !gam,H-C5'-C4'-H
+HN8  CN8B CN7  CN8      0.195   1         0.0 !gam, carbocylic, 25P1
+!======== HN7 CN8B CN7 ON6 = H-C5'-C4'-O4'
+HN8  CN8B CN7  ON6      0.195   1         0.0 !gam,H-C5'-C4'-O4'
+HN8  CN8B CN7  ON6B     0.195   1         0.0 !gam, RNA
+!======== HN7 CN7 CN8B ON2 =  H-C4'-C5'-O5'
+! When O5' is ON2 (phosphodiester linkage):
+HN7  CN7  CN8B ON2      0.195	3         0.0 !gam H-C4'-C5'-O5'
+! When O5' is ON5 (5TER patch):
+HN7  CN7  CN8B ON5      0.195   3         0.0 !gam
+HN8  CN8  CN8  ON6      0.195   1         0.0 !gam,H-C5'-C4'-O4'
+! terms for 5MET patch
+CN9  CN7  CN7  CN8B     0.5     4       180.0 !cn8 -> cn9
+HN7  CN7  CN9  HN9      0.195   3         0.0 !cn8 -> cn9
+CN7  CN7  CN9  HN9      0.195   3         0.0 !cn8 -> cn9
+ON6  CN7  CN9  HN9      0.195   3         0.0 !cn7 -> cn9
+HN7  CN7  CN7  CN9      0.195   3         0.0 !cn8 -> cn9
+ON2  CN7  CN7  CN9      0.2     4         0.0 !cn8b -> cn9
+ON2  CN7  CN7  CN9      0.8     3       180.0 !cn8b -> cn9
+CN8  CN7  CN7  CN9      0.5     4       180.0 !cn8b -> cn9
+
+!======== CN8 CN7 CN7 CN8B = C2'-C3'-C4'-C5'
+! This term is well suited to modify the puckering surfaces, in 
+! particular because it is present in THF5P 
+CN8  CN7  CN7  CN8B     0.5     4       180.0 !del lowers 180 deg. 
+CN7B CN7  CN7  CN8B     0.2     4       180.0 !del, RNA
+!======== CN8B CN7 CN7 ON2 = C5'-C4'-C3'-O3' 
+! These terms affect the c2endo/c3endo energy difference
+! When O3' is ON2 (3'-5' phosphodiester linkage)
+ON2  CN7  CN7  CN8B      0.2      4       0.0 !del
+! the following term controls the location of the barrier at ~75 deg.
+ON2  CN7  CN7  CN8B      0.8      3     180.0 !del,decreases P [100,250]
+! When O3' is ON5 (patch 3TER) 
+ON5  CN7  CN7  CN8B      0.2      4       0.0 !
+ON5  CN7  CN7  CN8B      0.8      3     180.0 !
+!======== ON6 CN7 CN7 ON2 = O4'-C4'-C3'-O3' 
+! These terms contribute to delta
+! These terms are present in THF3P and THFM3P but not in THF5P
+! When O3' is ON2 (3'-5' phosphodiester linkage)
+ON2  CN7  CN7  ON6       0.5     6        0.0 !del, good for amplitudes
+ON2  CN7  CN7  ON6       0.3     5        0.0 !del, impact on amplitudes
+ON2  CN7  CN7  ON6       0.6     4      180.0 !del, increases c2'endo
+ON2  CN7  CN7  ON6       0.2     3        0.0 !
+ON2  CN7  CN7  ON6B      0.4     6        0.0 !del, RNA, good for amplitudes
+ON2  CN7  CN7  ON6B      0.0     5        0.0 !del, RNA, impact on amplitudes
+ON2  CN7  CN7  ON6B      0.0     4      180.0 !del, RNA, increases c2'endo
+ON2  CN7  CN7  ON6B      1.6     3        0.0 !del, RNA, increases C2'endo
+! for ndph: make identical to ON2  CN7  CN7  ON6B
+ON2  CN7B CN7B ON6B      0.4     6        0.0 !del, RNA, good for amplitudes
+ON2  CN7B CN7B ON6B      0.0     5        0.0 !del, RNA, impact on amplitudes
+ON2  CN7B CN7B ON6B      0.0     4      180.0 !del, RNA, increases c2'endo
+ON2  CN7B CN7B ON6B      1.6     3        0.0 !del, RNA, increases C2'endo
+! When O3' is ON5 (patch 3TER)
+ON5  CN7  CN7  ON6       0.5     6        0.0 !  
+ON5  CN7  CN7  ON6       0.3     5        0.0 !  
+ON5  CN7  CN7  ON6       0.6     4      180.0 !  
+ON5  CN7  CN7  ON6       0.2     3        0.0 ! 
+ON5  CN7  CN7  ON6B      0.4     6        0.0 !RNA
+ON5  CN7  CN7  ON6B      0.0     5        0.0 !RNA
+ON5  CN7  CN7  ON6B      0.0     4      180.0 !RNA
+ON5  CN7  CN7  ON6B      1.6     3        0.0 !RNA. increases c2'endo
+
+!======== CN8B CN7 ON6 CN7B = C5'-C4'-O4'-C1' 
+! This term can be used to adjust the c2'endo/c3'endo  
+! energy difference in THF5P
+CN7B ON6  CN7  CN8B      0.8     3         0.0 ! P [30,80] 
+CN7B ON6B CN7  CN8B      2.0     3         0.0 ! To lower barrier in RNA
+CN7B ON6B CN7  CN9       2.0     3         0.0 ! To lower barrier in RNA, 5MET
+!======== ON2 CN7 CN8 CN7B = O3'-C3'-C2'-C1' 
+! This term can be used to adjust the c2'endo/c3'endo
+! When O3' is ON2 
+ON2  CN7  CN8  CN7B      0.8     6         0.0 !  
+ON2  CN7  CN8  CN7B      0.4     5         0.0 ! Moves the barrier right 
+ON2  CN7  CN8  CN7B      2.0     3       180.0 !  
+ON2  CN7  CN7B CN7B      0.6     6         0.0 ! RNA
+ON2  CN7  CN7B CN7B      0.0     5         0.0 ! RNA c2/c3 endo in RNA 
+ON2  CN7  CN7B CN7B      1.6     3       180.0 !
+!When O3' is ON5 (patch 3TER)
+ON5  CN7  CN8  CN7B      0.8     6         0.0 !
+ON5  CN7  CN8  CN7B      0.4     5         0.0 !
+ON5  CN7  CN8  CN7B      2.0     3       180.0 !
+ON5  CN7  CN7B CN7B      0.6     6         0.0 ! RNA, c2/c3 endo
+ON5  CN7  CN7B CN7B      0.0     5         0.0 ! RNA
+ON5  CN7  CN7B CN7B      1.6     3       180.0 ! RNA
+!======== ON2 CN7 CN8 HN8 = O3'-C3'-C2'-H 
+ON2  CN7  CN8  HN8       0.195   3         0.0 ! 
+ON5  CN7  CN8  HN8       0.195   3       180.0 !
+ON2  CN7  CN7B HN7       0.195   3         0.0 ! RNA
+ON5  CN7  CN7B HN7       0.195   3       180.0 ! RNA
+!======== HN7 CN7 CN7 ON2 = H-C4'-C3'-O3' 
+HN7  CN7  CN7  ON2       0.195   3         0.0
+HN7  CN7  CN7  ON5       0.195   3         0.0
+!======== CN7 CN7 ON2 P = C4'-C3'-O3'-P 
+CN7  CN7  ON2  P2        0.6     5         0.0 !eps, adm, 2011 DNA update
+CN7  CN7  ON2  P2        0.2     4         0.0 !eps, locat of 200 mimima, adm, 2011 DNA update
+CN7  CN7  ON2  P2        0.0     3       180.0 !eps, barE beteen minima, adm, 2011 DNA update
+CN7  CN7  ON2  P2        0.4     2         0.0 !eps, relE of 200 vs 275 min, adm, 2011 DNA update
+CN7  CN7  ON2  P2        1.9     1       180.0 !eps, adm, 2011 DNA update
+CN7  CN7  ON2  P         0.6     5         0.0 !eps, RNA
+CN7  CN7  ON2  P         0.2     4         0.0 !eps, locat of 200 mimima, RNA
+CN7  CN7  ON2  P         0.0     3       180.0 !eps, barE beteen minima, RNA
+CN7  CN7  ON2  P         0.4     2         0.0 !eps, relE of 200 vs 275 min, RNA
+CN7  CN7  ON2  P         1.9     1       180.0 !eps, RNA
+!======== CN8 CN7 ON2 P = C2'-C3'-O3'-P 
+! This term is involved in epsilon
+CN8  CN7  ON2  P         2.5     1       180.0 ! 3-terminal phosphate
+CN8  CN7  ON2  P2        1.9     1       180.0 ! adm, 2011 DNA update new param, eps
+CN7B CN7  ON2  P         2.5     1       180.0 !eps, RNA 
+CN7B CN7B ON2  P         2.5     1       180.0 !eps, NADPH and bkbmod
+CN7  CN7B ON2  P         2.5     1       180.0 !eps, NADPH and bkbmod
+! base on thfalloh
+! the following differ significantly from the protein based
+! alcohol parameters (based on ethanol, see above)
+CN7  CN7  ON5  HN5       0.5     3         0.0
+CN7  CN7  ON5  HN5       0.3     2       180.0
+CN7  CN7  ON5  HN5        1.5     1        0.0
+CN8  CN7  ON5  HN5       0.5     3         0.0
+CN8  CN7  ON5  HN5       1.0     2       180.0
+CN8  CN7  ON5  HN5       0.3     1         0.0
+CN7B CN7  ON5  HN5       0.8     3         0.0 ! RNA
+CN7B CN7  ON5  HN5       0.5     1         0.0 ! RNA
+! Was simply transfered from HN7  CN7  ON2  P
+! adm jr. should convert to alcohol term (see ribose etc)
+HN7  CN7  ON5  HN5       0.0     3         0.0
+HN7  CN7  CN8B HN8       0.195   3         0.0 !gam H-C4'-C5'-H
+HN7  CN7  CN7  CN8B      0.195   3         0.0 !gam H-C3'-C4'-C5'
+!@@@@@@ End of torsions involving exocyclic atoms:
+!@@@@@@ Begining of torsions for endocyclic atoms only:
+CN8  CN7B ON6  CN7       0.6     6       180.0 !C2'-C1'-O4'-C4'
+CN8  CN7  CN7  ON6       1.0     4         0.0 ! adm, 2011 DNA update new param, C2'-C3'-C4'-O4'; lowers c3'endo
+CN8  CN7  CN7  ON6       0.3     5       180.0 ! adm, 2011 DNA update new param, C2'-C3'-C4'-O4'; position of minima
+CN8  CN7  CN7  ON6       0.3     6       180.0 ! adm, 2011 DNA update new param, C2'-C3'-C4'-O4'; position of minima
+CN7B CN7B ON6B CN7       0.0     6         0.0 ! RNA, Lowers barrier
+CN7B CN7  CN7  ON6B      0.0     3         0.0 ! RNA
+!======== CN7 CN8 CN7B ON6 for nucleosides, transfered from =========
+!======== CN7 CN8  CN8  ON6 from thfoh ==============================
+CN7  CN8  CN7B ON6       0.6     6         0.0 ! C3'-C2'-C1'-O4', adjust barrier
+CN7  CN7B CN7B ON6B      0.4     6         0.0 ! RNA
+!======== C1'-C2'-C3'-C4' ========
+CN7B CN8  CN7  CN7       0.4      6        0.0 ! good for amplitudes
+CN7B CN7B CN7  CN7       0.0      6        0.0 ! RNA
+!======== CN7 CN7 ON6 CN7B for nucleosides, transfered from ========
+!======== CN7 CN7 ON6 CN8 from thfohch3 ============================
+CN7  CN7  ON6  CN7B      0.6      6      180.0 ! C3'-C4'-O4'-C1'
+CN7  CN7  ON6B CN7B      0.0      6      180.0 ! RNA
+!======== Directly adjusted with TM3P
+HN7  CN7  CN7  CN8       0.0      3        0.0 !puc,H-C3'-C4'-C5'
+!======== HN7 CN7 CN7 ON6 = H-C2'-C3'-O4'
+HN7  CN7  CN8  CN7B      0.195    3       0.0 !H-C3'-C2'-C1'
+HN7  CN7B CN8  CN7       0.195    3       0.0 !H-C1'-C2'-C3'
+HN7  CN7  CN7  ON6       0.195    3     180.0 ! useful
+HN8  CN8  CN7B ON6       0.195    3       0.0 !H-C2'-C1'-O4'
+HN7  CN7  CN7  HN7       0.195    3       0.0 !H-C4'-C3'-H
+HN7  CN7B CN8  HN8       0.195    3       0.0 !H-C1'-C2'-H 
+HN7  CN7  CN8  HN8       0.195    3       0.0 !H-C3'-C2'-H
+HN8  CN8  CN7  CN7       0.195    3       0.0 ! useful *cccc*
+HN7  CN7  ON6  CN7B      0.195    3       0.0 !H-C3'-C2'-C1'
+HN7  CN7B ON6  CN7       0.000    3       0.0 !H-C1'-O4'-C4'
+HN7  CN7  CN7  ON6B      0.195    3     180.0 ! RNA
+HN9  CN9  CN7  ON6B      0.195    3     180.0 ! RNA, 5MET
+HN8  CN8  CN7B ON6B      0.195    3       0.0 ! RNA
+HN7  CN7B ON6B CN7       0.000    3       0.0 ! RNA
+HN7  CN7  ON6B CN7B      0.195    3       0.0 ! RNA
+HN7  CN7  CN7B CN7B      0.195    3       0.0 ! RNA, H-C3'-C2'-C1'
+HN7  CN7B CN7B CN7       0.195    3       0.0 ! RNA, H-C1'-C2'-C3'
+HN7  CN7B CN7B ON6B      0.195    3       0.0 ! RNA, H-C2'-C1'-O4'
+!@@@@@@ End of torsions for endocyclic atoms only
+
+!@@@@@@ Begining of torsions specifically defined for RNA @@@@@@
+! N9-C1'-C2'-O2':
+NN2  CN7B CN7B ON5       0.000    3       0.0 ! Adenine and cytosine
+NN2B CN7B CN7B ON5       0.000    3       0.0 ! Guanine and uracil
+ON5  CN7B CN7B HN7       0.000    3       0.0 ! 
+HN7  CN7B CN7B HN7       0.000    3       0.0 ! 
+CN7  CN7  CN7B ON5       0.000    3       0.0
+ON6B CN7B CN7B ON5       0.000    3       0.0
+ON5  CN7B CN7  ON2       0.000    3       0.0
+! for ndph
+ON5  CN7  CN7B ON2       0.000    3       0.0
+ON5  CN7B CN7  ON5       0.000    3       0.0
+HN7  CN7B ON5  HN5       0.000    3       0.0
+!ejd, 2010 RNA update
+HN5  ON5  CN7B CN7B      0.000    6     180.0 ! ejd, 2010 RNA update
+HN5  ON5  CN7B CN7B      0.400    3       0.0 ! shifts min, ejd, 2010 RNA update
+HN5  ON5  CN7B CN7B      0.400    2       0.0 ! ejd, 2010 RNA update
+HN5  ON5  CN7B CN7B      0.800    1       0.0 ! height of right barrier and can shift min, ejd, 2010 RNA update
+!to C3'
+HN5  ON5  CN7B CN7       0.200    3       0.0 ! ejd, 2010 RNA update
+HN5  ON5  CN7B CN7       0.000    2     180.0 ! ejd, 2010 RNA update
+HN5  ON5  CN7B CN7       2.000    1       0.0 ! height of left side barrier, ejd, 2010 RNA update
+!@@@@@@ End of torsions specifically defined for RNA @@@@@@
+
+!Collection of parameters that were previously incorrectly categorized or labeled
+CN7B ON6  CN7  CN9       0.0     3         0.0 ! added for sugar model compounds
+HN7  CN7  CN7B ON5       0.195   3         0.0 ! for nadp/nadph (NOT!), adm jr.
+HN7  CN7B CN7  CN7       0.195   3         0.0 ! for nadp/nadph (NOT!), adm jr.
+HN7  CN7  CN7  CN7B      0.195   3         0.0 ! for nadp/nadph (NOT!), adm jr.
+HN7  CN7  CN7B HN7       0.195   3         0.0 ! for nadp/nadph (NOT!), adm jr.
+
+IMPROPER
+!
+!V(improper) = Kpsi(psi - psi0)**2
+!
+!Kpsi: kcal/mole/rad**2
+!psi0: degrees
+!note that the second column of numbers (0) is ignored
+!
+!atom types           Kpsi                   psi0
+!
+!
+HN2  X    X    NN2      1.0     0     0.0     !C, adm jr. 11/97
+NN2B CN4  CN5  HN2      7.0     0     0.0     !G, adm jr. 11/97
+HN1  X    X    NN1      4.0     0     0.0     !G, adm jr. 11/97
+NN1  CN2  HN1  HN1      6.0     0     0.0     !A,C adm jr. 11/97
+CN1  X    X    ON1     90.0     0     0.0     !U
+CN1T X    X    ON1     90.0     0     0.0     !U
+CN1  NN2G CN5G ON1     90.0     0     0.0     !G
+CN1T NN2B NN2U ON1    110.0     0     0.0     !T/O2, adm jr. 11/97
+CN1  NN2U CN3T ON1     90.0     0     0.0     !T/O4, adm jr. 11/97
+CN1  X    X    ON1C    80.0     0     0.0     !C, par_32, adm jr. 10/2/91
+CN2  X    X    NN1     90.0     0     0.0     !C, 
+CN2  NN3G NN2G NN1     40.0     0     0.0     !G
+CN2  NN3A CN5  NN1     40.0     0     0.0     !A
+CN2  NN3  CN3  NN1     60.0     0     0.0     !C, 
+CN9  X    X    CN3T    14.0     0     0.0     !T, adm jr. 11/97
+
+! Wildcards used to minimize memory requirements
+NONBONDED  NBXMOD 5  ATOM CDIEL FSHIFT VATOM VDISTANCE VFSWITCH -
+     CUTNB 14.0  CTOFNB 12.0  CTONNB 10.0  EPS 1.0  E14FAC 1.0  WMIN 1.5
+!
+!V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6]
+!
+!epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j)
+!Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j
+!
+!atom  ignored    epsilon      Rmin/2   ignored   eps,1-4       Rmin/2,1-4
+!
+HN1      0.0       -0.0460    0.2245 
+HN2      0.0       -0.0460    0.2245 
+HN3      0.0       -0.046     1.1000 !adm jr. aromatic Hvdw 
+HN4      0.0       -0.0460    0.2245
+HN5      0.0       -0.0460    0.2245
+HN6      0.0       -0.0220    1.3200
+HN7      0.0       -0.0220    1.3200
+HN8      0.0       -0.0280    1.3400 ! Hydrogen bound to CN8
+HN9      0.0       -0.0240    1.3400 ! Hydrogen bound to CN9
+!
+NN1      0.0        -0.20     1.85
+NN2      0.0        -0.20     1.85
+NN2B     0.0        -0.20     1.85 ! From NN2, for N9 in guanines
+NN2G     0.0        -0.20     1.85
+NN2U     0.0        -0.20     1.85
+NN3      0.0        -0.20     1.85
+NN3A     0.0        -0.20     1.85 
+NN3G     0.0        -0.20     1.85 
+NN4      0.0        -0.20     1.85
+NN6      0.0        -0.20     1.85
+!
+ON1      0.0       -0.1200    1.70  
+ON1C     0.0       -0.1200    1.70 
+ON2      0.0       -0.1521    1.77   
+ON3      0.0       -0.1200    1.70  
+ON4      0.0       -0.1521    1.77  
+ON5      0.0       -0.1521    1.77  
+ON6      0.0       -0.1521    1.77  
+ON6B     0.0       -0.1521    1.77  
+!
+! base ring C vdw param, 11/14/97, adm jr
+CN1      0.0       -0.10      1.9000
+CN1T     0.0       -0.10      1.9000
+CN2      0.0       -0.10      1.9000
+CN3      0.0       -0.09      1.9000
+CN3T     0.0       -0.09      1.9000 ! T, adm jr.
+CN4      0.0       -0.075     1.9000
+CN5      0.0       -0.075     1.9000
+CN5G     0.0       -0.075     1.9000
+CN7      0.0       -0.02      2.275  0.0   -0.01 1.90 !equivalent to protein CT1
+CN7B     0.0       -0.02      2.275  0.0   -0.01 1.90 !equivalent to protein CT1
+! alkane optimized terms below, Yin and MacKerell, 1998, JCC, In press
+CN8      0.0       -0.0560    2.010  0.0   -0.01 1.90 !
+CN8B     0.0       -0.0560    2.010  0.0   -0.01 1.90 !
+CN9      0.0       -0.0780    2.040  0.0   -0.01 1.90 !
+!
+P        0.0       -0.585     2.15  
+P2       0.0       -0.585     2.15  
+
+NBFIX
+!               Emin        Rmin
+!            (kcal/mol)     (A)
+!
+
+HBOND CUTHB 0.5  ! If you want to do hbond analysis (only), then use
+                 ! READ PARAM APPEND CARD
+                 ! to append hbond parameters from the file: par_hbond.inp
+
+END

tests/0-forcefields/par_all36m_prot.prm

@@ -0,0 +1,3411 @@
+*>>>> CHARMM36 All-Hydrogen Parameter File for Proteins <<<<<<<<<<
+*>>>>> Includes phi, psi cross term map (CMAP) correction <<<<<<<<
+*>>>>>>>>>>>>>>>>>>>>>>>>>> Jan. 2016 <<<<<<<<<<<<<<<<<<<<<<<<<<<<
+* All comments to the CHARMM web site: www.charmm.org
+*             parameter set discussion forum
+*
+
+!updated 2016/1, modified alanine CMAP and acid-guanidinium NBFIX
+
+!references
+!
+!Huang, J. et al. Manuscript in preparation: 2016 modification of
+!the additive all-atom C36 protein force field.
+!
+!Robert B. Best, R.B., Xiao Zhu, X., Shim, J., Lopes, P.
+!Mittal, J., Feig, M. and MacKerell, A.D., Jr. Optimization of the
+!additive CHARMM all-atom protein force field targeting improved
+!sampling of the backbone phi, psi and sidechain chi1 and chi2
+!dihedral angles. In preparation
+!
+!MacKerell, A.D., Jr., Feig, M. and Brooks, III, C.L. "Improved
+!treatment of the protein backbone in empirical force fields," Journal
+!of the American Chemical Society, 126: 698-699, 2004
+!
+!MacKerell, Jr., A. D.; Bashford, D.; Bellott, M.; Dunbrack Jr., R.L.;
+!Evanseck, J.D.; Field, M.J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.;
+!Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F.T.K.; Mattos,
+!C.; Michnick, S.; Ngo, T.; Nguyen, D.T.; Prodhom, B.; Reiher, III,
+!W.E.; Roux, B.; Schlenkrich, M.; Smith, J.C.; Stote, R.; Straub, J.;
+!Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M.  All-atom
+!empirical potential for molecular modeling and dynamics Studies of
+!proteins.  Journal of Physical Chemistry B, 1998, 102, 3586-3616.
+
+ATOMS
+MASS  -1  H          1.00800 ! polar H
+MASS  -1  HC         1.00800 ! N-ter H
+MASS  -1  HA         1.00800 ! nonpolar H
+MASS  -1  HP         1.00800 ! aromatic H
+MASS  -1  HB1        1.00800 ! backbone H
+MASS  -1  HB2        1.00800 ! aliphatic backbone H, to CT2
+MASS  -1  HR1        1.00800 ! his he1, (+) his HG,HD2
+MASS  -1  HR2        1.00800 ! (+) his HE1
+MASS  -1  HR3        1.00800 ! neutral his HG, HD2
+MASS  -1  HS         1.00800 ! thiol hydrogen
+MASS  -1  HE1        1.00800 ! for alkene; RHC=CR
+MASS  -1  HE2        1.00800 ! for alkene; H2C=CR
+MASS  -1  HA1        1.00800 ! alkane, CH, new LJ params (see toppar_all22_prot_aliphatic_c27.str)
+MASS  -1  HA2        1.00800 ! alkane, CH2, new LJ params (see toppar_all22_prot_aliphatic_c27.str)
+MASS  -1  HA3        1.00800 ! alkane, CH3, new LJ params (see toppar_all22_prot_aliphatic_c27.str)
+MASS  -1  C         12.01100 ! carbonyl C, peptide backbone
+MASS  -1  CA        12.01100 ! aromatic C
+MASS  -1  CT        12.01100 ! aliphatic sp3 C, new LJ params, no hydrogens, see retinol stream file for parameters
+MASS  -1  CT1       12.01100 ! aliphatic sp3 C for CH
+MASS  -1  CT2       12.01100 ! aliphatic sp3 C for CH2
+MASS  -1  CT2A      12.01100 ! from CT2 (GLU, HSP chi1/chi2 fitting) 05282010, zhu
+MASS  -1  CT3       12.01100 ! aliphatic sp3 C for CH3
+MASS  -1  CPH1      12.01100 ! his CG and CD2 carbons
+MASS  -1  CPH2      12.01100 ! his CE1 carbon
+MASS  -1  CPT       12.01100 ! trp C between rings
+MASS  -1  CY        12.01100 ! TRP C in pyrrole ring
+MASS  -1  CP1       12.01100 ! tetrahedral C (proline CA)
+MASS  -1  CP2       12.01100 ! tetrahedral C (proline CB/CG)
+MASS  -1  CP3       12.01100 ! tetrahedral C (proline CD)
+MASS  -1  CC        12.01100 ! carbonyl C, asn,asp,gln,glu,cter,ct2
+MASS  -1  CD        12.01100 ! carbonyl C, pres aspp,glup,ct1
+MASS  -1  CS        12.01100 ! thiolate carbon
+MASS  -1  CE1       12.01100 ! for alkene; RHC=CR
+MASS  -1  CE2       12.01100 ! for alkene; H2C=CR
+MASS  -1  CAI       12.01100 ! aromatic C next to CPT in trp
+MASS  -1  N         14.00700 ! proline N
+MASS  -1  NR1       14.00700 ! neutral his protonated ring nitrogen
+MASS  -1  NR2       14.00700 ! neutral his unprotonated ring nitrogen
+MASS  -1  NR3       14.00700 ! charged his ring nitrogen
+MASS  -1  NH1       14.00700 ! peptide nitrogen
+MASS  -1  NH2       14.00700 ! amide nitrogen
+MASS  -1  NH3       14.00700 ! ammonium nitrogen
+MASS  -1  NC2       14.00700 ! guanidinium nitrogen
+MASS  -1  NY        14.00700 ! TRP N in pyrrole ring
+MASS  -1  NP        14.00700 ! Proline ring NH2+ (N-terminal)
+MASS  -1  O         15.99900 ! carbonyl oxygen
+MASS  -1  OB        15.99900 ! carbonyl oxygen in acetic acid
+MASS  -1  OC        15.99900 ! carboxylate oxygen
+MASS  -1  OH1       15.99900 ! hydroxyl oxygen
+MASS  -1  OS        15.99940 ! ester oxygen
+MASS  -1  S         32.06000 ! sulphur
+MASS  -1  SM        32.06000 ! sulfur C-S-S-C type
+MASS  -1  SS        32.06000 ! thiolate sulfur
+
+
+BONDS
+!
+!V(bond) = Kb(b - b0)**2
+!
+!Kb: kcal/mole/A**2
+!b0: A
+!
+!atom type Kb          b0
+!
+NH2  CT1   240.000     1.4550 ! From LSN NH2-CT2
+!
+!Indole/Tryptophan
+CA   CAI   305.000     1.3750 ! from CA CA
+CAI  CAI   305.000     1.3750 ! atm, methylindole, fit CCDSS
+CPT  CA    300.000     1.3600 ! atm, methylindole, fit CCDSS
+CPT  CAI   300.000     1.3600 ! atm, methylindole, fit CCDSS
+CPT  CPT   360.000     1.3850 ! atm, methylindole, fit CCDSS
+CY   CA    350.000     1.3650 ! trj, adm jr., 5/08/91, indole CCDB structure search
+CY   CAI   350.000     1.3650 ! from CY CA
+CY   CPT   350.000     1.4300 ! atm, methylindole, fit CDS data
+CY   CT3   375.000     1.4920 ! atm, methylindole, fit CDS data
+CY   CT2   375.000     1.4920 ! atm, methylindole, fit CDS data
+HP   CAI   340.000     1.0800 ! from HP CA
+HP   CY    350.000     1.0800 ! trp, adm jr., 12/30/91
+NY   CA    270.000     1.3700 ! trp, adm jr., 12/30/91
+NY   CPT   270.000     1.3700 ! atm, methylindole, from CCDS 1/17/04
+NY   H     537.500     0.9760 ! atm, methylindole, 1/17/04
+CA   CA    305.000     1.3750 ! ALLOW   ARO
+                ! benzene, JES 8/25/89
+CE1  CE1   440.000     1.3400   ! 
+		! for butene; from propene, yin/adm jr., 12/95
+CE1  CE2   500.000     1.3420   ! 
+		! for propene, yin/adm jr., 12/95
+CE1  CT2   365.000     1.5020   ! 
+		! for butene; from propene, yin/adm jr., 12/95
+CE1  CT3   383.000     1.5040   ! 
+		! for butene, yin/adm jr., 12/95
+CE2  CE2   510.000     1.3300   ! 
+		! for ethene, yin/adm jr., 12/95
+CP1  C     250.000     1.4900 ! ALLOW PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CP1  CC    250.000     1.4900 ! ALLOW PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CP1  CD    200.000     1.4900 ! ALLOW PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CP2  CP1   222.500     1.5270 ! ALLOW PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CP2  CP2   222.500     1.5370 ! ALLOW PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CP3  CP2   222.500     1.5370 ! ALLOW PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CPH1 CPH1  410.000     1.3600 ! ALLOW ARO
+                ! histidine, adm jr., 6/27/90
+CT1  C     250.000     1.4900 ! ALLOW   ALI PEP POL ARO
+                ! Ala Dipeptide ab initio calc's (LK) fixed from 10/90 (5/91)
+CT1  CC    200.000     1.5220 ! ALLOW   POL
+                ! adm jr. 4/05/91, for asn,asp,gln,glu and cters
+CT1  CD    200.000     1.5220 ! ALLOW   POL
+                ! adm jr. 5/02/91, acetic acid pure solvent
+CT1  CT1   222.500     1.5000 ! ALLOW   ALI
+                ! alkane update, adm jr., 3/2/92
+CT2  C     250.000     1.4900 ! ALLOW   ALI PEP POL ARO
+                ! Ala Dipeptide ab initio calc's (LK) fixed from 10/90 (5/91)
+CT2  CA    230.000     1.4900 ! ALLOW   ALI ARO
+                ! phe,tyr, JES 8/25/89
+CT2  CC    200.000     1.5220 ! ALLOW   POL
+                ! adm jr. 4/05/91, for asn,asp,gln,glu and cters
+CT2  CD    200.000     1.5220 ! ALLOW   POL
+                ! adm jr. 5/02/91, acetic acid pure solvent
+CT2  CPH1  229.630     1.5000 ! ALLOW ARO
+                ! his, adm jr., 7/22/89, FC from CT2CT, BL from crystals
+CT2  CT1   222.500     1.5380 ! ALLOW   ALI
+                ! alkane update, adm jr., 3/2/92
+CT2  CT2   222.500     1.5300 ! ALLOW   ALI
+                ! alkane update, adm jr., 3/2/92
+CT3  C     250.000     1.4900 ! ALLOW   ALI PEP POL ARO
+                ! Ala Dipeptide ab initio calc's (LK) fixed from 10/90 (5/91)
+CT3  CA    230.000     1.4900 ! ALLOW   ALI ARO
+                ! toluene, adm jr. 3/7/92
+CT3  CC    200.000     1.5220 ! ALLOW   POL
+                ! adm jr. 4/05/91, for asn,asp,gln,glu and cters
+CT3  CD    200.000     1.5220 ! ALLOW   POL
+                ! adm jr. 5/02/91, acetic acid pure solvent
+CT3  CPH1  229.630     1.5000 ! ALLOW ARO
+                ! his, adm jr., 7/22/89, FC from CT2CT, BL from crystals
+CT3  CS    190.000     1.5310 ! ALLOW   SUL
+                ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
+CT3  CT1   222.500     1.5380 ! ALLOW   ALI
+                ! alkane update, adm jr., 3/2/92
+CT3  CT2   222.500     1.5280 ! ALLOW   ALI
+                ! alkane update, adm jr., 3/2/92
+CT3  CT3   222.500     1.5300 ! ALLOW   ALI
+                ! alkane update, adm jr., 3/2/92
+H    CD    330.000     1.1100 ! ALLOW   PEP POL ARO
+                ! adm jr. 5/02/91, acetic acid pure solvent
+HA1  CC    317.130     1.1000 ! ALLOW POL
+                ! adm jr., 5/13/91, formamide geometry and vibrations
+HA2  CP2   309.000     1.1110 ! ALLOW PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+HA2  CP3   309.000     1.1110 ! ALLOW PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+HA2  CS    300.000     1.1110 ! ALLOW   SUL
+                ! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
+HA3  CS    300.000     1.1110 ! ALLOW   SUL
+                ! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
+HA1  CT1   309.000     1.1110 ! ALLOW   ALI
+                ! alkane update, adm jr., 3/2/92
+HA2  CT2   309.000     1.1110 ! ALLOW   ALI
+                ! alkane update, adm jr., 3/2/92
+HA3  CT3   322.000     1.1110 ! ALLOW   ALI
+                ! alkane update, adm jr., 3/2/92
+!HA   CY    330.000     1.0800 ! ALLOW   ARO
+                ! JWK 05/14/91 new r0 from indole
+HE1  CE1   360.500     1.1000   ! 
+		! for propene, yin/adm jr., 12/95
+HE2  CE2   365.000     1.1000   ! 
+		! for ethene, yin/adm jr., 12/95
+HB1  CP1   330.000     1.0800 ! ALLOW PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+HB1  CT1   330.000     1.0800 ! ALLOW   PEP
+                ! Alanine Dipeptide ab initio calc's (LK)
+HB2  CT2   330.000     1.0800 ! ALLOW   PEP
+                ! Alanine Dipeptide ab initio calc's (LK)
+!HB3  CT3   330.000     1.0800 ! ALLOW   PEP
+                ! Alanine Dipeptide ab initio calc's (LK)
+HP   CA    340.000     1.0800 ! ALLOW   ARO
+                ! phe,tyr JES 8/25/89
+HR1  CPH1  375.000     1.0830 ! ALLOW ARO
+                ! his, adm jr., 6/27/90
+HR1  CPH2  340.000     1.0900 ! ALLOW ARO
+                ! his, adm jr., 6/28/29
+HR2  CPH2  333.000     1.0700 ! ALLOW ARO
+                ! his, adm jr., 6/27/90
+HR3  CPH1  365.000     1.0830 ! ALLOW ARO
+                ! adm jr., 3/24/92, maintain old aliphatic H VDW params
+N    C     260.000     1.3000 ! ALLOW PEP POL ARO PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+N    CP1   320.000     1.4340 ! ALLOW PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+N    CP3   320.000     1.4550 ! ALLOW PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NC2  C     450.000     1.3650 ! ALLOW   PEP POL ARO
+                ! mp2/6-311g** mgua vib. data, adm jr., 1/04
+NC2  CT2   390.000     1.4900 ! ALLOW   ALI POL
+                ! mp2/6-311g** mgua vib. data, adm jr., 1/04
+NC2  CT3   390.000     1.4900 ! ALLOW   ALI POL
+                ! mp2/6-311g** mgua vib. data, adm jr., 1/04
+NC2  HC    455.000     1.0000 ! ALLOW   POL
+                ! 405.0->455.0 GUANIDINIUM (KK)
+NH1  C     370.000     1.3450 ! ALLOW   PEP POL ARO
+                ! Alanine Dipeptide ab initio calc's (LK)
+NH1  CT1   320.000     1.4300 ! ALLOW   ALI PEP POL ARO
+                ! NMA Gas & Liquid Phase IR Spectra (LK)
+NH1  CT2   320.000     1.4300 ! ALLOW   ALI PEP POL ARO
+                ! NMA Gas & Liquid Phase IR Spectra (LK)
+NH1  CT3   320.000     1.4300 ! ALLOW   ALI PEP POL ARO
+                ! NMA Gas & Liquid Phase IR Spectra (LK)
+NH1  H     440.000     0.9970 ! ALLOW   PEP POL ARO
+                ! Alanine Dipeptide ab initio calc's (LK)
+NH1  HC    405.000     0.9800 ! ALLOW   PEP POL ARO
+                ! (DS)
+NH2  CC    430.000     1.3600 ! ALLOW   PEP POL ARO
+                ! adm jr. 4/10/91, acetamide
+NH2  CT2   240.000     1.4550
+                ! from NH2  CT3, neutral glycine, adm jr.
+NH2  CT3   240.000     1.4550 ! ALLOW   POL
+                ! methylamine geom/freq, adm jr., 6/2/92
+NH2  H     480.000     1.0000 ! ALLOW   POL
+                ! adm jr. 8/13/90 acetamide geometry and vibrations
+NH2  HC    460.000     1.0000 ! ALLOW   POL
+                ! methylamine geom/freq, adm jr., 6/2/92
+NH3  CT1   200.000     1.4800 ! ALLOW   ALI POL
+                ! new stretch and bend; methylammonium (KK 03/10/92)
+NH3  CT2   200.000     1.4800 ! ALLOW   ALI POL
+                ! new stretch and bend; methylammonium (KK 03/10/92)
+NH3  CT3   200.000     1.4800 ! ALLOW   ALI POL
+                ! new stretch and bend; methylammonium (KK 03/10/92)
+NH3  HC    403.000     1.0400 ! ALLOW   POL
+                ! new stretch and bend; methylammonium (KK 03/10/92)
+NP   CP1   320.000     1.4850 ! ALLOW PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NP   CP3   320.000     1.5020 ! ALLOW PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NP   HC    460.000     1.0060 ! ALLOW PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NR1  CPH1  400.000     1.3800 ! ALLOW ARO
+                ! his, ADM JR., 7/20/89
+NR1  CPH2  400.000     1.3600 ! ALLOW ARO
+                ! his, ADM JR., 7/20/89
+NR1  H     466.000     1.0000 ! ALLOW ARO
+                ! his, ADM JR., 7/20/89
+NR2  CPH1  400.000     1.3800 ! ALLOW ARO
+                ! his, ADM JR., 7/20/89
+NR2  CPH2  400.000     1.3200 ! ALLOW ARO
+                ! his, ADM JR., 7/20/89
+NR3  CPH1  380.000     1.3700 ! ALLOW ARO
+                ! his, adm jr., 6/28/90
+NR3  CPH2  380.000     1.3200 ! ALLOW ARO
+                ! his, adm jr., 6/27/90
+NR3  H     453.000     1.0000 ! ALLOW ARO
+                ! his, adm jr., 6/27/90
+O    C     620.000     1.2300 ! ALLOW   PEP POL ARO
+                ! Peptide geometry, condensed phase (LK)
+O    CC    650.000     1.2300 ! ALLOW   PEP POL ARO
+                ! adm jr. 4/10/91, acetamide
+OB   CC    750.000     1.2200 ! ALLOW   PEP POL ARO
+                ! adm jr., 10/17/90, acetic acid vibrations and geom.
+OB   CD    750.000     1.2200 ! ALLOW   PEP POL ARO
+                ! adm jr. 5/02/91, acetic acid pure solvent
+OC   CA    525.000     1.2600 ! ALLOW   PEP POL ARO ION
+                ! adm jr. 8/27/91, phenoxide
+OC   CC    525.000     1.2600 ! ALLOW   PEP POL ARO ION
+                ! adm jr. 7/23/91, acetic acid
+OC   CT2   450.000     1.3300 ! ALLOW   ALC
+                ! ethoxide 6-31+G* geom/freq, adm jr., 6/1/92
+OC   CT3   450.000     1.3300 ! ALLOW   ALC
+                ! methoxide 6-31+G* geom/freq, adm jr., 6/1/92
+OH1  CA    334.300     1.4110 ! ALLOW   ARO ALC
+                ! MeOH, EMB 10/10/89,
+OH1  CD    230.000     1.4000 ! ALLOW   PEP POL ARO ALC
+                ! adm jr. 5/02/91, acetic acid pure solvent
+OH1  CT1   428.000     1.4200 ! ALLOW   ALI ALC ARO
+                ! methanol vib fit EMB 11/21/89
+OH1  CT2   428.000     1.4200 ! ALLOW   ALI ALC ARO
+                ! methanol vib fit EMB 11/21/89
+OH1  CT3   428.000     1.4200 ! ALLOW   ALI ALC ARO
+                ! methanol vib fit EMB 11/21/89
+OH1  H     545.000     0.9600 ! ALLOW   ALC ARO
+                ! EMB 11/21/89 methanol vib fit
+OS   CD    150.000     1.3340 ! ALLOW POL PEP
+                ! adm jr. 5/02/91, acetic acid pure solvent
+OS   CT3   340.000     1.4300 ! ALLOW POL PEP
+                ! adm jr., 4/05/91, for PRES CT1 from methylacetate
+S    CT2   198.000     1.8180 ! ALLOW   ALI SUL ION
+                ! fitted to C-S s   9/26/92 (FL)
+S    CT3   240.000     1.8160 ! ALLOW   ALI SUL ION
+                ! fitted to C-S s   9/26/92 (FL)
+S    HS    275.000     1.3250 ! ALLOW   SUL ION
+                ! methanethiol pure solvent, adm jr., 6/22/92
+SM   CT2   214.000     1.8160 ! ALLOW   SUL ION
+                ! improved CSSC surface in DMDS  5/15/92 (FL)
+SM   CT3   214.000     1.8160 ! ALLOW   SUL ION
+                ! improved CSSC surface in DMDS  5/15/92 (FL)
+SM   SM    173.000     2.0290 ! ALLOW   SUL ION
+                ! improved CSSC surface in DMDS  5/15/92 (FL)
+SS   CS    205.000     1.8360 ! ALLOW   SUL
+                ! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
+HR1  CD    330.000     1.1100 ! acetaldehyde, benzaldehyde, 3ALP
+O    CD    720.000     1.2050 ! acetaldehyde, benzaldehyde, 3ALP. from stream/toppar_all27_na_bkb_modifications.str
+CT2A CT1   222.500     1.5380 ! from CT2  CT1, Zhu
+CT2  CT2A  222.500     1.5300 ! from CT2  CT2, Zhu
+CT2A HA2   309.000     1.1110 ! from HA2  CT2, Zhu
+CT2A CPH1  229.630     1.5000 ! from CT2  CPH1, Zhu
+!ASP, CT2->CT2A
+CT2A CC    200.000     1.5220 ! from CT2  CC, jshim
+! RESI CYSM and PRES CYSD
+CT1  CS    190.000     1.5380 ! from CT3 CS but lengthened; compare CT3 CT2 with CT2 CT1; kevo
+
+ANGLES
+!
+!V(angle) = Ktheta(Theta - Theta0)**2
+!
+!V(Urey-Bradley) = Kub(S - S0)**2
+!
+!Ktheta: kcal/mole/rad**2
+!Theta0: degrees
+!Kub: kcal/mole/A**2 (Urey-Bradley)
+!S0: A
+!
+!atom types     Ktheta    Theta0   Kub     S0
+!
+H    NH2  CT1   50.000    111.00              ! From LSN HC-NH2-CT2
+H    NH2  CT2   50.000    111.00              ! From LSN HC-NH2-CT2, Neutral Gly Nterminus
+NH2  CT1  CT1   67.700    110.00              ! From LSN NH2-CT2-CT2
+NH2  CT1  CT2   67.700    110.00              ! From LSN NH2-CT2-CT2
+NH2  CT1  CT3   67.700    110.00              ! From LSN NH2-CT2-CT2
+CT1  CD   OH1   55.000    110.50              ! From ASPP CT2-CD-OH1
+CT3  CT1  CD    52.000    108.00              ! Ala cter
+NH2  CT1  HB1   38.000    109.50   50.00   2.1400 ! From LSN NH2-CT2-HA
+NH2  CT1  C     50.000    107.00              ! From ALA Dipep. NH1-CT2-C
+NH2  CT2  C     50.000    107.00              ! From ALA Dipep. NH1-CT2-C, Neutral Gly Nterminus
+!
+!Indole/Tryptophan
+CAI  CAI  CA    40.000    120.00   35.00   2.41620 ! from CA CA CA
+CAI  CA   CA    40.000    120.00   35.00   2.41620 ! from CA CA CA
+CPT  CA   CA    50.000    113.20 ! atm, methylindole, 1/17/04
+CPT  CPT  CA    50.000    110.00 ! atm, methylindole, 1/17/04
+CPT  CAI  CA    50.000    113.20 ! atm, methylindole, 1/17/04
+CPT  CPT  CAI   50.000    110.00 ! atm, methylindole, 1/17/04
+CPT  CY   CA    85.000    106.40   25.00   2.26100 ! atm, methylindole, 1/17/04
+CPT  NY   CA    85.000    112.00 ! atm, methylindole, 1/17/04
+CT2  CY   CA    30.000    127.00 ! atm, methylindole, CT3  CY   CA
+CT2  CY   CPT   30.000    126.70 ! atm, methylindole, 1/17/04
+CT3  CY   CA    30.000    127.00 ! atm, methylindole, CT3  CY   CA
+CT3  CY   CPT   30.000    126.70 ! atm, methylindole, 1/17/04
+CY   CPT  CA   130.000    133.50 ! atm, methylindole, 1/17/04
+CY   CPT  CAI  130.000    133.50 ! atm, methylindole, 1/17/04
+CY   CPT  CPT   85.000    108.00 ! atm, methylindole, 1/17/04
+CY   CT2  CT1   58.350    114.00 ! from TRP crystal, JWK
+CY   CT2  CT3   58.350    114.00 ! from TRP crystal, JWK
+H    NY   CA    28.000    126.00 ! trp, adm jr., 12/30/91
+H    NY   CAI   28.000    126.00 ! trp, adm jr., 12/30/91
+H    NY   CPT   28.000    126.00 ! trp, adm jr., 12/30/91
+HA2  CT2  CY    55.000    109.50 ! atm, methylindole, 1/17/04
+HA3  CT3  CY    55.000    109.50 ! atm, methylindole, 1/17/04
+HP   CA   CAI   30.000    120.00   22.00   2.15250 ! from HP CA CA
+HP   CAI  CA    30.000    120.00   22.00   2.15250 ! from HP CA CA
+HP   CA   CPT   30.000    122.00   22.00   2.14600 ! trp, adm jr., 12/30/91
+HP   CAI  CPT   30.000    122.00   22.00   2.14600 ! from HP CA CPT
+HP   CA   CY    32.000    125.00   25.00   2.17300 ! JWK 05/14/91 new theta0 and r0UB from indole
+HP   CY   CA    32.000    126.40   25.00   2.18600 ! trp, adm jr., 12/30/91
+HP   CY   CPT   32.000    126.40   25.00   2.25500 ! JWK 05/14/91 new theta0 and r0UB from indole
+NY   CA   CY    85.000    110.50   25.00   2.24000 ! trp, adm jr., 12/30/91
+NY   CA   HP    32.000    125.00   25.00   2.17700 ! JWK 05/14/91 new theta0 and r0UB from indole
+NY   CPT  CA   130.000    129.50 ! atm, methylindole, 1/17/04
+NY   CPT  CAI  130.000    129.50 ! atm, methylindole, 1/17/04
+NY   CPT  CPT   95.000    107.40 ! atm, methylindole, 1/17/04
+CA   CA   CA    40.000    120.00   35.00   2.41620 ! ALLOW   ARO
+                ! JES 8/25/89
+CE1  CE1  CT2    48.00    123.50   !
+                ! for 2-butene, yin/adm jr., 12/95
+CE1  CE1  CT3    48.00    123.50   ! 
+		! for 2-butene, yin/adm jr., 12/95
+CE1  CT2  CT3    32.00    112.20   ! 
+		! for 1-butene; from propene, yin/adm jr., 12/95
+CE2  CE1  CT2    48.00    126.00   ! 
+		! for 1-butene; from propene, yin/adm jr., 12/95
+CE2  CE1  CT3    47.00    125.20   ! 
+		! for propene, yin/adm jr., 12/95
+CP1  N    C      60.000   117.0000 ! ALLOW PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CP2  CP1  C      52.000   112.3000 ! ALLOW PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CP2  CP1  CC     52.000   112.3000 ! ALLOW PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CP2  CP1  CD     50.000   112.3000 ! ALLOW PRO PEP
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CP2  CP2  CP1    70.000   108.5000 ! ALLOW PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CP3  CP2  CP2    70.000   108.5000 ! ALLOW PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CP3  N    C      60.000   117.0000 ! ALLOW PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CP3  N    CP1   100.000   114.2000 ! ALLOW PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CP3  NP   CP1   100.000   111.0000 ! ALLOW PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CPH2 NR1  CPH1  130.000   107.5000 ! ALLOW ARO
+                ! his, adm jr., 6/27/90
+CPH2 NR2  CPH1  130.000   104.0000 ! ALLOW ARO
+                ! his, adm jr., 6/27/90
+CPH2 NR3  CPH1  145.000   108.0000 ! ALLOW ARO
+                ! his, ADM JR., 7/20/89
+CT1  CT1  C      52.000   108.0000 ! ALLOW   ALI PEP POL ARO
+                ! Alanine Dipeptide ab initio calc's (LK)
+CT1  CT1  CC     52.000   108.0000 ! ALLOW   ALI PEP POL ARO
+                ! adm jr. 4/05/91, for asn,asp,gln,glu and cters
+CT1  CT1  CD     52.000   108.0000 ! ALLOW   ALI PEP POL ARO
+                ! adm jr. 6/27/2012, for Thr with CT1 patch
+CT1  CT1  CT1   53.350    111.00    8.00   2.56100 ! ALLOW ALI
+                ! alkane update, adm jr., 3/2/92
+CT1  CT2  CA     51.800   107.5000 ! ALLOW   ALI ARO
+                ! PARALLH19 (JES)
+CT1  CT2  CC     52.000   108.0000 ! ALLOW   ALI PEP POL ARO
+                ! adm jr. 4/05/91, for asn,asp,gln,glu and cters
+CT1  CT2  CD     52.000   108.0000 ! ALLOW   ALI PEP POL ARO
+                ! adm jr. 5/02/91, acetic acid pure solvent
+CT1  CT2  CPH1   58.350   113.0000 ! ALLOW ARO
+                ! his, ADM JR., 7/22/89, from CT2CT2CT, U-B omitted
+CT1  CT2  CT1   58.350    113.50   11.16   2.56100 ! ALLOW   ALI
+                ! alkane frequencies (MJF), alkane geometries (SF)
+CT1  NH1  C      50.000   120.0000 ! ALLOW   ALI PEP POL ARO
+                ! NMA Vib Modes (LK)
+CT2  CA   CA     45.800   122.3000 ! ALLOW   ALI ARO
+                ! PARALLH19 (JES)
+CT2  CPH1 CPH1   45.800   130.0000 ! ALLOW ARO
+                ! his, ADM JR., 7/22/89, FC=>CT2CA CA,BA=> CRYSTALS
+CT2  CT1  C      52.000   108.0000 ! ALLOW   ALI PEP POL ARO
+                ! Alanine Dipeptide ab initio calc's (LK)
+CT2  CT1  CC     52.000   108.0000 ! ALLOW   ALI PEP POL ARO
+                ! adm jr. 4/05/91, for asn,asp,gln,glu and cters
+CT2A CT1  CC     52.000   108.0000 ! ALLOW   ALI PEP POL ARO
+                ! adm jr. 4/05/91, for asn,asp,gln,glu and cters
+CT2  CT1  CD     52.000   108.0000 ! ALLOW   ALI PEP POL ARO
+                ! adm jr. 5/02/91, acetic acid pure solvent
+CT2  CT1  CT1   53.350    111.00    8.00   2.56100 ! ALLOW   ALI
+                ! alkane update, adm jr., 3/2/92
+CT2  CT2  C      52.000   108.0000 ! ALLOW   ALI PEP POL ARO
+                ! from CT2  CT1  C, for lactams, adm jr.
+CT2  CT2  CC     52.000   108.0000 ! ALLOW   ALI PEP POL ARO
+                ! adm jr. 4/05/91, for asn,asp,gln,glu and cters
+CT3  CT2  CC     52.000   108.0000 ! ALLOW   ALI PEP POL ARO
+                ! adm jr. 4/05/91, for asn,asp,gln,glu and cters
+CT2  CT2  CD     52.000   108.0000 ! ALLOW   ALI PEP POL ARO
+                ! adm jr. 5/02/91, acetic acid pure solvent
+CT2A CT2  CD     52.000   108.0000 ! for GLUP, ZHU
+CT2  CT2  CT1   58.350    113.50   11.16   2.56100 ! ALLOW   ALI
+                ! alkane frequencies (MJF), alkane geometries (SF)
+CT2  CT2  CT2   58.350    113.60   11.16   2.56100 ! ALLOW   ALI
+                ! alkane update, adm jr., 3/2/92
+CT2  CT3  CT1   58.350    113.50   11.16   2.56100 ! ALLOW   ALI
+                ! alkane frequencies (MJF), alkane geometries (SF)
+CT2  NC2  C      62.300   120.0000 ! ALLOW   ALI POL PEP ARO
+                ! 107.5->120.0 to make planar Arg (KK)
+CT2  NH1  C      50.000   120.0000 ! ALLOW   ALI PEP POL ARO
+                ! NMA Vib Modes (LK)
+CT2  OS   CD    40.000    109.60   30.00   2.26510 ! ALLOW  POL PEP
+                ! adm jr. 5/02/91, acetic acid pure solvent
+CT3  CA   CA     45.800   122.3000 ! ALLOW   ALI ARO
+                ! toluene, adm jr., 3/7/92
+CT3  CPH1 CPH1   45.800   130.0000 ! ALLOW ARO
+                ! his, ADM JR., 7/22/89, FC=>CT2CA CA,BA=> CRYSTALS
+CT3  CT1  C      52.000   108.0000 ! ALLOW   ALI PEP POL ARO
+                ! Alanine Dipeptide ab initio calc's (LK)
+CT3  CT1  CC     52.000   108.0000 ! ALLOW   ALI PEP POL ARO
+                ! adm jr. 4/09/92, for ALA cter
+CT3  CT1  CT1   53.350    108.50    8.00   2.56100 ! ALLOW   ALI
+                ! alkane update, adm jr., 3/2/92
+CT3  CT1  CT2   53.350    114.00    8.00   2.56100 ! ALLOW   ALI
+                ! alkane update, adm jr., 3/2/92
+CT3  CT1  CT3   53.350    114.00    8.00   2.56100 ! ALLOW   ALI
+                ! alkane update, adm jr., 3/2/92
+CT3  CT2  CA     51.800   107.5000 ! ALLOW   ALI ARO
+                ! ethylbenzene, adm jr., 3/7/92
+CT3  CT2  CPH1   58.350   113.0000 ! ALLOW ARO
+                ! his, ADM JR., 7/22/89, from CT2CT2CT, U-B omitted
+CT3  CT2  CT1   58.350    113.50   11.16   2.56100 ! ALLOW   ALI
+                ! alkane frequencies (MJF), alkane geometries (SF)
+CT3  CT2  CT2   58.000    115.00    8.00   2.56100 ! ALLOW   ALI
+                ! alkane update, adm jr., 3/2/92
+CT3  CT2  CT3   53.350    114.00    8.00   2.56100 ! ALLOW   ALI
+                ! alkane update, adm jr., 3/2/92
+CT3  NC2  C      62.300   120.0000 ! ALLOW   ALI POL PEP ARO
+                ! methylguanidinium, adm jr., 3/26/92
+CT3  NH1  C      50.000   120.0000 ! ALLOW   ALI PEP POL ARO
+                ! NMA Vib Modes (LK)
+CT3  OS   CD    40.000    109.60   30.00   2.26510 ! ALLOW  POL PEP
+                ! adm jr. 5/02/91, acetic acid pure solvent
+CT3  S    CT2    34.000    95.0000 ! ALLOW   ALI SUL ION
+                ! expt. MeEtS,    3/26/92 (FL)
+H    NH1  C      34.000   123.0000 ! ALLOW   PEP POL ARO
+                ! NMA Vib Modes (LK)
+H    NH1  CT1    35.000   117.0000 ! ALLOW   PEP POL ARO ALI
+                ! NMA Vibrational Modes (LK)
+H    NH1  CT2    35.000   117.0000 ! ALLOW   PEP POL ARO ALI
+                ! NMA Vibrational Modes (LK)
+H    NH1  CT3    35.000   117.0000 ! ALLOW   PEP POL ARO ALI
+                ! NMA Vibrational Modes (LK)
+H    NH2  CC     50.000   120.0000 ! ALLOW   POL PEP ARO
+                ! his, adm jr. 8/13/90 acetamide geometry and vibrations
+H    NH2  H      23.000   120.0000 ! ALLOW   POL
+                ! adm jr. 8/13/90 acetamide geometry and vibrations
+H    NR1  CPH1  30.000    125.50   20.00   2.15000 ! ALLOW ARO
+                ! his, adm jr., 6/27/90
+H    NR1  CPH2  30.000    127.00   20.00   2.14000 ! ALLOW ARO
+                ! his, adm jr., 6/27/90
+H    NR3  CPH1  25.000    126.00   15.00   2.13000 ! ALLOW ARO
+                ! his, adm jr., 6/27/90
+H    NR3  CPH2  25.000    126.00   15.00   2.09000 ! ALLOW ARO
+                ! his, adm jr., 6/27/90
+H    OH1  CA     65.000   108.0000 ! ALLOW   ALC ARO
+                ! JES 8/25/89 phenol
+H    OH1  CD     55.000   115.0000 ! ALLOW   ALC ARO PEP POL
+                ! adm jr. 5/02/91, acetic acid pure solvent
+H    OH1  CT1    57.500   106.0000 ! ALLOW   ALC ARO ALI
+                ! methanol vib fit EMB 11/21/89
+H    OH1  CT2    57.500   106.0000 ! ALLOW   ALC ARO ALI
+                ! methanol vib fit EMB 11/21/89
+H    OH1  CT3    57.500   106.0000 ! ALLOW   ALC ARO ALI
+                ! methanol vib fit EMB 11/21/89
+HA2  CP2  CP1   33.430    110.10   22.53   2.17900 ! ALLOW ALI PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+HA2  CP2  CP2   26.500    110.10   22.53   2.17900 ! ALLOW ALI PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+HA2  CP2  CP3   26.500    110.10   22.53   2.17900 ! ALLOW ALI PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+HA2  CP2  HA2   35.500    109.00    5.40   1.80200 ! ALLOW ALI PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+HA2  CP3  CP2   26.500    110.10   22.53   2.17900 ! ALLOW ALI PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+HA2  CP3  HA2   35.500    109.00    5.40   1.80200 ! ALLOW ALI PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+HA2  CS   CT3   34.600    110.10   22.53   2.17900 ! ALLOW SUL
+                ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
+HA2  CS   HA2   35.500    108.40   14.00   1.77500 ! ALLOW SUL
+                ! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
+HA3  CS   HA3   35.500    108.40   14.00   1.77500 ! ALLOW SUL
+                ! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
+HA1  CT1  C     33.000    109.50   30.00   2.16300 ! ALLOW   ALI PEP POL ARO
+                ! alanine dipeptide, LK, replaced, adm jr., 5/09/91
+HA1  CT1  CD    33.000    109.50   30.00   2.16300 ! ALLOW   ALI PEP POL ARO
+                ! adm jr. 5/02/91, acetic acid pure solvent
+HA1  CT1  CT1   34.500    110.10   22.53   2.17900 ! ALLOW   ALI
+                ! alkane update, adm jr., 3/2/92
+HA1  CT1  CT2   34.500    110.10   22.53   2.17900 ! ALLOW   ALI
+                ! alkane update, adm jr., 3/2/92
+HA1  CT1  CT3   34.500    110.10   22.53   2.17900 ! ALLOW   ALI
+                ! alkane update, adm jr., 3/2/92
+HA1  CT1  HA1   35.500    109.00    5.40   1.80200 ! TEST for test cpd
+                ! based on HA   CT2  HA
+HA2  CT2  C     33.000    109.50   30.00   2.16300 ! ALLOW   ALI PEP POL ARO
+                ! alanine dipeptide, LK, replaced, adm jr., 5/09/91
+HA2  CT2  CA     49.300   107.5000 ! ALLOW   ALI ARO
+                ! PARALLH19 (JES)
+HA2  CT2  CC    33.000    109.50   30.00   2.16300 ! ALLOW   ALI PEP POL ARO
+                ! adm jr. 4/05/91, for asn,asp,gln,glu and cters
+HA2  CT2  CD    33.000    109.50   30.00   2.16300 ! ALLOW   ALI PEP POL ARO
+                ! adm jr. 5/02/91, acetic acid pure solvent
+HA2  CT2  CE1    45.00    111.50   ! 
+		! for 1-butene; from propene, yin/adm jr., 12/95
+HA2  CT2  CPH1   33.430   109.5000 ! ALLOW ARO
+                ! his, ADM JR., 7/22/89, from CT2CT2HA, U-B OMITTED
+HA2  CT2  CT1   26.500    110.10   22.53   2.17900 ! ALLOW   ALI
+                ! alkane frequencies (MJF), alkane geometries (SF)
+HA2  CT2  CT2   26.500    110.10   22.53   2.17900 ! ALLOW   ALI
+                ! alkane update, adm jr., 3/2/92
+HA2  CT2  CT3   34.600    110.10   22.53   2.17900 ! ALLOW   ALI
+                ! alkane update, adm jr., 3/2/92
+HA2  CT2  HA2   35.500    109.00    5.40   1.80200 ! ALLOW   ALI
+                ! alkane update, adm jr., 3/2/92
+HA3  CT3  C     33.000    109.50   30.00   2.16300 ! ALLOW   ALI PEP POL ARO
+                ! alanine dipeptide, LK, replaced, adm jr., 5/09/91
+HA3  CT3  CA     49.300   107.5000 ! ALLOW   ALI ARO
+                ! toluene, adm jr. 3/7/92
+HA3  CT3  CC    33.000    109.50   30.00   2.16300 ! ALLOW   ALI PEP POL ARO
+                ! adm jr. 4/05/91, for asn,asp,gln,glu and cters
+HA3  CT3  CD    33.000    109.50   30.00   2.16300 ! ALLOW   ALI PEP POL ARO
+                ! adm jr. 5/02/91, acetic acid pure solvent
+HA3  CT3  CE1    42.00    111.50   ! 
+		! for 2-butene, yin/adm jr., 12/95
+HA3  CT3  CPH1   33.430   109.5000 ! ALLOW ARO
+                ! his, ADM JR., 7/22/89, from CT2CT2HA, U-B OMITTED
+HA3  CT3  CS    34.600    110.10   22.53   2.17900 ! ALLOW SUL
+                ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
+HA3  CT3  CT1   33.430    110.10   22.53   2.17900 ! ALLOW   ALI
+                ! alkane frequencies (MJF), alkane geometries (SF)
+HA3  CT3  CT2   34.600    110.10   22.53   2.17900 ! ALLOW   ALI
+                ! alkane update, adm jr., 3/2/92
+HA3  CT3  CT3   37.500    110.10   22.53   2.17900 ! ALLOW   ALI
+                ! alkane update, adm jr., 3/2/92
+HA3  CT3  HA3   35.500    108.40    5.40   1.80200 ! ALLOW   ALI
+                ! alkane update, adm jr., 3/2/92
+HE1  CE1  CE1    52.00    119.50   ! 
+		! for 2-butene, yin/adm jr., 12/95
+HE1  CE1  CE2    42.00    118.00   ! 
+		! for propene, yin/adm jr., 12/95
+HE1  CE1  CT2    40.00    116.00   ! 
+		! for 1-butene; from propene, yin/adm jr., 12/95
+HE1  CE1  CT3    22.00    117.00   ! 
+		! for propene, yin/adm jr., 12/95
+HE2  CE2  CE1    45.00    120.50   ! 
+		! for propene, yin/adm jr., 12/95
+HE2  CE2  CE2    55.50    120.50   ! 
+		! for ethene, yin/adm jr., 12/95
+HE2  CE2  HE2    19.00    119.00   ! 
+		! for propene, yin/adm jr., 12/95
+HB1  CP1  C      50.000   112.0000 ! ALLOW PEP PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+HB1  CP1  CC     50.000   112.0000 ! ALLOW PEP PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+HB1  CP1  CD     50.000   112.0000 ! ALLOW PEP POL PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+HB1  CP1  CP2    35.000   118.0000 ! ALLOW PEP PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+HB1  CT1  C      50.000   109.5000 ! ALLOW  PEP
+                ! Alanine Dipeptide ab initio calc's (LK)
+HB1  CT1  CC     50.000   109.5000 ! ALLOW  PEP POL
+                ! adm jr. 4/05/91, for asn,asp,gln,glu and cters
+HB1  CT1  CD     50.000   109.5000 ! ALLOW  PEP POL
+                ! adm jr. 5/02/91, acetic acid pure solvent
+HB1  CT1  CT1    35.000   111.0000 ! ALLOW  PEP
+                ! Alanine Dipeptide ab initio calc's (LK)
+HB1  CT1  CT2    35.000   111.0000 ! ALLOW  PEP
+                ! Alanine Dipeptide ab initio calc's (LK)
+HB1  CT1  CT3    35.000   111.0000 ! ALLOW  PEP
+                ! Alanine Dipeptide ab initio calc's (LK)
+HB2  CT2  C      50.000   109.5000 ! ALLOW  PEP
+                ! Alanine Dipeptide ab initio calc's (LK)
+HB2  CT2  CC     50.000   109.5000 ! ALLOW  PEP POL
+                ! adm jr. 4/05/91, for asn,asp,gln,glu and cters
+HB2  CT2  CD     50.000   109.5000 ! ALLOW  PEP POL
+                ! adm jr. 5/02/91, acetic acid pure solvent
+HB2  CT2  HB2    36.000   115.0000 ! ALLOW   PEP
+                ! Alanine Dipeptide ab initio calc's (LK)
+HC   NC2  C      49.000   120.0000 ! ALLOW   POL PEP ARO
+                ! 35.3->49.0 GUANIDINIUM (KK)
+HC   NC2  CT2    40.400   120.0000 ! ALLOW   POL ALI
+                ! 107.5->120.0 to make planar Arg (KK)
+HC   NC2  CT3    40.400   120.0000 ! ALLOW   POL ALI
+                ! methylguanidinium, adm jr., 3/26/92
+HC   NC2  HC     25.000   120.0000 ! ALLOW   POL
+                ! 40.0->25.0 GUANIDINIUM (KK)
+HC   NH2  CT2    50.000   111.0000 ! ALLOW   POL
+                ! from HC NH2 CT3, neutral glycine, adm jr.
+HC   NH2  CT3    50.000   111.0000 ! ALLOW   POL
+                ! methylamine geom/freq, adm jr., 6/2/92
+HC   NH2  HC     39.000   106.5000 ! ALLOW   POL
+                ! 40.0->25.0 GUANIDINIUM (KK)
+HC   NH3  CT1   30.000    109.50   20.00   2.07400 ! ALLOW   POL ALI
+                ! new stretch and bend; methylammonium (KK 03/10/92)
+HC   NH3  CT2   30.000    109.50   20.00   2.07400 ! ALLOW   POL ALI
+                ! new stretch and bend; methylammonium (KK 03/10/92)
+HC   NH3  CT3   30.000    109.50   20.00   2.07400 ! ALLOW   POL ALI
+                ! new stretch and bend; methylammonium (KK 03/10/92)
+HC   NH3  HC     44.000   109.5000 ! ALLOW   POL
+                ! new stretch and bend; methylammonium (KK 03/10/92)
+HC   NP   CP1   33.000    109.50    4.00   2.05600 ! ALLOW POL ALI PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+HC   NP   CP3   33.000    109.50    4.00   2.05600 ! ALLOW POL ALI PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+HC   NP   HC     51.000   107.5000 ! ALLOW PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+HP   CA   CA    30.000    120.00   22.00   2.15250 ! ALLOW   ARO
+                ! JES 8/25/89 benzene
+HR1  CPH1 CPH1  22.000    130.00   15.00   2.21500 ! ALLOW ARO
+                ! adm jr., 6/27/90, his
+HR3  CPH1 CPH1  25.000    130.00   20.00   2.20000 ! ALLOW ARO
+                ! adm jr., 3/24/92, maintain old aliphatic H VDW params
+HS   S    CT2    38.800    95.0000 ! ALLOW   SUL ION ALI
+                ! methanethiol pure solvent, adm jr., 6/22/92
+HS   S    CT3    43.000    95.0000 ! ALLOW   SUL ION ALI
+                ! methanethiol pure solvent, adm jr., 6/22/92
+N    C    CP1    20.000   112.5000 ! ALLOW PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+N    C    CT1    20.000   112.5000 ! ALLOW ALI PEP POL ARO PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+N    C    CT2    20.000   112.5000 ! ALLOW ALI PEP POL ARO PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+N    C    CT3    20.000   112.5000 ! ALLOW ALI PEP POL ARO PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+N    CP1  C      50.000   108.2000 ! ALLOW PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+N    CP1  CC     50.000   108.2000 ! ALLOW PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+N    CP1  CD     50.000   108.2000 ! ALLOW PRO PEP
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+N    CP1  CP2    70.000   110.8000 ! ALLOW PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+N    CP1  HB1    48.000   112.0000 ! ALLOW PEP PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+N    CP3  CP2    70.000   110.5000 ! ALLOW PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+N    CP3  HA2    48.000   108.0000 ! ALLOW PEP PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NC2  C    NC2   40.000    120.00   70.00   2.31
+                ! mp2/6-311g** mgua vib data, adm jr., 1/04
+                ! N-N distances: 2.29001, 2.31146, 2.33240
+NC2  CT2  CT2    67.700   107.5000 ! ALLOW   ALI POL
+                ! arg, (DS)
+NC2  CT2  HA2    56.500   107.5000 ! ALLOW   ALI POL
+                ! mp2/6-311g** mgua vib data, adm jr., 1/04
+NC2  CT3  HA3    56.5000   107.5000 ! ALLOW   ALI POL
+                ! mp2/6-311g** mgua vib data, adm jr., 1/04
+NH1  C    CP1    80.000   116.5000 ! ALLOW PEP PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NH1  C    CT1    80.000   116.5000 ! ALLOW   ALI PEP POL ARO
+                ! NMA Vib Modes (LK)
+NH1  C    CT2    80.000   116.5000 ! ALLOW   ALI PEP POL ARO
+                ! NMA Vib Modes (LK)
+NH1  C    CT3    80.000   116.5000 ! ALLOW   ALI PEP POL ARO
+                ! NMA Vib Modes (LK)
+NH1  CT1  C      50.000   107.0000 ! ALLOW   PEP POL ARO ALI
+                ! Alanine Dipeptide ab initio calc's (LK)
+NH1  CT1  CC     50.000   107.0000 ! ALLOW   PEP POL ARO ALI
+                ! adm jr. 4/05/91, for asn,asp,gln,glu and cters
+NH1  CT1  CD     50.000   107.0000 ! ALLOW   PEP POL ARO ALI
+                ! adm jr. 5/02/91, acetic acid pure solvent
+NH1  CT1  CT1    70.000   113.5000 ! ALLOW   ALI PEP POL ARO
+                ! Alanine Dipeptide ab initio calc's (LK)
+NH1  CT1  CT2    70.000   113.5000 ! ALLOW   ALI PEP POL ARO
+                ! Alanine Dipeptide ab initio calc's (LK)
+NH1  CT1  CT3    70.000   113.5000 ! ALLOW   ALI PEP POL ARO
+                ! Alanine Dipeptide ab initio calc's (LK)
+NH1  CT1  HB1    48.000   108.0000 ! ALLOW PEP
+                ! Alanine Dipeptide ab initio calc's (LK)
+NH1  CT2  C      50.000   107.0000 ! ALLOW   PEP POL ARO ALI
+                ! Alanine Dipeptide ab initio calc's (LK)
+NH1  CT2  CC     50.000   107.0000 ! ALLOW   PEP POL ARO ALI
+                ! adm jr. 5/20/92, for asn,asp,gln,glu and cters
+NH1  CT2  CD     50.000   107.0000 ! ALLOW   PEP POL ARO ALI
+                ! adm jr. 5/02/91, acetic acid pure solvent
+NH1  CT2  CT2    70.000   113.5000 ! ALLOW   ALI PEP POL ARO
+                ! from NH1  CT1  CT2, for lactams, adm jr.
+NH1  CT2  HA2    51.500   109.5000 ! ALLOW   ALI PEP POL ARO
+                ! from NH1  CT3  HA, for lactams, adm jr.
+NH1  CT2  HB2    48.000   108.0000 ! ALLOW PEP
+                ! Alanine Dipeptide ab initio calc's (LK)
+NH1  CT3  HA3    51.500   109.5000 ! ALLOW   ALI PEP POL ARO
+                ! NMA crystal (JCS)
+NH2  CC   CP1    80.000   112.5000 ! ALLOW ALI PEP POL ARO PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NH2  CC   CT1   50.000    116.50   50.00   2.45000 ! ALLOW   ALI PEP POL ARO
+                ! adm jr. 8/13/90 acetamide geometry and vibrations
+NH2  CC   CT2   50.000    116.50   50.00   2.45000 ! ALLOW   ALI PEP POL ARO
+                ! adm jr. 8/13/90 acetamide geometry and vibrations
+NH2  CC   CT3   50.000    116.50   50.00   2.45000 ! ALLOW   ALI PEP POL ARO
+                ! adm jr. 8/13/90 acetamide geometry and vibrations
+NH2  CC   HA1   44.000    111.00   50.00   1.98000 ! ALLOW POL
+                ! adm jr., 5/13/91, formamide geometry and vibrations
+NH2  CT2  HB2   38.000    109.50   50.00   2.14000
+                !from NH2  CT3  HA, neutral glycine, adm jr.
+NH2  CT2  CD    52.000   108.0000
+                !from CT2 CT2 CD, neutral glycine, adm jr.
+NH2  CT2  CT2    67.700   110.0000 ! ALLOW   ALI POL
+                !from NH3  CT2  CT2, neutral lysine
+NH2  CT2  HA2   38.000    109.50   50.00   2.14000
+                !from NH2  CT3  HA, neutral lysine
+NH2  CT3  HA3   38.000    109.50   50.00   2.14000 ! ALLOW POL
+                ! methylamine geom/freq, adm jr., 6/2/92
+NH3  CT1  C      43.700   110.0000 ! ALLOW   PEP POL ARO ALI
+                ! new aliphatics, adm jr., 2/3/92
+NH3  CT1  CC     43.700   110.0000 ! ALLOW   PEP POL ARO ALI
+                ! adm jr. 4/05/91, for asn,asp,gln,glu and cters
+NH3  CT1  CT1    67.700   110.0000 ! ALLOW   ALI POL
+                ! new aliphatics, adm jr., 2/3/92
+NH3  CT1  CT2    67.700   110.0000 ! ALLOW   ALI POL
+                ! new aliphatics, adm jr., 2/3/92
+NH3  CT1  CT3    67.700   110.0000 ! ALLOW   ALI POL
+                ! new aliphatics, adm jr., 2/3/92
+NH3  CT1  HB1    51.500   107.5000 ! ALLOW   ALI POL PEP
+                ! new aliphatics, adm jr., 2/3/92
+NH3  CT2  C      43.700   110.0000 ! ALLOW   PEP POL ARO ALI
+                ! alanine (JCS)
+NH3  CT2  CC     43.700   110.0000 ! ALLOW   PEP POL ARO ALI
+                ! adm jr. 4/05/91, for asn,asp,gln,glu and cters
+NH3  CT2  CD     43.700   110.0000 ! ALLOW   PEP POL ARO ALI
+                ! adm jr. 5/02/91, acetic acid pure solvent
+NH3  CT2  CT2    67.700   110.0000 ! ALLOW   ALI POL
+                ! methylammonium
+NH3  CT2  CT3    67.700   110.0000 ! ALLOW   ALI POL
+                ! ethylammonium
+NH3  CT2  HA2   45.000    107.50   35.00   2.10100 ! ALLOW   ALI POL
+                ! new stretch and bend; methylammonium (KK 03/10/92)
+NH3  CT2  HB2    51.500   107.5000 ! ALLOW   ALI POL PEP
+                ! for use on NTER -- from NH3 CT2HA (JCS) -- (LK)
+NH3  CT3  HA3   45.000    107.50   35.00   2.10100 ! ALLOW   ALI POL
+                ! new stretch and bend; methylammonium (KK 03/10/92)
+NP   CP1  C      50.000   106.0000 ! ALLOW PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NP   CP1  CC     50.000   106.0000 ! ALLOW PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NP   CP1  CD     50.000   106.0000 ! ALLOW PRO PEP
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NP   CP1  CP2    70.000   108.5000 ! ALLOW PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NP   CP1  HB1    51.500   107.5000 ! ALLOW ALI POL PEP PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NP   CP3  CP2    70.000   108.5000 ! ALLOW PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NP   CP3  HA2    51.500   109.1500 ! ALLOW PEP PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NR1  CPH1 CPH1  130.000   106.0000 ! ALLOW ARO
+                ! his, ADM JR., 7/20/89
+NR1  CPH1 CT2    45.800   124.0000 ! ALLOW ARO
+                ! his, ADM JR., 7/22/89, FC FROM CA CT2CT
+NR1  CPH1 CT3    45.800   124.0000 ! ALLOW ARO
+                ! his, ADM JR., 7/22/89, FC FROM CA CT2CT
+NR1  CPH1 HR3   25.000    124.00   20.00   2.14000 ! ALLOW ARO
+                ! adm jr., 3/24/92, maintain old aliphatic H VDW params
+NR1  CPH2 HR1   25.000    122.50   20.00   2.14000 ! ALLOW ARO
+                ! his, adm jr., 6/27/90
+NR2  CPH1 CPH1  130.000   110.0000 ! ALLOW ARO
+                ! his, ADM JR., 7/20/89
+NR2  CPH1 CT2    45.800   120.0000 ! ALLOW ARO
+                ! his, ADM JR., 7/22/89, FC FROM CA CT2CT
+NR2  CPH1 HR3   25.000    120.00   20.00   2.14000 ! ALLOW ARO
+                ! adm jr., 3/24/92, maintain old aliphatic H VDW params
+NR2  CPH2 HR1   25.000    125.00   20.00   2.12000 ! ALLOW ARO
+                ! his, adm jr., 6/27/90
+NR2  CPH2 NR1   130.000   112.5000 ! ALLOW ARO
+                ! his, adm jr., 6/27/90
+NR3  CPH1 CPH1  145.000   108.0000 ! ALLOW ARO
+                ! his, ADM JR., 7/20/89
+NR3  CPH1 CT2    45.800   122.0000 ! ALLOW ARO
+                ! his, ADM JR., 7/22/89, FC FROM CA CT2CT
+NR3  CPH1 HR1   22.000    122.00   15.00   2.18000 ! ALLOW ARO
+                ! his, adm jr., 6/27/90
+NR3  CPH2 HR2   32.000    126.00   25.00   2.14000 ! ALLOW ARO
+                ! his, adm jr., 6/27/90
+NR3  CPH2 NR3   145.000   108.0000 ! ALLOW ARO
+                ! his, ADM JR., 7/20/89
+O    C    CP1    80.000   118.0000 ! ALLOW PEP PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+O    C    CT1    80.000   121.0000 ! ALLOW   ALI PEP POL ARO
+                ! Alanine Dipeptide ab initio calc's (LK)
+O    C    CT2    80.000   121.0000 ! ALLOW   ALI PEP POL ARO
+                ! Alanine Dipeptide ab initio calc's (LK)
+O    C    CT3    80.000   121.0000 ! ALLOW   ALI PEP POL ARO
+                ! Alanine Dipeptide ab initio calc's (LK)
+O    C    H      50.000   121.7000 ! ALLOW   PEP POL ARO
+                ! acetaldehyde (JCS)
+O    C    N      80.000   122.5000 ! ALLOW PRO PEP POL ARO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+O    C    NH1    80.000   122.5000 ! ALLOW   PEP POL ARO
+                ! NMA Vib Modes (LK)
+O    CC   CP1    80.000   118.0000 ! ALLOW ALI PEP POL ARO PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+O    CC   CT1   15.000    121.00   50.00   2.44000 ! ALLOW   ALI PEP POL ARO
+                ! adm jr. 4/10/91, acetamide update
+O    CC   CT2   15.000    121.00   50.00   2.44000 ! ALLOW   ALI PEP POL ARO
+                ! adm jr. 4/10/91, acetamide update
+O    CC   CT3   15.000    121.00   50.00   2.44000 ! ALLOW   ALI PEP POL ARO
+                ! adm jr. 4/10/91, acetamide update
+O    CC   HA1    44.000   122.0000 ! ALLOW POL
+                ! adm jr., 5/13/91, formamide geometry and vibrations
+O    CC   NH2   75.000    122.50   50.00   2.37000 ! ALLOW   POL PEP ARO
+                ! adm jr. 4/10/91, acetamide update
+OB   CD   CP1   70.000    125.00   20.00   2.44200 ! ALLOW ALI PEP POL ARO PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+OB   CD   CT1   70.000    125.00   20.00   2.44200 ! ALLOW   ALI PEP POL ARO
+                ! adm jr. 5/02/91, acetic acid pure solvent
+OB   CD   CT2   70.000    125.00   20.00   2.44200 ! ALLOW   ALI PEP POL ARO
+                ! adm jr. 5/02/91, acetic acid pure solvent
+OB   CD   CT3   70.000    125.00   20.00   2.44200 ! ALLOW   ALI PEP POL ARO
+                ! adm jr. 5/02/91, acetic acid pure solvent
+OC   CA   CA     40.000   120.0000 ! ALLOW  POL ARO
+                ! adm jr. 8/27/91, phenoxide
+OC   CC   CP1   40.000    118.00   50.00   2.38800 ! ALLOW ALI PEP POL ARO ION PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+OC   CC   CT1   40.000    118.00   50.00   2.38800 ! ALLOW   ALI PEP POL ARO ION
+                ! adm jr. 7/23/91, correction, ACETATE (KK)
+OC   CC   CT2   40.000    118.00   50.00   2.38800 ! ALLOW   ALI PEP POL ARO ION
+                ! adm jr. 7/23/91, correction, ACETATE (KK)
+OC   CC   CT3   40.000    118.00   50.00   2.38800 ! ALLOW   ALI PEP POL ARO ION
+                ! adm jr. 7/23/91, correction, ACETATE (KK)
+OC   CC   OC   100.000    124.00   70.00   2.22500 ! ALLOW   POL ION PEP ARO
+                ! adm jr. 7/23/91, correction, ACETATE (KK)
+OC   CT2  CT3    65.000   122.0000 ! ALLOW  ALC
+                ! ethoxide 6-31+G* geom/freq, adm jr., 6/1/92
+OC   CT2  HA2    65.000   118.3000 ! ALLOW  ALC
+                ! ethoxide 6-31+G* geom/freq, adm jr., 6/1/92
+OC   CT3  HA3    65.000   118.3000 ! ALLOW  ALC
+                ! methoxide 6-31+G* geom/freq, adm jr., 6/1/92
+OH1  CA   CA     45.200   120.0000 ! ALLOW   ARO ALC
+                ! PARALLH19 WITH [122.3] (JES)
+OH1  CD   CT2    55.000   110.5000 ! ALLOW   ALI PEP POL ARO ALC
+                ! adm jr, 10/17/90, acetic acid vibrations
+OH1  CD   CT3    55.000   110.5000 ! ALLOW   ALI PEP POL ARO ALC
+                ! adm jr, 10/17/90, acetic acid vibrations
+OH1  CD   OB    50.000    123.00  210.00   2.26200 ! ALLOW   PEP POL ARO ALC
+                ! adm jr, 10/17/90, acetic acid vibrations
+OH1  CT1  CT1    75.700   110.1000 ! ALLOW   ALI ALC ARO
+                ! MeOH, EMB, 10/10/89
+OH1  CT1  CT3    75.700   110.1000 ! ALLOW   ALI ALC ARO
+                ! MeOH, EMB, 10/10/89
+OH1  CT1  HA1    45.900   108.8900 ! ALLOW   ALI ALC ARO
+                ! MeOH, EMB, 10/10/89
+OH1  CT2  CT1    75.700   110.1000 ! ALLOW   ALI ALC ARO
+                ! MeOH, EMB, 10/10/89
+OH1  CT2  CT2    75.700   110.1000 ! ALLOW   ALI ALC ARO
+                ! MeOH, EMB, 10/10/89
+OH1  CT2  CT3    75.700   110.1000 ! ALLOW   ALI ALC ARO
+                ! MeOH, EMB, 10/10/89
+OH1  CT2  HA2    45.900   108.8900 ! ALLOW   ALI ALC ARO
+                ! MeOH, EMB, 10/10/89
+OH1  CT3  HA3    45.900   108.8900 ! ALLOW   ALI ALC ARO
+                ! MeOH, EMB, 10/10/89
+OS   CD   CP1   55.000    109.00   20.00   2.32600 ! ALLOW POL PEP PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+OS   CD   CT1   55.000    109.00   20.00   2.32600 ! ALLOW POL PEP
+                ! adm jr., 4/05/91, for PRES CT1 from methylacetate
+OS   CD   CT2   55.000    109.00   20.00   2.32600 ! ALLOW POL PEP
+                ! adm jr., 4/05/91, for PRES CT1 from methylacetate
+OS   CD   CT3   55.000    109.00   20.00   2.32600 ! ALLOW POL PEP
+                ! adm jr., 4/05/91, for PRES CT1 from methylacetate
+OS   CD   OB    90.000    125.90  160.00   2.25760 ! ALLOW  PEP POL
+                ! adm jr. 3/19/92, from lipid methyl acetate
+OS   CT2  HA2    60.000   109.5000 ! ALLOW PEP POL
+                ! adm jr. 4/05/91, for PRES CT1 from methyl acetate
+OS   CT3  HA3    60.000   109.5000 ! ALLOW PEP POL
+                ! adm jr. 4/05/91, for PRES CT1 from methyl acetate
+S    CT2  CT1    58.000   112.5000 ! ALLOW   ALI SUL ION
+                ! as in expt.MeEtS & DALC crystal,  5/15/92
+S    CT2  CT2    58.000   114.5000 ! ALLOW   ALI SUL ION
+                ! expt. MeEtS,     3/26/92 (FL)
+S    CT2  CT3    58.000   114.5000 ! ALLOW   ALI SUL ION
+                ! expt. MeEtS,     3/26/92 (FL)
+S    CT2  HA2    46.100   111.3000 ! ALLOW   ALI SUL ION
+                ! vib. freq. and HF/6-31G* geo. (DTN) 8/24/90
+S    CT3  HA3    46.100   111.3000 ! ALLOW   ALI SUL ION
+                ! vib. freq. and HF/6-31G* geo. (DTN) 8/24/90
+SM   CT2  CT1    58.000   112.5000 ! ALLOW   ALI SUL ION
+                ! as in expt.MeEtS & DALC crystal,  5/15/92
+SM   CT2  CT3    58.000   112.5000 ! ALLOW   ALI SUL ION
+                ! diethyldisulfide, as in expt.MeEtS & DALC crystal,  5/15/92
+SM   CT2  HA2    38.000   111.0000 ! ALLOW   ALI SUL ION
+                ! new S-S atom type 8/24/90
+SM   CT3  HA3    38.000   111.0000 ! ALLOW   ALI SUL ION
+                ! new S-S atom type 8/24/90
+SM   SM   CT2    72.500   103.3000 ! ALLOW   ALI SUL ION
+                ! expt. dimethyldisulfide,    3/26/92 (FL)
+SM   SM   CT3    72.500   103.3000 ! ALLOW   ALI SUL ION
+                ! expt. dimethyldisulfide,    3/26/92 (FL)
+SS   CS   CT3    55.000   118.0000 ! ALLOW SUL
+                ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
+SS   CS   HA2    40.000   112.3000 ! ALLOW SUL
+                ! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
+SS   CS   HA3    40.000   112.3000 ! ALLOW SUL
+                ! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
+O    CD   HR1    75.000   121.0000 ! acetaldehyde, benzaldehyde, 3ALP, retinal
+!For GLU/HSP, Zhu
+NH1  CT1  CT2A   70.000   113.5000 ! from NH1  CT1  CT2
+HB1  CT1  CT2A   35.000   111.0000 ! from HB1  CT1  CT2
+CT2A CT1  C      52.000   108.0000 ! from CT2  CT1  C
+CT1  CT2A HA2    26.500   110.1000  22.53   2.17900 ! from HA2  CT2  CT1
+CT1  CT2A CT2    58.350   113.5000  11.16   2.56100 ! from CT2  CT2  CT1
+HA2  CT2A HA2    35.500   109.0000   5.40   1.80200 ! from HA2  CT2  HA2
+HA2  CT2A CT2    26.500   110.1000  22.53   2.17900 ! from HA2  CT2  CT2
+CT2A CT2  HA2    26.500   110.1000  22.53   2.17900 ! from HA2  CT2  CT2
+CT2A CT2  CC     52.000   108.0000 ! from CT2  CT2  CC
+CT1  CT2A CPH1   58.350   113.0000 ! from CT1  CT2  CPH1 
+HA2  CT2A CPH1   33.430   109.5000 ! from HA2  CT2  CPH1
+CT2A CPH1 CPH1   45.800   130.0000 ! from CT2  CPH1 CPH1
+CT2A CPH1 NR3    45.800   122.0000 ! from NR3  CPH1 CT2
+!ASP, CT2->CT2A, jshim
+CT1  CT2A CC     52.000   108.0000 ! from CT1  CT2  CC
+HA2  CT2A CC     33.000   109.5000  30.00   2.16300 ! from HA2  CT2  CC
+OC   CC   CT2A   40.000   118.0000  50.00   2.38800 ! from OC   CC   CT2
+NH3  CT1  CT2A   67.700   110.0000 ! from NH3  CT1  CT2
+CT2A CT1  CD     52.000   108.0000 ! from CT2  CT1  CD
+! RESI CYSM and PRES CYSD
+NH2  CT1  CS     67.700   110.0000 ! from NH2  CT1  CT2 , kevo
+CS   CT1  C      52.000   108.0000 ! from CT2  CT1  C   , kevo
+CS   CT1  CC     52.000   108.0000 ! from CT2  CT1  CC  , kevo
+CS   CT1  CD     52.000   108.0000 ! from CT2  CT1  CD  , kevo
+HB1  CT1  CS     35.000   111.0000 ! from HB1  CT1  CT2 , kevo
+NH1  CT1  CS     70.000   113.5000 ! from NH1  CT1  CT2 , kevo
+NH3  CT1  CS     67.700   110.0000 ! from NH3  CT1  CT2 , kevo
+SS   CS   CT1    55.000   118.0000 ! from SS   CS   CT3 , kevo
+HA2  CS   CT1    34.600   110.10    22.53   2.17900 ! from HA2 CS CT3 to be consistent with SS CS CT1, kevo
+! PRES SERD
+OC   CT2  CT1    65.000   122.0000 ! from OC   CT2  CT3 , kevo
+
+DIHEDRALS
+!
+!V(dihedral) = Kchi(1 + cos(n(chi) - delta))
+!
+!Kchi: kcal/mole
+!n: multiplicity
+!delta: degrees
+!
+!atom types             Kchi    n   delta
+!
+!Neutral N terminus
+NH2  CT1  C    O        0.0000  1     0.00
+NH2  CT2  C    O        0.0000  1     0.00   ! Neutral Gly Nterminus
+NH2  CT1  C    NH1      0.0000  1     0.00
+NH2  CT2  C    NH1      0.0000  1     0.00   ! Neutral Gly Nterminus
+H    NH2  CT1  CT1      0.0000  1     0.00
+H    NH2  CT1  C        0.0000  1     0.00
+H    NH2  CT2  C        0.0000  1     0.00   ! Neutral Gly Nterminus
+H    NH2  CT1  HB1      0.1100  3     0.00   ! From LSN HC-NH2-CT2-HA
+H    NH2  CT2  HB2      0.1100  3     0.00   ! From LSN HC-NH2-CT2-HA, Neutral Gly Nterminus
+H    NH2  CT1  CT2      0.1100  3     0.00   ! From LSN HC-NH2-CT2-CT2
+H    NH2  CT1  CT3      0.1100  3     0.00   ! From LSN HC-NH2-CT2-CT2
+!Indole/Tryptophan
+CAI  CA   CA   CAI      3.1000  2   180.00 ! from CA CA CA CA
+CA   CPT  CPT  CA       3.0000  2   180.00 ! atm, methylindole, 1/17/04	
+CAI  CPT  CPT  CAI      3.0000  2   180.00 ! atm, methylindole, 1/17/04	
+CA   CY   CPT  CA       3.0000  2   180.00 ! atm, methylindole, 1/17/04
+CA   CY   CPT  CAI      3.0000  2   180.00 ! atm, methylindole, 1/17/04
+CA   NY   CPT  CA       3.0000  2   180.00 ! atm, methylindole, 1/17/04
+CPT  CA   CA   CA       3.0000  2   180.00 ! JWK 05/14/91 fit to indole
+CPT  CPT  CA   CA       3.0000  2   180.00 ! JWK 05/14/91 fit to indole
+CA   NY   CPT  CAI      3.0000  2   180.00 ! atm, methylindole, 1/17/04
+CPT  CAI  CA   CA       3.0000  2   180.00 ! JWK 05/14/91 fit to indole
+CPT  CPT  CAI  CA       3.0000  2   180.00 ! JWK 05/14/91 fit to indole
+CPT  CPT  CY   CA       5.0000  2   180.00 ! atm, methylindole, 1/17/04
+CPT  CPT  NY   CA       6.5000  2   180.00 ! atm, methylindole, 1/17/04
+CT3  CY   CPT  CA       2.5000  2   180.00 ! atm, methylindole, r6r5
+CT3  CY   CPT  CAI      2.5000  2   180.00 ! atm, methylindole, r6r5
+CT3  CY   CPT  CPT      3.0000  2   180.00 ! atm, methylindole, meth
+CT2  CY   CPT  CA       2.5000  2   180.00 ! atm, methylindole, r6r5
+CT2  CY   CPT  CAI      2.5000  2   180.00 ! atm, methylindole, r6r5
+CT2  CY   CPT  CPT      3.0000  2   180.00 ! atm, methylindole, meth
+CY   CA   NY   CPT      6.0000  2   180.00 ! atm, methylindole, 1/17/04
+CY   CPT  CA   CA       4.0000  2   180.00 ! atm, methylindole, 1/17/04
+CY   CPT  CPT  CA       4.0000  2   180.00 ! atm, methylindole, 1/17/04
+CY   CPT  CAI  CA       4.0000  2   180.00 ! atm, methylindole, 1/17/04
+CY   CPT  CPT  CAI      4.0000  2   180.00 ! atm, methylindole, 1/17/04
+H    NY   CA   CY       0.0500  2   180.00 ! atm, methylindole, 1/17/04
+H    NY   CPT  CA       0.2000  2   180.00 ! atm, methylindole, 1/17/04
+H    NY   CPT  CAI      0.2000  2   180.00 ! atm, methylindole, 1/17/04
+H    NY   CPT  CPT      0.8500  2   180.00 ! atm, methylindole, 1/17/04
+HP   CAI  CA   CA       4.2000  2   180.00 ! from HP CA CA CA
+HP   CA   CA   CPT      3.0000  2   180.00 ! JWK 05/14/91 fit to indole
+HP   CA   CPT  CPT      3.0000  2   180.00 ! JWK indole 05/14/91
+HP   CA   CPT  CY       4.0000  2   180.00 ! atm, methylindole, 1/17/04
+HP   CA   CA   CAI      4.2000  2   180.00 ! from HP CA CA CA
+HP   CA   CAI  CPT      3.0000  2   180.00 ! from HP CA CA CPT
+HP   CAI  CA   HP       2.4000  2   180.00 ! from HP CA CA HP
+HP   CAI  CPT  CPT      3.0000  2   180.00 ! from HP CA CPT CPT
+HP   CAI  CPT  CY       4.0000  2   180.00 ! from HP CA CPT CY, r6r5
+HP   CA   CY   CPT      2.8000  2   180.00 ! adm jr., 12/30/91, for jwk
+HP   CA   CY   CT3      1.2000  2   180.00 ! atm, methylindole
+HP   CA   CY   CT2      1.2000  2   180.00 ! atm, methylindole
+HP   CA   NY   CPT      2.6000  2   180.00 ! adm jr., 12/30/91, for jwk
+HP   CA   NY   H        0.4000  2   180.00 ! JWK 05/14/91 fit to indole
+HP   CY   CA   HP       1.0000  2   180.00 ! JWK 05/14/91 fit to indole
+HP   CY   CPT  CA       2.8000  2   180.00 ! JWK 05/14/91 fit to indole
+HP   CY   CPT  CAI      2.8000  2   180.00 ! JWK 05/14/91 fit to indole
+HP   CY   CPT  CPT      2.6000  2   180.00 ! JWK 05/14/91 fit to indole
+NY   CA   CY   CPT      5.0000  2   180.00 ! atm, methylindole, 1/17/04
+NY   CA   CY   CT3      2.5000  2   180.00 ! atm, methylindole, from NY   CA   CY   CT3
+NY   CA   CY   CT2      2.5000  2   180.00 ! atm, methylindole, from NY   CA   CY   CT3
+NY   CA   CY   HP       3.5000  2   180.00 ! JWK indole 05/14/91
+NY   CPT  CA   CA       3.0000  2   180.00 ! atm, methylindole, 1/17/04, r6r5 
+NY   CPT  CA   HP       3.0000  2   180.00 ! JWK 05/14/91 fit to indole, r6r5
+NY   CPT  CPT  CA       4.0000  2   180.00 ! atm, methylindole, 1/17/04, bfly
+NY   CPT  CAI  CA       3.0000  2   180.00 ! atm, methylindole, 1/17/04
+NY   CPT  CAI  HP       3.0000  2   180.00 ! JWK 05/14/91 fit to indole, r6r5
+NY   CPT  CPT  CAI      4.0000  2   180.00 ! atm, methylindole, 1/17/04, bfly
+NY   CPT  CPT  CY       6.5000  2   180.00 ! JWK 05/14/91 fit to indole,  r5 t1
+CT3  CT2  CY   CA       0.3800  2     0.00 ! trp, from ethylbenzene, adm jr., 3/7/92
+CT3  CT2  CY   CPT      0.2500  2   180.00 ! atm 1/14/04 3-ethylindole
+CT3  CT2  CY   CPT      0.3000  3     0.00 ! atm 1/14/04 3-ethylindole
+HA3  CT3  CY   CA       0.0100  3     0.00 ! atm, methylindole, 1/17/04
+HA3  CT3  CY   CPT      0.2000  3     0.00 ! atm, methylindole, 1/17/04
+HA2  CT2  CY   CA       0.0100  3     0.00 ! atm, methylindole, 1/17/04
+HA2  CT2  CY   CPT      0.2000  3     0.00 ! atm, methylindole, 1/17/04
+X    CS   SS   X        0.0000  3     0.20 ! guess
+                !from methanethiol, HS S CT3 HA
+                !adm jr., 7/01
+C    CT1  NH1  C        0.2000  1   180.00 ! ALLOW PEP
+                ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c
+C    CT2  NH1  C        0.2000  1   180.00 ! ALLOW PEP
+                ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c
+C    N    CP1  C        0.8000  3     0.00 ! ALLOW PRO PEP
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CA   CA   CA   CA       3.1000  2   180.00 ! ALLOW   ARO
+                ! JES 8/25/89
+!CA   CT2  CT1  C        0.0400  3     0.00 ! ALLOW   ARO
+                ! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92
+CC   CP1  N    C        0.8000  3     0.00 ! ALLOW PRO PEP
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CC   CT1  CT2  CA       0.0400  3     0.00 ! ALLOW   ARO
+                ! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92
+CC   CT1  NH1  C        0.2000  1   180.00 ! ALLOW PEP POL
+                ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c
+!CC   CT2  NH1  C        0.2000  1   180.00 ! ALLOW PEP POL
+!                ! Alanine dipeptide; NMA; acetate; etc. adm jr., 3/3/93c
+CC   CT2  NH1  C        2.0000  1   180.00 ! ALLOW PEP POL
+                ! Based on Gly3 data from graf et al, RB 7/1/11
+CD   CP1  N    C        0.0000  1   180.00 ! ALLOW PRO PEP
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CD   CT1  NH1  C        0.2000  1   180.00 ! ALLOW PEP POL
+                ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c
+!CD   CT2  NH1  C        0.2000  1   180.00 ! ALLOW PEP POL
+!               ! Alanine dipeptide; NMA; acetate; etc. backbon adm jr., 3/3/93c
+CD   CT2  NH1  C        2.0000  1   180.00 ! ALLOW PEP POL
+                ! Based on Gly3 data from graf et al, RB 7/1/11
+CE1  CE1  CT3  HA3      0.0300  3     0.00 ! 
+		! for butene, yin/adm jr., 12/95
+CE2  CE1  CT2  CT3      0.5000  1   180.00 !
+                ! 1-butene, adm jr., 2/00 update
+CE2  CE1  CT2  CT3      1.3000  3   180.00 !
+		! 1-butene, adm jr., 2/00 update
+CE2  CE1  CT2  HA2      0.1200  3     0.00 ! 
+		! for butene, yin/adm jr., 12/95
+CE2  CE1  CT3  HA3      0.0500  3   180.00 ! 
+		! for propene, yin/adm jr., 12/95
+CP1  C    N    CP1      2.7500  2   180.00 ! ALLOW PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CP1  C    N    CP1      0.3000  4     0.00 ! ALLOW PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CP2  CP1  N    C        0.8000  3     0.00 ! ALLOW PRO PEP
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CP2  CP3  N    C        0.0000  3   180.00 ! ALLOW PRO PEP
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CP2  CP3  N    CP1      0.1000  3     0.00 ! ALLOW PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CP2  CP3  NP   CP1      0.0800  3     0.00 ! ALLOW PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CP3  N    C    CP1      2.7500  2   180.00 ! ALLOW PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CP3  N    C    CP1      0.3000  4     0.00 ! ALLOW PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CP3  N    CP1  C        0.1000  3     0.00 ! ALLOW PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CP3  N    CP1  CC       0.1000  3     0.00 ! ALLOW PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CP3  N    CP1  CP2      0.1000  3     0.00 ! ALLOW PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CP3  NP   CP1  C        0.0800  3     0.00 ! ALLOW PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CP3  NP   CP1  CC       0.0800  3     0.00 ! ALLOW PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CP3  NP   CP1  CD       0.0800  3     0.00 ! ALLOW PRO PEP
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CP3  NP   CP1  CP2      0.0800  3     0.00 ! ALLOW PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CPH2 NR1  CPH1 CPH1    14.0000  2   180.00 ! ALLOW ARO
+                ! his, ADM JR., 7/20/89
+CPH2 NR2  CPH1 CPH1    14.0000  2   180.00 ! ALLOW ARO
+                ! his, ADM JR., 7/20/89
+CPH2 NR3  CPH1 CPH1    12.0000  2   180.00 ! ALLOW ARO
+                ! his, ADM JR., 7/20/89
+CT1  C    N    CP1      2.7500  2   180.00 ! ALLOW PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CT1  C    N    CP1      0.3000  4     0.00 ! ALLOW PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CT1  C    N    CP3      2.7500  2   180.00 ! ALLOW PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CT1  C    N    CP3      0.3000  4     0.00 ! ALLOW PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CT1  C    NH1  CT1      1.6000  1     0.00 !  ALLOW PEP
+                ! Revised to adjust NMA cis/trans energy difference. (LK)
+CT1  C    NH1  CT1      2.5000  2   180.00 !  ALLOW PEP
+                ! Gives appropriate NMA cis/trans barrier. (LK)
+CT1  CT1  NH1  C        1.8000  1     0.00 ! ALLOW PEP
+                ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c
+CT1  NH1  C    CP1      1.6000  1     0.00 ! ALLOW PEP PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CT1  NH1  C    CP1      2.5000  2   180.00 ! ALLOW PEP PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CT2  C    N    CP1      2.7500  2   180.00 ! ALLOW PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CT2  C    N    CP1      0.3000  4     0.00 ! ALLOW PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CT2  C    N    CP3      2.7500  2   180.00 ! ALLOW PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CT2  C    N    CP3      0.3000  4     0.00 ! ALLOW PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CT2  C    NH1  CT1      1.6000  1     0.00 !  ALLOW PEP
+                ! Revised to adjust NMA cis/trans energy difference. (LK)
+CT2  C    NH1  CT1      2.5000  2   180.00 !  ALLOW PEP
+                ! Gives appropriate NMA cis/trans barrier. (LK)
+CT2  C    NH1  CT2      1.6000  1     0.00 !  ALLOW PEP
+                ! Revised to adjust NMA cis/trans energy difference. (LK)
+CT2  C    NH1  CT2      2.5000  2   180.00 !  ALLOW PEP
+                ! Gives appropriate NMA cis/trans barrier. (LK)
+CT2  C    NH1  CT3      1.6000  1     0.00 !  ALLOW PEP
+                ! from CT2  C    NH1  CT2, adm jr. 10/21/96
+CT2  C    NH1  CT3      2.5000  2   180.00 !  ALLOW PEP
+                ! from CT2  C    NH1  CT2, adm jr. 10/21/96
+CT2  CA   CA   CA       3.1000  2   180.00 ! ALLOW   ARO
+                ! JES 8/25/89 toluene and ethylbenzene
+CT2  CPH1 NR1  CPH2     3.0000  2   180.00 ! ALLOW ARO
+                ! his, ADM JR., 7/22/89, FROM HA CPH1 NR1 CPH2
+CT2  CPH1 NR2  CPH2     3.0000  2   180.00 ! ALLOW ARO
+                ! his, ADM JR., 7/22/89, FROM HA CPH1 NR2 CPH2
+CT2  CPH1 NR3  CPH2     2.5000  2   180.00 ! ALLOW ARO
+                ! his, adm jr., 6/27/90
+CT2  CT1  NH1  C        1.8000  1     0.00 ! ALLOW PEP
+                ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c
+CT2  CT2  CPH1 CPH1     0.4000  1     0.00 ! ALLOW ARO
+                ! 4-methylimidazole 4-21G//6-31G* rot bar. ADM JR., 9/4/89
+!aliphatic chain parameters compatible with the revised side-chain parameters, from all22_carb>>all27_lip>>all31
+                ! lower butane gauche conformer
+CT2  CT2  CT2  CT2      0.10    2   180.00 ! alkane, 4/98, adm jr.
+CT2  CT2  CT2  CT2      0.15    4     0.00 ! alkane, 4/98, adm jr.
+CT2  CT2  CT2  CT2      0.10    6   180.00 ! alkane, 4/98, adm jr.
+CT2  CT2  CT2  CT3      0.10    2   180.00 ! alkane, 4/98, adm jr.
+CT2  CT2  CT2  CT3      0.15    4     0.00 ! alkane, 4/98, adm jr.
+CT2  CT2  CT2  CT3      0.10    6   180.00 ! alkane, 4/98, adm jr.
+!
+CT2  CT2  NH1  C        1.8000  1     0.00 ! ALLOW PEP
+                ! from CT2  CT1  NH1  C, for lactams, adm jr.
+CT2  NH1  C    CP1      1.6000  1     0.00 ! ALLOW PEP PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CT2  NH1  C    CP1      2.5000  2   180.00 ! ALLOW PEP PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CT2  NH1  C    CT1      1.6000  1     0.00 !  ALLOW PEP
+                ! Revised to adjust NMA cis/trans energy difference. (LK)
+CT2  NH1  C    CT1      2.5000  2   180.00 !  ALLOW PEP
+                ! Gives appropriate NMA cis/trans barrier. (LK)
+CT2  SM   SM   CT2      1.0000  1     0.00 ! ALLOW   ALI SUL ION
+                ! improved CSSC dihedral in DMDS  5/15/92 (FL)
+CT2  SM   SM   CT2      4.1000  2     0.00 ! ALLOW   ALI SUL ION
+                ! mp 6-311G** dimethyldisulfide,  3/26/92 (FL)
+CT2  SM   SM   CT2      0.9000  3     0.00 ! ALLOW   ALI SUL ION
+                ! improved CSSC dihedral in DMDS  5/15/92 (FL)
+CT3  C    N    CP1      2.7500  2   180.00 ! ALLOW PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CT3  C    N    CP1      0.3000  4     0.00 ! ALLOW PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CT3  C    N    CP3      2.7500  2   180.00 ! ALLOW PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CT3  C    N    CP3      0.3000  4     0.00 ! ALLOW PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CT3  C    NH1  CT1      1.6000  1     0.00 !  ALLOW PEP
+                ! Revised to adjust NMA cis/trans energy difference. (LK)
+CT3  C    NH1  CT1      2.5000  2   180.00 !  ALLOW PEP
+                ! Gives appropriate NMA cis/trans barrier. (LK)
+CT3  C    NH1  CT2      1.6000  1     0.00 !  ALLOW PEP
+                ! for acetylated GLY N-terminus, adm jr.
+CT3  C    NH1  CT2      2.5000  2   180.00 !  ALLOW PEP
+                ! for acetylated GLY N-terminus, adm jr.
+CT3  C    NH1  CT3      1.6000  1     0.00 !  ALLOW PEP
+                ! Revised to adjust NMA cis/trans energy difference. (LK)
+CT3  C    NH1  CT3      2.5000  2   180.00 !  ALLOW PEP
+                ! Gives appropriate NMA cis/trans barrier. (LK)
+CT3  CA   CA   CA       3.1000  2   180.00 ! ALLOW   ARO
+                ! toluene, adm jr., 3/7/92
+CT3  CE1  CE2  HE2      5.2000  2   180.00 ! 
+		! for propene, yin/adm jr., 12/95
+CT3  CPH1 NR1  CPH2     3.0000  2   180.00 ! ALLOW ARO
+                ! his, ADM JR., 7/22/89, FROM HA CPH1 NR1 CPH2
+CT3  CT1  NH1  C        1.8000  1     0.00 ! ALLOW PEP
+                ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c
+CT3  CT2  CA   CA       0.2300  2   180.00 ! ALLOW   ARO ALI
+                ! ethylbenzene ethyl rotation, adm jr. 3/7/92
+CT3  CT2  CPH1 CPH1     0.2000  1     0.00 ! ALLOW ARO
+                ! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92
+CT3  CT2  CPH1 CPH1     0.2700  2     0.00 ! ALLOW ARO
+                ! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92
+CT3  CT2  CPH1 CPH1     0.0000  3     0.00 ! ALLOW ARO
+                ! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92
+CT3  CT2  S    CT3      0.2400  1   180.00 ! ALOW    ALI SUL ION
+                ! expt. MeEtS,      3/26/92 (FL)
+CT3  CT2  S    CT3      0.3700  3     0.00 ! ALOW    ALI SUL ION
+                ! DTN 8/24/90
+CT3  NH1  C    CP1      1.6000  1     0.00 ! ALLOW PEP PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CT3  NH1  C    CP1      2.5000  2   180.00 ! ALLOW PEP PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CT3  NH1  C    CT1      1.6000  1     0.00 !  ALLOW PEP
+                ! Revised to adjust NMA cis/trans energy difference. (LK)
+CT3  NH1  C    CT1      2.5000  2   180.00 !  ALLOW PEP
+                ! Gives appropriate NMA cis/trans barrier. (LK)
+CT3  S    CT2  CT2      0.2400  1   180.00 ! ALOW    ALI SUL ION
+                ! expt. MeEtS,      3/26/92 (FL)
+CT3  S    CT2  CT2      0.3700  3     0.00 ! ALOW    ALI SUL ION
+                ! expt. MeEtS,      3/26/92 (FL)
+CT3  SM   SM   CT3      1.0000  1     0.00 ! ALLOW   ALI SUL ION
+                ! improved CSSC dihedral in DMDS  5/15/92 (FL)
+CT3  SM   SM   CT3      4.1000  2     0.00 ! ALLOW   ALI SUL ION
+                ! mp 6-311G** dimethyldisulfide,   3/26/92 (FL)
+CT3  SM   SM   CT3      0.9000  3     0.00 ! ALLOW   ALI SUL ION
+                ! improved CSSC dihedral in DMDS  5/15/92 (FL)
+H    NH1  C    CP1      2.5000  2   180.00 ! ALLOW PEP PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+H    NH1  C    CT1      2.5000  2   180.00 !  ALLOW PEP
+                ! Gives appropriate NMA cis/trans barrier. (LK)
+H    NH1  C    CT2      2.5000  2   180.00 !  ALLOW PEP
+                ! Gives appropriate NMA cis/trans barrier. (LK)
+H    NH1  C    CT3      2.5000  2   180.00 !  ALLOW PEP
+                ! Gives appropriate NMA cis/trans barrier. (LK)
+H    NH1  CT1  C        0.0000  1     0.00 ! ALLOW PEP
+                ! Alanine Dipeptide ab initio calc's (LK)
+H    NH1  CT1  CC       0.0000  1     0.00 ! ALLOW PEP POL
+                ! adm jr. 4/05/91, for asn,asp,gln,glu and cters
+H    NH1  CT1  CD       0.0000  1     0.00 ! ALLOW PEP POL
+                ! adm jr. 5/02/91, acetic acid pure solvent
+H    NH1  CT1  CT1      0.0000  1     0.00 ! ALLOW PEP
+                ! Alanine Dipeptide ab initio calc's (LK)
+H    NH1  CT1  CT2      0.0000  1     0.00 ! ALLOW PEP
+                ! Alanine Dipeptide ab initio calc's (LK)
+H    NH1  CT1  CT3      0.0000  1     0.00 ! ALLOW PEP
+                ! Alanine Dipeptide ab initio calc's (LK)
+H    NH1  CT2  C        0.0000  1     0.00 ! ALLOW PEP
+                ! Alanine Dipeptide ab initio calc's (LK)
+H    NH1  CT2  CC       0.0000  1     0.00 ! ALLOW PEP POL
+                ! Alanine dipeptide; NMA; acetate; etc. backbone param. RLD 3/22/92
+H    NH1  CT2  CD       0.0000  1     0.00 ! ALLOW PEP POL
+                ! adm jr. 5/02/91, acetic acid pure solvent
+H    NH1  CT2  CT2      0.0000  1     0.00 ! ALLOW PEP
+                ! from H    NH1  CT2  CT3, for lactams, adm jr.
+H    NH1  CT2  CT3      0.0000  1     0.00 ! ALLOW PEP
+                ! Alanine Dipeptide ab initio calc's (LK)
+H    NH2  CC   CT1      1.4000  2   180.00 !  ALLOW   PEP POL ARO PRO
+                ! adm jr. 4/10/91, acetamide update
+H    NH2  CC   CT2      1.4000  2   180.00 !  ALLOW   PEP POL ARO PRO
+                ! adm jr. 4/10/91, acetamide update
+H    NH2  CC   CT3      1.4000  2   180.00 !  ALLOW   PEP POL ARO PRO
+                ! adm jr. 4/10/91, acetamide update
+H    NH2  CC   CP1      2.5000  2   180.00 ! ALLOW PEP POL ARO PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+H    NR1  CPH1 CPH1     1.0000  2   180.00 ! ALLOW ARO
+                ! his, adm jr., 7/20/89
+H    NR1  CPH1 CT2      1.0000  2   180.00 ! ALLOW ARO
+                ! his, adm jr., 7/22/89, FROM HA CPH1 NR1 H
+H    NR1  CPH1 CT3      1.0000  2   180.00 ! ALLOW ARO
+                ! his, adm jr., 7/22/89, FROM HA CPH1 NR1 H
+H    NR3  CPH1 CPH1     1.4000  2   180.00 ! ALLOW ARO
+                ! his, adm jr., 6/27/90
+H    NR3  CPH1 CT2      3.0000  2   180.00 ! ALLOW ARO
+                ! his, adm jr., 7/22/89, FROM HC NR3 CPH1 HA
+H    NR3  CPH1 CT3      3.0000  2   180.00 ! ALLOW ARO
+                ! his, adm jr., 7/22/89, FROM HC NR3 CPH1 HA
+H    OH1  CA   CA       0.9900  2   180.00 ! ALLOW   ARO ALC
+                ! phenol OH rot bar, 3.37 kcal/mole, adm jr. 3/7/92
+H    OH1  CT1  CT3      1.3300  1     0.00 ! ALLOW ALC
+                ! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
+H    OH1  CT1  CT3      0.1800  2     0.00 ! ALLOW ALC
+                ! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
+H    OH1  CT1  CT3      0.3200  3     0.00 ! ALLOW ALC
+                ! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
+H    OH1  CT2  CT2      1.3000  1     0.00 ! ALLOW ALC
+                ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
+H    OH1  CT2  CT2      0.3000  2     0.00 ! ALLOW ALC
+                ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
+H    OH1  CT2  CT2      0.4200  3     0.00 ! ALLOW ALC
+                ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
+H    OH1  CT2  CT3      1.3000  1     0.00 ! ALLOW ALC
+                ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
+H    OH1  CT2  CT3      0.3000  2     0.00 ! ALLOW ALC
+                ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
+H    OH1  CT2  CT3      0.4200  3     0.00 ! ALLOW ALC
+                ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
+HA1  CC   NH2  H        1.4000  2   180.00 !  ALLOW PEP POL
+                ! adm jr. 4/10/91, acetamide update
+HA2  CP3  N    C        0.0000  3   180.00 ! ALLOW PRO PEP
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+HA2  CP3  N    CP1      0.1000  3     0.00 ! ALLOW PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+HA2  CP3  NP   CP1      0.0800  3     0.00 ! ALLOW PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+HA1  CT1  CT2  CA       0.0400  3     0.00 ! ALLOW   ARO
+                ! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92
+HA2  CT2  CPH1 CPH1     0.0000  3     0.00 ! ALLOW ARO
+                ! 4-methylimidazole 4-21G//6-31G* rot bar. adm jr., 9/4/89
+HA2  CT2  NH1  C        0.0000  3     0.00 ! ALLOW PEP
+                ! LK for autogenerate dihe, sp2-methyl, no dihedral potential
+HA2  CT2  NH1  H        0.0000  3     0.00 ! ALLOW PEP
+                ! LK for autogenerate dihe, sp2-methyl, no dihedral potential
+HA2  CT2  S    CT3      0.2800  3     0.00 ! ALLOW   ALI SUL ION
+                ! DTN 8/24/90
+HA3  CT3  CPH1 CPH1     0.0000  3     0.00 ! ALLOW ARO
+                ! 4-methylimidazole 4-21G//6-31G* rot bar. adm jr., 9/4/89
+HA3  CT3  CS   HA2      0.1600  3     0.00 ! ALLOW SUL
+                ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
+HA3  CT3  CS   HA3      0.1600  3     0.00 ! ALLOW SUL
+                ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
+HA3  CT3  CT2  CA       0.0400  3     0.00 ! ALLOW   ARO
+                ! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92
+HA3  CT3  NH1  C        0.0000  3     0.00 ! ALLOW PEP
+                ! LK for autogenerate dihe, sp2-methyl, no dihedral potential
+HA3  CT3  NH1  H        0.0000  3     0.00 ! ALLOW PEP
+                ! LK for autogenerate dihe, sp2-methyl, no dihedral potential
+HA3  CT3  S    CT2      0.2800  3     0.00 ! ALLOW   ALI SUL ION
+                ! DTN 8/24/90
+HE1  CE1  CE1  HE1      1.0000  2   180.00 ! 
+                ! 2-butene, adm jr., 8/98 update
+CT3  CE1  CE1  HE1      1.0000  2   180.00 !
+                ! 2-butene, adm jr., 8/98 update
+HE1  CE1  CE2  HE2      5.2000  2   180.00 ! 
+		! for propene, yin/adm jr., 12/95
+HE1  CE1  CT2  HA2      0.0000  3     0.00
+		! butene, adm jr., 2/00 update
+HE1  CE1  CT2  CT3      0.1200  3     0.00 ! 
+		! for butene, yin/adm jr., 12/95
+HE1  CE1  CT3  HA3      0.0000  3     0.00
+		! butene, adm jr., 2/00 update
+HE2  CE2  CE1  CT2      5.2000  2   180.00 ! 
+		! for butene, yin/adm jr., 12/95
+HB1  CP1  N    C        0.8000  3     0.00 ! ALLOW PRO PEP
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+HB1  CP1  N    CP3      0.1000  3     0.00 ! ALLOW PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+HB1  CP1  NP   CP3      0.0800  3     0.00 ! ALLOW PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+HB1  CT1  NH1  C        0.0000  1     0.00 ! ALLOW PEP
+                ! Alanine Dipeptide ab initio calc's (LK)
+HB1  CT1  NH1  H        0.0000  1     0.00 ! ALLOW PEP
+                ! Alanine Dipeptide ab initio calc's (LK)
+HB2  CT2  NH1  C        0.0000  1     0.00 ! ALLOW PEP
+                ! Alanine Dipeptide ab initio calc's (LK)
+HB2  CT2  NH1  H        0.0000  1     0.00 ! ALLOW PEP
+                ! Alanine Dipeptide ab initio calc's (LK)
+HC   NH2  CT2  HB2      0.1100  3     0.00
+                !from X CT3 NH2 X, neutral glycine, adm jr.
+HC   NH2  CT2  CD       0.1100  3     0.00
+                !from X CT3 NH2 X, neutral glycine, adm jr.
+HC   NH2  CT2  CT2       0.1100  3     0.00
+                !from X CT3 NH2 X, neutral lysine
+HC   NH2  CT2  HA2      0.1100  3     0.00
+                !from X CT3 NH2 X, neutral lysine
+HC   NP   CP1  C        0.0800  3     0.00 ! ALLOW PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+HC   NP   CP1  CC       0.0800  3     0.00 ! ALLOW PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+HC   NP   CP1  CD       0.0800  3     0.00 ! ALLOW PRO PEP
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+HC   NP   CP1  CP2      0.0800  3     0.00 ! ALLOW PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+HC   NP   CP1  HB1      0.0800  3     0.00 ! ALLOW PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+HC   NP   CP3  CP2      0.0800  3     0.00 ! ALLOW PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+HC   NP   CP3  HA2      0.0800  3     0.00 ! ALLOW PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+HP   CA   CA   CA       4.2000  2   180.00 ! ALLOW   ARO
+                ! JES 8/25/89 benzene
+HP   CA   CA   CT2      4.2000  2   180.00 ! ALLOW   ARO
+                ! JES 8/25/89 toluene and ethylbenzene
+HP   CA   CA   CT3      4.2000  2   180.00 ! ALLOW   ARO
+                ! toluene, adm jr., 3/7/92
+HP   CA   CA   HP       2.4000  2   180.00 ! ALLOW   ARO
+                ! JES 8/25/89 benzene
+HR1  CPH1 CPH1 CT2      1.0000  2   180.00 ! ALLOW ARO
+                ! his, adm jr., 6/27/90
+HR1  CPH1 CPH1 CT3      1.0000  2   180.00 ! ALLOW ARO
+                ! his, adm jr., 6/27/90
+HR1  CPH1 CPH1 HR1      1.0000  2   180.00 ! ALLOW ARO
+                ! his, adm jr., 6/27/90, his
+HR1  CPH1 NR3  CPH2     2.5000  2   180.00 ! ALLOW ARO
+                ! his, adm jr., 6/27/90
+HR1  CPH1 NR3  H        3.0000  2   180.00 ! ALLOW ARO
+                ! his, adm jr., 6/27/90
+HR1  CPH2 NR1  CPH1     3.0000  2   180.00 ! ALLOW ARO
+                ! his, adm jr., 6/27/90
+HR1  CPH2 NR1  H        1.0000  2   180.00 ! ALLOW ARO
+                ! his, adm jr., 6/27/90
+HR1  CPH2 NR2  CPH1     3.0000  2   180.00 ! ALLOW ARO
+                ! his, adm jr., 6/27/90
+HR2  CPH2 NR3  CPH1     3.0000  2   180.00 ! ALLOW ARO
+                ! his, adm jr., 6/27/90
+HR2  CPH2 NR3  H        0.0000  2   180.00 ! ALLOW ARO
+                ! his, adm jr., 6/27/90, YES, 0.0
+HR3  CPH1 CPH1 CT2      2.0000  2   180.00 ! ALLOW ARO
+                ! adm jr., 3/24/92, maintain old aliphatic H VDW params
+HR3  CPH1 CPH1 CT3      2.0000  2   180.00 ! ALLOW ARO
+                ! adm jr., 3/24/92, maintain old aliphatic H VDW params
+HR3  CPH1 CPH1 HR3      2.0000  2   180.00 ! ALLOW ARO
+                ! adm jr., 3/24/92, maintain old aliphatic H VDW params
+HR3  CPH1 NR1  CPH2     3.0000  2   180.00 ! ALLOW ARO
+                ! adm jr., 3/24/92, maintain old aliphatic H VDW params
+HR3  CPH1 NR1  H        1.0000  2   180.00 ! ALLOW ARO
+                ! adm jr., 3/24/92, maintain old aliphatic H VDW params
+HR3  CPH1 NR2  CPH2     3.0000  2   180.00 ! ALLOW ARO
+                ! adm jr., 3/24/92, maintain old aliphatic H VDW params
+HS   S    CT2  CT3      0.2400  1     0.00 ! ALLOW   ALI SUL ION
+                ! ethanethiol C-C-S-H surface, adm jr., 4/18/93
+HS   S    CT2  CT3      0.1500  2     0.00 ! ALLOW   ALI SUL ION
+                ! ethanethiol C-C-S-H surface, adm jr., 4/18/93
+HS   S    CT2  CT3      0.2700  3     0.00 ! ALLOW   ALI SUL ION
+                ! ethanethiol C-C-S-H surface, adm jr., 4/18/93
+HS   S    CT2  HA2      0.2000  3     0.00 ! ALLOW   ALI SUL ION
+                ! methanethiol pure solvent, adm jr., 6/22/92
+HS   S    CT3  HA3      0.2000  3     0.00 ! ALLOW   ALI SUL ION
+                ! methanethiol pure solvent, adm jr., 6/22/92
+N    C    CP1  CP2      0.4000  1     0.00 ! ALLOW PEP PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+N    C    CP1  CP2      0.6000  2     0.00 ! ALLOW PEP PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+N    C    CP1  HB1      0.4000  1   180.00 ! ALLOW PEP PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+N    C    CP1  HB1      0.6000  2     0.00 ! ALLOW PEP PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+N    C    CP1  N        0.3000  1     0.00 ! ALLOW PEP PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+N    C    CP1  N       -0.3000  4     0.00 ! ALLOW PEP PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+N    C    CT1  CT1      0.0000  1     0.00 ! ALLOW PEP PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+N    C    CT1  CT2      0.0000  1     0.00 ! ALLOW PEP PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+N    C    CT1  CT3      0.0000  1     0.00 ! ALLOW PEP PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+N    C    CT1  HB1      0.0000  1     0.00 ! ALLOW PEP PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+N    C    CT2  HB2      0.0000  1     0.00 ! ALLOW PEP PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+N    C    CT3  HA3      0.0000  1     0.00 ! ALLOW PEP PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+N    CT1  CT2  CA       0.0400  3     0.00 ! ALLOW   ARO
+                ! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92
+NH1  C    CP1  CP2      0.4000  1     0.00 ! ALLOW PEP PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NH1  C    CP1  CP2      0.6000  2     0.00 ! ALLOW PEP PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NH1  C    CP1  HB1      0.4000  1   180.00 ! ALLOW PEP PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NH1  C    CP1  HB1      0.6000  2     0.00 ! ALLOW PEP PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NH1  C    CP1  N        0.3000  1     0.00 ! ALLOW PEP PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NH1  C    CP1  N       -0.3000  4     0.00 ! ALLOW PEP PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NH1  C    CT1  CT1      0.0000  1     0.00 !   ALLOW PEP
+                ! ala dipeptide corrxn for new C VDW Rmin, 4/10/93 (LK)
+NH1  C    CT1  CT2      0.0000  1     0.00 !   ALLOW PEP
+                ! ala dipeptide corrxn for new C VDW Rmin, 4/10/93 (LK)
+NH1  C    CT1  CT3      0.0000  1     0.00 !   ALLOW PEP
+                ! ala dipeptide corrxn for new C VDW Rmin, 4/10/93 (LK)
+NH1  C    CT1  HB1      0.0000  1     0.00 !   ALLOW PEP
+                ! Alanine Dipeptide ab initio calc's (LK)
+NH1  C    CT1  NH1      0.6000  1     0.00 !   ALLOW PEP
+                ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93
+NH1  C    CT2  CT2      0.0000  1     0.00 !   ALLOW PEP
+                ! from NH1  C    CT1  CT2, for lactams, adm jr.
+NH1  C    CT2  HA2      0.0000  3     0.00 ! ALLOW PEP
+                ! LK for autogenerate dihe, sp2-methyl, no dihedral potential
+NH1  C    CT2  HB2      0.0000  1     0.00 !   ALLOW PEP
+                ! Alanine Dipeptide ab initio calc's (LK)
+NH1  C    CT2  NH1      0.6000  1     0.00 !   ALLOW PEP
+                ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93
+NH1  C    CT3  HA3      0.0000  3     0.00 ! ALLOW PEP
+                ! LK for autogenerate dihe, sp2-methyl, no dihedral potential
+NH1  CT1  C    N        0.4000  1     0.00 ! ALLOW PEP PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NH1  CT2  C    N        0.4000  1     0.00 ! ALLOW PEP PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NH2  CC   CP1  CP2      0.4000  1     0.00 ! ALLOW PEP PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NH2  CC   CP1  CP2      0.6000  2     0.00 ! ALLOW PEP PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NH2  CC   CP1  HB1      0.4000  1   180.00 ! ALLOW PEP PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NH2  CC   CP1  HB1      0.6000  2     0.00 ! ALLOW PEP PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NH2  CC   CP1  N        0.3000  1     0.00 ! ALLOW PEP PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NH2  CC   CP1  N       -0.3000  4     0.00 ! ALLOW PEP PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NH2  CC   CT2  HA2      0.0000  3   180.00 ! ALLOW POL
+                ! adm jr., 8/13/90 acetamide geometry and vibrations
+NH3  CT1  C    N        0.4000  1     0.00 ! ALLOW PEP PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NH3  CT1  C    NH1      0.6000  1     0.00 ! ALLOW PEP PRO
+                ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93
+NH3  CT1  CC   NH2      0.4000  1     0.00 ! ALLOW PEP PRO
+                ! Alanine dipeptide; NMA; acetate; etc. backbone param. RLD 3/22/92
+NH3  CT2  C    N        0.4000  1     0.00 ! ALLOW PEP PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+!!!NH3  CT2  C    NH1      0.4000  1     0.00 ! ALLOW PEP PRO
+!!!                ! adm jr. 3/24/92, for PRES GLYP
+NH3  CT2  C    NH1      1.0000  1     0.00 ! ALLOW PEP PRO
+                ! RB 1/07/11, based on graf et al Gly 3 N-ter J-couplings for PRES GLYP
+NH3  CT2  CC   NH2      0.4000  1     0.00 ! ALLOW PEP PRO
+                ! Alanine dipeptide; NMA; acetate; etc. backbone param. RLD 3/22/92
+NP   CP1  C    N        0.3000  1     0.00 ! ALLOW PEP PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NP   CP1  C    NH1      0.3000  1     0.00 ! ALLOW PEP PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NP   CP1  CC   NH2      0.3000  1     0.00 ! ALLOW PEP PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NR1  CPH1 CPH1 CT2      3.0000  2   180.00 ! ALLOW ARO
+                ! his, ADM JR., 7/22/89, FROM NR1 CPH1 CPH1 HA
+NR1  CPH1 CPH1 CT3      3.0000  2   180.00 ! ALLOW ARO
+                ! his, ADM JR., 7/22/89, FROM NR1 CPH1 CPH1 HA
+NR1  CPH1 CPH1 HR3      3.0000  2   180.00 ! ALLOW ARO
+                ! adm jr., 3/24/92, maintain old aliphatic H VDW params
+NR1  CPH1 CT2  CT2      0.1900  3     0.00 ! ALLOW ARO
+                ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89
+NR1  CPH1 CT2  CT3      0.1900  3     0.00 ! ALLOW ARO
+                ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89
+NR1  CPH1 CT2  HA2      0.1900  3     0.00 ! ALLOW ARO
+                ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89
+NR1  CPH1 CT3  HA3      0.1900  3     0.00 ! ALLOW ARO
+                ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89
+NR1  CPH2 NR2  CPH1    14.0000  2   180.00 ! ALLOW ARO
+                ! his, ADM JR., 7/20/89
+NR2  CPH1 CPH1 CT2      3.0000  2   180.00 ! ALLOW ARO
+                ! his, ADM JR., 7/22/89, FROM NR2 CPH1 CPH1 HA
+NR2  CPH1 CPH1 CT3      3.0000  2   180.00 ! ALLOW ARO
+                ! his, ADM JR., 7/22/89, FROM NR2 CPH1 CPH1 HA
+NR2  CPH1 CPH1 HR3      3.0000  2   180.00 ! ALLOW ARO
+                ! adm jr., 3/24/92, maintain old aliphatic H VDW params
+NR2  CPH1 CPH1 NR1     14.0000  2   180.00 ! ALLOW ARO
+                ! his, ADM JR., 7/20/89
+!NR2  CPH1 CT2  CT1      0.1900  3     0.00 ! ALLOW ARO
+                ! HIS CB-CG TORSION,
+NR2  CPH1 CT2  CT2      0.1900  3     0.00 ! ALLOW ARO
+                ! HIS CB-CG TORSION,
+NR2  CPH1 CT2  CT3      0.1900  3     0.00 ! ALLOW ARO
+                ! HIS CB-CG TORSION,
+NR2  CPH1 CT2  HA2      0.1900  3     0.00 ! ALLOW ARO
+                ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89
+NR2  CPH1 CT3  HA3      0.1900  3     0.00 ! ALLOW ARO
+                ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89
+NR2  CPH2 NR1  CPH1    14.0000  2   180.00 ! ALLOW ARO
+                ! his, ADM JR., 7/20/89
+NR2  CPH2 NR1  H        1.0000  2   180.00 ! ALLOW ARO
+                ! his, ADM JR., 7/20/89
+NR3  CPH1 CPH1 CT2      2.5000  2   180.00 ! ALLOW ARO
+                ! his, adm jr., 6/27/90
+NR3  CPH1 CPH1 CT3      2.5000  2   180.00 ! ALLOW ARO
+                ! his, adm jr., 6/27/90
+NR3  CPH1 CPH1 HR1      2.5000  2   180.00 ! ALLOW ARO
+                ! his, adm jr., 6/27/90
+NR3  CPH1 CPH1 NR3     12.0000  2   180.00 ! ALLOW ARO
+                ! his, adm jr., 6/27/90
+NR3  CPH1 CT2  CT2      0.1900  3     0.00 ! ALLOW ARO
+                ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89
+NR3  CPH1 CT2  CT3      0.1900  3     0.00 ! ALLOW ARO
+                ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89
+NR3  CPH1 CT2  HA2      0.1900  3     0.00 ! ALLOW ARO
+                ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89
+NR3  CPH1 CT3  HA3      0.1900  3     0.00 ! ALLOW ARO
+                ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89
+NR3  CPH2 NR3  CPH1    12.0000  2   180.00 ! ALLOW ARO
+                ! his, ADM JR., 7/20/89
+NR3  CPH2 NR3  H        1.4000  2   180.00 ! ALLOW ARO
+                ! his, adm jr., 6/27/90
+O    C    CP1  CP2      0.4000  1   180.00 ! ALLOW PEP PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+O    C    CP1  CP2      0.6000  2     0.00 ! ALLOW PEP PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+O    C    CP1  HB1      0.4000  1     0.00 ! ALLOW PEP PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+O    C    CP1  HB1      0.6000  2     0.00 ! ALLOW PEP PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+O    C    CP1  N       -0.3000  4     0.00 ! ALLOW PEP PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+O    C    CT1  CT1      1.4000  1     0.00 !   ALLOW PEP
+                ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c
+O    C    CT1  CT2      1.4000  1     0.00 !   ALLOW PEP
+                ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c
+O    C    CT1  CT3      1.4000  1     0.00 !   ALLOW PEP
+                ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c
+O    C    CT1  HB1      0.0000  1     0.00 !   ALLOW PEP
+                ! Alanine Dipeptide ab initio calc's (LK)
+O    C    CT1  NH1      0.0000  1     0.00 !   ALLOW PEP
+                ! Alanine Dipeptide ab initio calc's (LK)
+O    C    CT1  NH3      0.0000  1     0.00 ! ALLOW PEP PRO
+                ! Backbone parameter set made complete RLD 8/8/90
+O    C    CT2  CT2      1.4000  1     0.00 !   ALLOW PEP
+                ! from O    C    CT1  CT2, for lactams, adm jr.
+O    C    CT2  HA2      0.0000  3   180.00 ! ALLOW POL
+                ! adm jr., 8/13/90 acetamide geometry and vibrations
+O    C    CT2  HB2      0.0000  1     0.00 !   ALLOW PEP
+                ! Alanine Dipeptide ab initio calc's (LK)
+O    C    CT2  NH1      0.0000  1     0.00 !   ALLOW PEP
+                ! Alanine Dipeptide ab initio calc's (LK)
+O    C    CT2  NH3      0.0000  1     0.00 ! ALLOW PEP PRO
+                ! Backbone parameter set made complete RLD 8/8/90
+O    C    CT3  HA3      0.0000  3   180.00 ! ALLOW POL
+                ! adm jr., 8/13/90 acetamide geometry and vibrations
+O    C    N    CP1      2.7500  2   180.00 ! ALLOW PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+O    C    N    CP1      0.3000  4     0.00 ! ALLOW PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+O    C    N    CP3      2.7500  2   180.00 ! ALLOW PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+O    C    N    CP3      0.3000  4     0.00 ! ALLOW PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+O    C    NH1  CT1      2.5000  2   180.00 !  ALLOW PEP
+                ! Gives appropriate NMA cis/trans barrier. (LK)
+O    C    NH1  CT2      2.5000  2   180.00 !  ALLOW PEP
+                ! Gives appropriate NMA cis/trans barrier. (LK)
+O    C    NH1  CT3      2.5000  2   180.00 !  ALLOW PEP
+                ! Gives appropriate NMA cis/trans barrier. (LK)
+O    C    NH1  H        2.5000  2   180.00 !  ALLOW PEP
+                ! Gives appropriate NMA cis/trans barrier. (LK)
+O    CC   CP1  CP2      0.4000  1   180.00 ! ALLOW PEP PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+O    CC   CP1  CP2      0.6000  2     0.00 ! ALLOW PEP PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+O    CC   CP1  HB1      0.4000  1     0.00 ! ALLOW PEP PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+O    CC   CP1  HB1      0.6000  2     0.00 ! ALLOW PEP PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+O    CC   CP1  N       -0.3000  4     0.00 ! ALLOW PEP PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+O    CC   CT2  HA2      0.0000  3   180.00 ! ALLOW POL
+                ! adm jr. 4/05/91, for asn,asp,gln,glu and cters
+O    CC   NH2  H        1.4000  2   180.00 !  ALLOW PEP POL ARO PRO
+                ! adm jr. 4/10/91, acetamide update
+OB   CD   OS   CT2      0.9650  1   180.00 ! ALLOW   PEP POL
+                ! adm jr. 3/19/92, from lipid methyl acetate
+OB   CD   OS   CT2      3.8500  2   180.00 ! ALLOW   PEP POL
+                ! adm jr. 3/19/92, from lipid methyl acetate
+OB   CD   OS   CT3      0.9650  1   180.00 ! ALLOW   PEP POL
+                ! adm jr. 3/19/92, from lipid methyl acetate
+OB   CD   OS   CT3      3.8500  2   180.00 ! ALLOW   PEP POL
+                ! adm jr. 3/19/92, from lipid methyl acetate
+OC   CA   CA   CA       3.1000  2   180.00 ! ALLOW   ARO
+                ! adm jr. 8/27/91, phenoxide
+OC   CA   CA   HP       4.2000  2   180.00 ! ALLOW   ARO
+                ! adm jr. 8/27/91, phenoxide
+OC   CC   CP1  CP2      0.1600  3     0.00 ! ALLOW PEP PRO POL
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+OC   CC   CP1  HB1      0.1600  3     0.00 ! ALLOW PEP PRO POL
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+OC   CC   CP1  N        0.1600  3     0.00 ! ALLOW PEP PRO POL
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+OC   CC   CP1  NP       0.1600  3     0.00 ! ALLOW PEP PRO POL
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+OC   CC   CT1  NH3      3.2000  2   180.00 ! ALLOW PEP PRO
+                ! adm jr. 4/17/94, zwitterionic glycine
+OC   CC   CT2  NH3      3.2000  2   180.00 ! ALLOW PEP PRO
+                ! adm jr. 4/17/94, zwitterionic glycine
+OH1  CA   CA   CA       3.1000  2   180.00 ! ALLOW   ARO
+                ! JES 8/25/89 phenol
+OH1  CA   CA   HP       4.2000  2   180.00 ! ALLOW   ARO
+                ! JES 8/25/89 phenol
+S    CT2  CT2  HA2      0.0100  3     0.00 ! ALLOW   ALI SUL ION
+                ! DTN 8/24/90
+SM   CT2  CT2  HA2      0.0100  3     0.00 ! ALLOW   ALI SUL ION
+                ! DTN 8/24/90
+SM   SM   CT2  CT1      0.3100  3     0.00 ! ALLOW  SUL ALI
+                ! S-S for cys-cys, dummy parameter for now ... DTN  9/04/90
+SM   SM   CT2  CT2      0.3100  3     0.00 ! ALLOW  SUL ALI
+                ! S-S for cys-cys, dummy parameter for now ... DTN  9/04/90
+SM   SM   CT2  CT3      0.3100  3     0.00 ! ALLOW  SUL ALI
+                ! S-S for cys-cys, dummy parameter for now ... DTN  9/04/90
+SM   SM   CT2  HA2      0.1580  3     0.00 ! ALLOW   ALI SUL ION
+                ! expt. dimethyldisulfide,    3/26/92 (FL)
+SM   SM   CT3  HA3      0.1580  3     0.00 ! ALLOW   ALI SUL ION
+                ! expt. dimethyldisulfide,    3/26/92 (FL)
+SS   CS   CT3  HA3      0.1500  3     0.00 ! ALLOW SUL
+                ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
+X    C    NC2  X        2.2500  2   180.00 ! ALLOW   PEP POL ARO
+                ! 9.0->2.25 GUANIDINIUM (KK)
+X    CD   OH1  X        2.0500  2   180.00 ! ALLOW   PEP POL ARO ALC
+                ! adm jr, 10/17/90, acetic acid C-Oh rotation barrier
+X    CD   OS   X        2.0500  2   180.00 ! ALLOW   PEP POL
+                ! adm jr. 3/19/92, from lipid methyl acetate
+X    CE1  CE1  X        0.1500  1     0.00
+                ! 2-butene, adm jr., 2/00 update
+X    CE1  CE1  X        8.5000  2   180.00
+                ! 2-butene, adm jr., 2/00 update
+X    CE2  CE2  X        4.9000  2   180.00 ! 
+		! for ethene, yin/adm jr., 12/95
+X    CP1  C    X        0.0000  6   180.00 ! ALLOW   POL PEP PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+X    CP1  CC   X        0.0000  6   180.00 ! ALLOW   POL PEP
+                ! changed to 0.0 RLD 5/19/92
+X    CP1  CD   X        0.0000  6   180.00 ! ALLOW   POL PEP
+                ! Alanine dipeptide; NMA; acetate; etc. backbone param. RLD 3/22/92
+X    CP1  CP2  X        0.1400  3     0.00 ! ALLOW PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+X    CP2  CP2  X        0.1600  3     0.00 ! ALLOW PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+X    CP3  CP2  X        0.1400  3     0.00 ! ALLOW PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+X    CT1  CC   X        0.0500  6   180.00 ! ALLOW   POL PEP
+                ! For side chains of asp,asn,glu,gln, (n=6) from KK(LK)
+X    CT1  CD   X        0.0000  6   180.00 ! ALLOW   POL PEP
+                ! adm jr. 3/19/92, from lipid methyl acetate
+X    CT1  CT1  X        0.2000  3     0.00 ! ALLOW   ALI
+                ! alkane update, adm jr., 3/2/92
+X    CT1  CT2  X        0.2000  3     0.00 ! ALLOW   ALI
+                ! alkane update, adm jr., 3/2/92
+X    CT1  CT3  X        0.2000  3     0.00 ! ALLOW   ALI
+                ! alkane update, adm jr., 3/2/92
+X    CT1  NH3  X        0.1000  3     0.00 ! ALLOW   ALI POL
+                ! 0.715->0.10 METHYLAMMONIUM (KK)
+X    CT1  OH1  X        0.1400  3     0.00 ! ALLOW   ALI ALC ARO
+                ! EMB  11/21/89 methanol vib fit
+X    CT1  OS   X       -0.1000  3     0.00 ! ALLOW   PEP POL
+                ! adm jr. 3/19/92, from lipid methyl acetate
+X    CT2  CA   X        0.0000  6     0.00 ! ALLOW   ALI ARO
+                ! toluene, adm jr., 3/7/92
+X    CT2  CC   X        0.0500  6   180.00 ! ALLOW   POL PEP
+                ! For side chains of asp,asn,glu,gln, (n=6) from KK(LK)
+X    CT2  CD   X        0.0000  6   180.00 ! ALLOW   POL PEP
+                ! adm jr. 3/19/92, from lipid methyl acetate
+X    CT2  CT2  X        0.1900  3     0.00 ! ALLOW   ALI
+                ! alkane, 4/98, yin and mackerell
+X    CT2  CT3  X        0.1600  3     0.00 ! ALLOW   ALI
+                ! alkane, 4/98, yin and mackerell
+X    CT2  NC2  X        0.0000  6   180.00 ! ALLOW   ALI POL
+                ! methylguanidinium, adm jr., 3/26/92
+X    CT2  NH3  X        0.1000  3     0.00 ! ALLOW   ALI POL
+                ! 0.715->0.10 METHYLAMMONIUM (KK)
+X    CT2  OH1  X        0.1400  3     0.00 ! ALLOW   ALI ALC ARO
+                ! EMB  11/21/89 methanol vib fit
+X    CT2  OS   X       -0.1000  3     0.00 ! ALLOW   PEP POL
+                ! adm jr. 3/19/92, from lipid methyl acetate
+X    CT3  CA   X        0.0000  6     0.00 ! ALLOW   ALI ARO
+                ! toluene, adm jr., 3/7/92
+X    CT3  CC   X        0.0500  6   180.00 ! ALLOW   POL PEP
+                ! For side chains of asp,asn,glu,gln, (n=6) from KK(LK)
+X    CT3  CD   X        0.0000  6   180.00 ! ALLOW   POL PEP
+                ! adm jr. 3/19/92, from lipid methyl acetate
+X    CT3  CT3  X        0.1525  3     0.00 ! ALLOW   ALI
+                ! alkane, 4/98, yin and mackerell
+X    CT3  NC2  X        0.0000  6   180.00 ! ALLOW   ALI POL
+                ! methylguanidinium, adm jr., 3/26/92
+X    CT3  NH2  X        0.1100  3     0.00 ! ALLOW   POL
+                ! methylamine geom/freq, adm jr., 6/2/92
+X    CT3  NH3  X        0.0900  3     0.00 ! ALLOW   ALI POL
+                ! fine-tuned to ab initio; METHYLAMMONIUM, KK 03/10/92
+X    CT3  OH1  X        0.1400  3     0.00 ! ALLOW   ALI ALC ARO
+                ! EMB  11/21/89 methanol vib fit
+X    CT3  OS   X       -0.1000  3     0.00 ! ALLOW   PEP POL
+                ! adm jr. 3/19/92, from lipid methyl acetate
+
+!chi1/chi2 fitting, Zhu, 2011
+!directly transferred parameters
+NH1  CT1  CT1  HA1      0.2000  3     0.00 ! From X    CT1  CT1  X
+HB1  CT1  CT1  HA1      0.2000  3     0.00 ! From X    CT1  CT1  X
+HB1  CT1  CT1  CT3      0.2000  3     0.00 ! From X    CT1  CT1  X
+HA1  CT1  CT1  C        0.2000  3     0.00 ! From X    CT1  CT1  X
+!
+NH1  CT1  CT2  HA2      0.2000  3     0.00 ! From X    CT1  CT2  X
+HB1  CT1  CT2  HA2      0.2000  3     0.00 ! From X    CT1  CT2  X
+HB1  CT1  CT2  OH1      0.2000  3     0.00 ! From X    CT1  CT2  X
+HB1  CT1  CT2  CT2      0.2000  3     0.00 ! From X    CT1  CT2  X
+HA2  CT2  CT1  C        0.2000  3     0.00 ! From X    CT1  CT2  X
+HA2  CT2  OH1  H        0.1400  3     0.00 ! From X    CT2  OH1  X      
+!
+CT1  CT2  CT2  HA2      0.1900  3     0.00 ! From X    CT2  CT2  X
+HA2  CT2  CT2  HA2      0.1900  3     0.00 ! From X    CT2  CT2  X
+HA2  CT2  CT2  CC       0.1900  3     0.00 ! From X    CT2  CT2  X
+!
+HB1  CT1  CT2  S        0.2000  3     0.00 ! From X    CT1  CT2  X
+!Arg
+CT2  CT2  CT2  HA2      0.1900  3     0.00 ! From X    CT2  CT2  X
+CT2  CT2  CT2  NC2      0.1900  3     0.00 ! From X    CT2  CT2  X
+CT2  CT2  NC2  HC       0.0000  6   180.00 ! From X    CT2  NC2  X
+CT2  CT2  NC2  C        0.0000  6   180.00 ! From X    CT2  NC2  X
+HA2  CT2  CT2  NC2      0.1900  3     0.00 ! From X    CT2  CT2  X
+CT2  NC2  C    NC2      2.2500  2   180.00 ! From X    C    NC2  X
+HA2  CT2  NC2  HC       0.0000  6   180.00 ! From X    CT2  NC2  X
+HA2  CT2  NC2  C        0.0000  6   180.00 ! From X    CT2  NC2  X
+NC2  C    NC2  HC       2.2500  2   180.00 ! From X    C    NC2  X
+!Asn
+HB1  CT1  CT2  CC       0.2000  3     0.00 ! From X    CT1  CT2  X
+!Trp
+HB1  CT1  CT2  CY       0.2000  3     0.00 ! From X    CT1  CT2  X
+!Asp
+HA2  CT2  CC   OC       0.0500  6   180.00 ! From X    CT2  CC   X
+!Hsd/Hse
+HB1  CT1  CT2  CPH1     0.2000  3     0.00 ! From X    CT1  CT2  X
+!Ile,Leu,Val
+CT1  CT1  CT3  HA3      0.2000  3     0.00 ! From X    CT1  CT3  X
+CT1  CT1  CT2  HA2      0.2000  3     0.00 ! From X    CT1  CT2  X
+HB1  CT1  CT1  CT2      0.2000  3     0.00 ! From X    CT1  CT1  X
+CT1  CT2  CT3  HA3      0.1600  3     0.00 ! From X    CT2  CT3  X
+HA1  CT1  CT3  HA3      0.2000  3     0.00 ! From X    CT1  CT3  X
+HA1  CT1  CT2  HA2      0.2000  3     0.00 ! From X    CT1  CT2  X
+HA1  CT1  CT2  CT3      0.2000  3     0.00 ! From X    CT1  CT2  X
+CT3  CT1  CT2  HA2      0.2000  3     0.00 ! From X    CT1  CT2  X
+CT3  CT1  CT2  CT3      0.2000  3     0.00 ! From X    CT1  CT2  X
+HA3  CT3  CT1  CT2      0.2000  3     0.00 ! From X    CT1  CT3  X
+HA2  CT2  CT3  HA3      0.1600  3     0.00 ! From X    CT2  CT3  X
+CT1  CT2  CT1  HA1      0.2000  3     0.00 ! From X    CT1  CT2  X
+HB1  CT1  CT2  CT1      0.2000  3     0.00 ! From X    CT1  CT2  X
+CT3  CT1  CT3  HA3      0.2000  3     0.00 ! From X    CT1  CT3  X
+!Lys
+CT2  CT2  CT2  NH3      0.1900  3     0.00 ! From X    CT2  CT2  X
+CT2  CT2  NH3  HC       0.1000  3     0.00 ! From X    CT2  NH3  X
+HA2  CT2  CT2  NH3      0.1900  3     0.00 ! From X    CT2  CT2  X
+HA2  CT2  NH3  HC       0.1000  3     0.00 ! From X    CT2  NH3  X
+!Tyr/Phe
+HB1  CT1  CT2  CA       0.2000  3     0.00 ! From X    CT1  CT2  X
+HA2  CT2  CA   CA       0.0000  6     0.00 ! From X    CT2  CA   X
+!Thr
+HB1  CT1  CT1  OH1      0.2000  3     0.00 ! From X    CT1  CT1  X
+HA1  CT1  OH1  H        0.1400  3     0.00 ! From X    CT1  OH1  X
+OH1  CT1  CT3  HA3      0.2000  3     0.00 ! From X    CT1  CT3  X
+!Gln
+CT2  CT2  CC   O        0.0500  6   180.00 ! From X    CT2  CC   X
+CT2  CT2  CC   NH2      0.0500  6   180.00 ! From X    CT2  CC   X
+!Glu
+CT2  CT2  CC   OC       0.0500  6   180.00 ! From X    CT2  CC   X
+!Glu/Hsp
+NH1  CT1  CT2A HA2      0.2000  3     0.00 ! From X    CT1  CT2  X
+NH3  CT1  CT2A CT2      0.2000  3     0.00 ! From X    CT1  CT2  X !N terminus
+CT1  CT2A CT2  HA2      0.1900  3     0.00 ! From X    CT2  CT2  X
+HB1  CT1  CT2A HA2      0.2000  3     0.00 ! From X    CT1  CT2  X
+HB1  CT1  CT2A CT2      0.2000  3     0.00 ! From X    CT1  CT2  X
+HA2  CT2A CT1  C        0.2000  3     0.00 ! From X    CT1  CT2  X
+HA2  CT2A CT1  CC       0.2000  3     0.00 ! RB: added for C-ter Glu
+HA2  CT2A CT2  HA2      0.1900  3     0.00 ! From X    CT2  CT2  X
+HA2  CT2A CT2  CC       0.1900  3     0.00 ! From X    CT2  CT2  X
+HB1  CT1  CT2A CPH1     0.2000  3     0.00 ! From X    CT1  CT2  X
+C    NH1  CT1  CT2A     1.8000  1     0.00 ! from CT2  CT1  NH1  C
+H    NH1  CT1  CT2A     0.0000  1     0.00 ! from H    NH1  CT1  CT2
+CT2A CT1  C    O        1.4000  1     0.00 ! from O    C    CT1  CT2
+CT2A CT1  C    NH1      0.0000  1     0.00 ! NH1  C    CT1  CT2
+CT2A CT1  C    N        0.0000  1     0.00 ! RB: added for GLU-PRO in UBQ
+! Glup
+CT1  CT2A CT2  CD       0.1900  3     0.00 ! From X    CT2  CT2  X
+HA2  CT2A CT2  CD       0.1900  3     0.00 ! From X    CT2  CT2  X
+CT2A CPH1 CPH1 HR1      1.0000  2   180.00 ! from HR1  CPH1 CPH1 CT2
+CT2A CPH1 CPH1 NR3      2.5000  2   180.00 ! from NR3  CPH1 CPH1 CT2
+CT2A CPH1 NR3  H        3.0000  2   180.00 ! from H    NR3  CPH1 CT2
+CT2A CPH1 NR3  CPH2     2.5000  2   180.00 ! from CT2  CPH1 NR3  CPH2
+HA2  CT2A CPH1 CPH1     0.0000  3     0.00 ! from HA2  CT2  CPH1 CPH1
+HA2  CT2A CPH1 NR3      0.1900  3     0.00 ! from NR3  CPH1 CT2  HA2
+
+! Fit dihedrals
+! Variable cutoff based on QM and weighted in favor of alphaR and EXT (5:5:1)
+! Shared dihedrals were fitted simultaneously
+
+! Group-fitted for Lys/Arg/Gln/Met
+C    CT1  CT2  CT2      0.3500  1   180.00 
+C    CT1  CT2  CT2      0.4200  2   180.00 
+C    CT1  CT2  CT2      1.9100  3   180.00 
+CT2  CT2  CT1  NH1      0.8800  1   180.00 
+CT2  CT2  CT1  NH1      0.0000  2   180.00 
+CT2  CT2  CT1  NH1      1.9000  3     0.00 
+CC   CT2  CT2  CT1      1.8400  1   180.00 
+CC   CT2  CT2  CT1      0.8400  2   180.00 
+CC   CT2  CT2  CT1      0.3900  3   180.00 
+CT1  CT2  CT2  CT2      0.6300  1   180.00 
+CT1  CT2  CT2  CT2      0.0100  2     0.00 
+CT1  CT2  CT2  CT2      0.1500  3     0.00 
+CT1  CT2  CT2  S        0.1400  1   180.00 
+CT1  CT2  CT2  S        0.5400  2     0.00 
+CT1  CT2  CT2  S        0.6900  3     0.00 
+! Fitted Asn 
+C    CT1  CT2  CC       1.4100  1   180.00 
+C    CT1  CT2  CC       1.2900  2   180.00 
+C    CT1  CT2  CC       0.5900  3   180.00 
+CC   CT2  CT1  NH1      0.2800  1   180.00 
+CC   CT2  CT1  NH1      0.5000  2   180.00 
+CC   CT2  CT1  NH1      0.3800  3     0.00 
+CT1  CT2  CC   NH2      0.6200  1   180.00 
+CT1  CT2  CC   NH2      0.6600  2   180.00 
+CT1  CT2  CC   NH2      0.7200  3   180.00 
+CT1  CT2  CC   O        0.4200  1   180.00 
+CT1  CT2  CC   O        0.1500  2   180.00 
+CT1  CT2  CC   O        0.9500  3   180.00 
+! Fitted Asp
+C    CT1  CT2A CC       1.6100  1   180.00 
+C    CT1  CT2A CC       1.2900  2   180.00 
+C    CT1  CT2A CC       0.5900  3   180.00 
+CC   CT2A CT1  NH1      0.6800  1   180.00 
+CC   CT2A CT1  NH1      0.1000  2   180.00 
+CC   CT2A CT1  NH1      0.3800  3     0.00 
+CT1  CT2A CC   OC       0.8400  1     0.00 
+CT1  CT2A CC   OC       0.9800  2   180.00 
+CT1  CT2A CC   OC       1.4600  3     0.00 
+! Fitted Cys
+CT1  CT2  S    HS       0.2000  1     0.00
+CT1  CT2  S    HS       0.6500  2     0.00
+CT1  CT2  S    HS       0.2200  3     0.00
+C    CT1  CT2  S        0.2400  1   180.00
+C    CT1  CT2  S        0.7500  2   180.00
+C    CT1  CT2  S        1.3500  3   180.00
+NH1  CT1  CT2  S        0.3400  1     0.00
+NH1  CT1  CT2  S        0.5000  2   180.00
+NH1  CT1  CT2  S        1.4300  3     0.00
+! Fitted Glu
+CC   CT2  CT2A CT1      0.0000  1   180.00
+CC   CT2  CT2A CT1      0.3800  2   180.00
+CC   CT2  CT2A CT1      0.5900  3   180.00
+C    CT1  CT2A CT2      0.1100  1     0.00
+C    CT1  CT2A CT2      0.9800  2   180.00
+C    CT1  CT2A CT2      1.6000  3   180.00
+CC   CT1  CT2A CT2      1.6000  3   180.00
+CT2  CT2A CT1  NH1      0.3000  1     0.00 
+CT2  CT2A CT1  NH1      0.3500  2     0.00
+CT2  CT2A CT1  NH1      1.7600  3     0.00
+! Group-fitted for Hsd/Hse
+CPH1 CPH1 CT2  CT1      1.7400  1     0.00
+CPH1 CPH1 CT2  CT1      0.1500  2     0.00
+CPH1 CPH1 CT2  CT1      0.7700  3   180.00
+CT1  CT2  CPH1 NR1      1.4900  1     0.00
+CT1  CT2  CPH1 NR1      0.0900  2   180.00
+CT1  CT2  CPH1 NR1      0.7900  3   180.00
+CT1  CT2  CPH1 NR2      1.0900  1     0.00
+CT1  CT2  CPH1 NR2      0.0900  2     0.00
+CT1  CT2  CPH1 NR2      0.6700  3   180.00
+C    CT1  CT2  CPH1     0.1800  1   180.00
+C    CT1  CT2  CPH1     0.6400  2   180.00
+C    CT1  CT2  CPH1     0.8700  3   180.00
+CPH1 CT2  CT1  NH1      0.0000  1     0.00
+CPH1 CT2  CT1  NH1      0.0000  2   180.00
+CPH1 CT2  CT1  NH1      0.9000  3     0.00
+! Fitted Hsp
+CPH1 CPH1 CT2A CT1      2.0400  1     0.00
+CPH1 CPH1 CT2A CT1      0.4400  2     0.00
+CPH1 CPH1 CT2A CT1      0.1300  3   180.00
+CT1  CT2A CPH1 NR3      0.5300  1   180.00
+CT1  CT2A CPH1 NR3      0.4200  2   180.00
+CT1  CT2A CPH1 NR3      0.3000  3   180.00
+C    CT1  CT2A CPH1     1.7500  1   180.00
+C    CT1  CT2A CPH1     0.1300  2     0.00
+C    CT1  CT2A CPH1     1.8600  3   180.00
+CPH1 CT2A CT1  NH1      1.0900  1   180.00
+CPH1 CT2A CT1  NH1      0.2200  2   180.00
+CPH1 CT2A CT1  NH1      2.3200  3     0.00
+! Group-fitted for Ile/Thr
+CT1  CT1  CT2  CT3      0.3800  1   180.00
+CT1  CT1  CT2  CT3      0.1300  2   180.00
+CT1  CT1  CT2  CT3      0.2900  3   180.00
+C    CT1  CT1  CT2      0.1000  1   180.00
+C    CT1  CT1  CT2      0.5200  2   180.00
+C    CT1  CT1  CT2      0.2900  3   180.00
+CT2  CT1  CT1  NH1      0.1200  1   180.00
+CT2  CT1  CT1  NH1      0.3600  2   180.00
+CT2  CT1  CT1  NH1      0.4100  3     0.00
+! Fitted Leu 
+CT1  CT2  CT1  CT3      0.0500  1     0.00
+CT1  CT2  CT1  CT3      0.1000  2   180.00
+CT1  CT2  CT1  CT3      0.0100  3   180.00
+C    CT1  CT2  CT1      0.3200  1   180.00
+C    CT1  CT2  CT1      0.6100  2   180.00
+C    CT1  CT2  CT1      0.7200  3   180.00
+CT1  CT2  CT1  NH1      0.4800  1   180.00
+CT1  CT2  CT1  NH1      0.4200  2   180.00
+CT1  CT2  CT1  NH1      0.6500  3     0.00
+! Group-fitted for Phe/Tyr
+CA   CA   CT2  CT1      1.0700  1     0.00
+CA   CA   CT2  CT1      0.2400  2   180.00
+CA   CA   CT2  CT1      0.1700  3   180.00
+C    CT1  CT2  CA       1.2800  1   180.00
+C    CT1  CT2  CA       0.9400  2   180.00
+C    CT1  CT2  CA       1.5700  3   180.00
+CA   CT2  CT1  NH1      0.5200  1   180.00
+CA   CT2  CT1  NH1      0.6200  2   180.00
+CA   CT2  CT1  NH1      1.5800  3     0.00
+! Fitted Ser
+CT1  CT2  OH1  H        0.0200  1     0.00
+CT1  CT2  OH1  H        0.5600  2     0.00
+CT1  CT2  OH1  H        0.4900  3     0.00
+C    CT1  CT2  OH1      0.6500  1   180.00
+C    CT1  CT2  OH1      0.2500  2   180.00
+C    CT1  CT2  OH1      1.1700  3   180.00
+NH1  CT1  CT2  OH1      0.1800  1   180.00
+NH1  CT1  CT2  OH1      0.1900  2   180.00
+NH1  CT1  CT2  OH1      1.4600  3     0.00
+! Group-fitted for Ile/Thr
+CT1  CT1  OH1  H        0.1800  1     0.00
+CT1  CT1  OH1  H        0.0600  2     0.00
+CT1  CT1  OH1  H        0.2500  3     0.00
+C    CT1  CT1  OH1      0.7900  1   180.00
+C    CT1  CT1  OH1      0.3900  2   180.00
+C    CT1  CT1  OH1      0.9900  3   180.00
+NH1  CT1  CT1  OH1      0.0900  1     0.00
+NH1  CT1  CT1  OH1      0.1900  2   180.00
+NH1  CT1  CT1  OH1      0.1700  3     0.00
+! Fitted Trp
+CA   CY   CT2  CT1      0.0300  1     0.00
+CA   CY   CT2  CT1      0.5500  2     0.00
+CA   CY   CT2  CT1      0.3900  3   180.00
+CPT  CY   CT2  CT1      0.3600  1   180.00
+CPT  CY   CT2  CT1      0.0500  2     0.00
+CPT  CY   CT2  CT1      0.1900  3   180.00
+C    CT1  CT2  CY       1.0900  1   180.00
+C    CT1  CT2  CY       0.5000  2   180.00
+C    CT1  CT2  CY       1.1700  3   180.00
+CY   CT2  CT1  NH1      0.2900  1   180.00
+CY   CT2  CT1  NH1      0.6600  2   180.00
+CY   CT2  CT1  NH1      1.1700  3     0.00
+! Fitted Val
+C    CT1  CT1  CT3      0.1400  1   180.00
+C    CT1  CT1  CT3      0.2600  2   180.00
+C    CT1  CT1  CT3      0.3300  3   180.00
+CT3  CT1  CT1  NH1      0.1800  1     0.00
+CT3  CT1  CT1  NH1      0.0600  2     0.00
+CT3  CT1  CT1  NH1      0.5900  3     0.00
+!ASP, CT2->CT2A, jshim
+H    NH1  CT2A CC       0.0000  1     0.00
+X    CT2A CC   X        0.0500  6   180.00
+HB1  CT1  CT2A CC       0.2000  3     0.00
+HA2  CT2A CC   OC       0.0500  6   180.00
+NH3  CT1  CT2A HA2      0.2000  3     0.00
+NH3  CT1  CT2A CC       0.2000  3     0.00
+CC   CT2A CT1  CC       0.2000  3     0.00
+!termini specific terms
+CPH1 CT2A CT1  CC       0.2000  3     0.00
+CPH1 CT2A CT1  NH3      0.2000  3     0.00
+CPH1 CT2A CT1  CD       0.2000  3     0.00 
+HA2  CT2A CT1  CD       0.2000  3     0.00     
+CT2  CT2A CT1  CD       0.2000  3     0.00
+! RESI CYSM and PRES CYSD
+H    NH2  CT1  CS       0.1100  3     0.00 ! from H    NH2  CT1  CT2 or H    NH2  CT1  CT2 , kevo
+CS   CT1  NH1  C        1.8000  1     0.00 ! from CT2  CT1  NH1  C   or CT2A CT1  NH1  C , kevo
+H    NH1  CT1  CS       0.0000  1     0.00 ! from H    NH1  CT1  CT2 or H    NH1  CT1  CT2 , kevo
+N    C    CT1  CS       0.0000  1     0.00 ! from N    C    CT1  CT2 or N    C    CT1  CT2 , kevo
+NH1  C    CT1  CS       0.0000  1     0.00 ! from NH1  C    CT1  CT2 or NH1  C    CT1  CT2 , kevo
+O    C    CT1  CS       1.4000  1     0.00 ! from O    C    CT1  CT2 or O    C    CT1  CT2 , kevo
+HA2  CS   CT1  C        0.2000  3     0.00 ! from HA2  CT2  CT1  C   or HA2  CT2A CT1  C , kevo
+NH1  CT1  CS   HA2      0.2000  3     0.00 ! from NH1  CT1  CT2  HA2 or NH1  CT1  CT2A HA2 , kevo
+HB1  CT1  CS   HA2      0.2000  3     0.00 ! from HB1  CT1  CT2  HA2 or HB1  CT1  CT2A HA2 , kevo
+HB1  CT1  CS   SS       0.2000  3     0.00 ! from HB1  CT1  CT2  S   or HB1  CT1  CT2A S , kevo
+C    CT1  CS   SS       0.2000  3     0.00 ! from X    CT1  CT2  X , kevo
+NH1  CT1  CS   SS       0.2000  3     0.00 ! from X    CT1  CT2  X , kevo
+! Termini 
+NH3  CT1  CS   HA2      0.2000  3     0.00 ! from X    CT1  CT2  X , kevo
+NH3  CT1  CS   SS       0.2000  3     0.00 ! from X    CT1  CT2  X , kevo
+NH2  CT1  CS   HA2      0.2000  3     0.00 ! from X    CT1  CT2  X , kevo
+NH2  CT1  CS   SS       0.2000  3     0.00 ! from X    CT1  CT2  X , kevo
+CC   CT1  CS   HA2      0.2000  3     0.00 ! from X    CT1  CT2  X , kevo
+CC   CT1  CS   SS       0.2000  3     0.00 ! from X    CT1  CT2  X , kevo
+CD   CT1  CS   HA2      0.2000  3     0.00 ! from X    CT1  CT2  X , kevo
+CD   CT1  CS   SS       0.2000  3     0.00 ! from X    CT1  CT2  X , kevo
+! PRES SERD
+NH1  CT1  CT2  OC       0.2000  3     0.00 ! from X    CT1  CT2  X , kevo
+NH2  CT1  CT2  OC       0.2000  3     0.00 ! from X    CT1  CT2  X , kevo
+NH3  CT1  CT2  OC       0.2000  3     0.00 ! from X    CT1  CT2  X , kevo
+C    CT1  CT2  OC       0.2000  3     0.00 ! from X    CT1  CT2  X , kevo
+CC   CT1  CT2  OC       0.2000  3     0.00 ! from X    CT1  CT2  X , kevo
+CD   CT1  CT2  OC       0.2000  3     0.00 ! from X    CT1  CT2  X , kevo
+HB1  CT1  CT2  OC       0.2000  3     0.00 ! from X    CT1  CT2  X , kevo
+
+IMPROPER
+!
+!V(improper) = Kpsi(psi - psi0)**2
+!
+!Kpsi: kcal/mole/rad**2
+!psi0: degrees
+!note that the second column of numbers (0) is ignored
+!
+!atom types           Kpsi                   psi0
+!
+HE2  HE2  CE2  CE2     3.0            0      0.00   ! 
+		! for ethene, yin/adm jr., 12/95
+HR1  NR1  NR2  CPH2    0.5000         0      0.0000 ! ALLOW ARO
+                ! his, adm jr., 7/05/90
+HR1  NR2  NR1  CPH2    0.5000         0      0.0000 ! ALLOW ARO
+                ! his, adm jr., 7/05/90
+HR3  CPH1 NR1  CPH1    0.5000         0      0.0000 ! ALLOW ARO
+                ! adm jr., 3/24/92, maintain old aliphatic H VDW params
+HR3  CPH1 NR2  CPH1    0.5000         0      0.0000 ! ALLOW ARO
+                ! adm jr., 3/24/92, maintain old aliphatic H VDW params
+HR3  CPH1 NR3  CPH1    1.0000         0      0.0000 ! ALLOW ARO
+                ! adm jr., 3/24/92, maintain old aliphatic H VDW params
+HR3  NR1  CPH1 CPH1    0.5000         0      0.0000 ! ALLOW ARO
+                ! adm jr., 3/24/92, maintain old aliphatic H VDW params
+HR3  NR2  CPH1 CPH1    0.5000         0      0.0000 ! ALLOW ARO
+                ! adm jr., 3/24/92, maintain old aliphatic H VDW params
+N    C    CP1  CP3     0.0000         0      0.0000 ! ALLOW PRO
+                ! 6-31g* AcProNH2 and ProNH2  RLD 5/19/92
+NC2  X    X    C      45.0000         0      0.0000 ! ALLOW   PEP POL ARO
+                ! mp2/6-311g** guan vibrational data, adm jr., 1/04
+C   HC    HC   NC2      0.0          0      0.0
+                ! mp2/6-311g** guan vibrational data, adm jr., 1/04
+NC2  X    X    HC      -2.0          0      0.0
+                ! mp2/6-311g** guan vibrational data, adm jr., 1/04
+NH1  X    X    H      20.0000         0      0.0000 ! ALLOW   PEP POL ARO
+                ! NMA Vibrational Modes (LK)
+NH2  X    X    H       4.0000         0      0.0000 ! ALLOW   POL
+                ! adm jr., 8/13/90 acetamide geometry and vibrations
+NR1  CPH1 CPH2 H       0.4500         0      0.0000 ! ALLOW ARO
+                ! his, adm jr., 7/05/90
+NR1  CPH2 CPH1 H       0.4500         0      0.0000 ! ALLOW ARO
+                ! his, adm jr., 7/05/90
+NR3  CPH1 CPH2 H       1.2000         0      0.0000 ! ALLOW ARO
+                ! his, adm jr., 6/27/90
+NR3  CPH2 CPH1 H       1.2000         0      0.0000 ! ALLOW ARO
+                ! his, adm jr., 6/27/90
+O    CP1  NH2  CC     45.0000         0      0.0000 ! ALLOW PEP POL PRO
+                ! 6-31g* AcProNH2 and ProNH2  RLD 5/19/92
+O    CT1  NH2  CC     45.0000         0      0.0000 ! ALLOW PEP POL
+                ! adm jr., 8/13/90 acetamide geometry and vibrations
+O    CT2  NH2  CC     45.0000         0      0.0000 ! ALLOW PEP POL
+                ! adm jr., 8/13/90 acetamide geometry and vibrations
+O    CT3  NH2  CC     45.0000         0      0.0000 ! ALLOW PEP POL
+                ! adm jr., 8/13/90 acetamide geometry and vibrations
+O    HA1  NH2  CC     45.0000         0      0.0000 ! ALLOW PEP POL PRO
+                ! adm jr., 5/13/91, formamide geometry and vibrations
+O    N    CT2  CC    120.0000         0      0.0000 ! ALLOW PEP POL PRO
+                ! 6-31g* AcProNH2 and ProNH2  RLD 5/19/92
+O    NH2  CP1  CC     45.0000         0      0.0000 ! ALLOW PEP POL PRO
+                ! 6-31g* AcProNH2 and ProNH2  RLD 5/19/92
+O    NH2  CT1  CC     45.0000         0      0.0000 ! ALLOW PEP POL
+                ! adm jr., 8/13/90 acetamide geometry and vibrations
+O    NH2  CT2  CC     45.0000         0      0.0000 ! ALLOW PEP POL
+                ! adm jr., 8/13/90 acetamide geometry and vibrations
+O    NH2  CT3  CC     45.0000         0      0.0000 ! ALLOW PEP POL
+                ! adm jr., 8/13/90 acetamide geometry and vibrations
+O    NH2  HA1  CC     45.0000         0      0.0000 ! ALLOW PEP POL
+                ! adm jr., 5/13/91, formamide geometry and vibrations
+O    X    X    C     120.0000         0      0.0000 ! ALLOW   PEP POL ARO
+                ! NMA Vibrational Modes (LK)
+OB   X    X    CD    100.0000         0      0.0000 ! ALLOW   ALC ARO POL
+                ! adm jr., 10/17/90, acetic acid vibrations
+OC   X    X    CC     96.0000         0      0.0000 ! ALLOW   PEP POL ARO ION
+                ! 90.0->96.0 acetate, single impr (KK)
+CC   X    X    CT1    96.0000         0      0.0000 ! ALLOW   PEP POL ARO ION
+                ! 90.0->96.0 acetate, single impr (KK)
+CC   X    X    CT2    96.0000         0      0.0000 ! ALLOW   PEP POL ARO ION
+                ! 90.0->96.0 acetate, single impr (KK)
+CC   X    X    CT3    96.0000         0      0.0000 ! ALLOW   PEP POL ARO ION
+                ! 90.0->96.0 acetate, single impr (KK)
+
+CMAP
+! 2D grid correction data. 
+! Finalfix3, Feig/Best/MacKerell 2010
+
+! Jing Huang/Alex MacKerell adjustments to correct for 
+! oversampling of alpha L conformation.  2016/1
+
+! alanine map
+C    NH1  CT1  C    NH1  CT1  C    NH1   24
+
+! insertion 1
+!-180
+    0.13     0.77     0.97     1.25     2.12
+    2.72     2.09     1.79     0.78    -0.69
+    1.00    -2.20    -4.83    -4.82    -4.91
+   -3.59    -2.77    -2.78    -2.45    -2.35
+   -2.34    -1.52    -0.95    -0.04
+
+!-165
+   -0.13     1.38     1.58     1.87     2.40
+    2.49     2.44     1.93     1.09     0.64
+    0.26    -2.80    -4.01    -4.14    -3.42
+   -2.60    -2.30    -1.50    -1.10    -0.86
+   -0.64    -0.21    -1.08    -1.12
+
+!-150
+    0.08     1.42     1.62     2.05     2.65
+    2.72     2.32     1.99     1.56     2.46
+   -0.23    -1.82    -2.58    -3.01    -2.55
+   -1.89    -1.35    -0.73     0.07    -0.23
+   -0.77    -1.28    -1.29    -0.82
+
+!-135
+    0.93     1.52     2.24     2.55     3.11
+    2.92     2.46     2.19     2.06     1.85
+    0.12    -1.18    -2.00    -2.28    -1.96
+   -1.34    -0.93     0.02     0.31    -0.52
+   -1.15    -0.98    -0.57    -0.44
+
+!-120
+    1.36     1.96     2.70     3.04     3.70
+    3.56     2.64     2.77     2.72     1.63
+    0.71    -0.79    -2.12    -2.63    -1.80
+   -0.43    -0.06     0.44     0.91    -0.55
+   -0.97    -0.86    -0.25     0.45
+
+!-105
+    2.05     2.54     2.82     3.09     3.37
+    3.55     3.07     2.90     2.96     2.12
+    0.91    -0.82    -2.09    -2.24    -1.46
+    0.21     0.08     0.77     1.04    -0.12
+   -0.32    -0.16     0.31     0.73
+
+!-90
+    1.45     2.75     2.74     3.16     3.45
+    3.34     3.18     3.90     3.34     2.44
+    0.91    -0.61    -1.51    -1.62    -0.96
+   -0.02     0.42     0.91     0.46     0.15
+   -0.07     0.02     0.28     0.75
+
+!-75
+    1.38     3.35     2.35     3.06     3.81
+    3.70     3.58     4.21     3.54     1.69
+    0.10    -0.68    -0.12    -0.43    -0.60
+    0.23     0.42     0.30     0.55     0.19
+   -0.25    -0.19    -0.25     0.47
+
+!-60
+    0.24     1.23     1.72     3.17     4.21
+    4.39     4.28     3.67     2.27    -0.48
+   -0.41    -0.04    -0.36    -0.82    -0.17
+    0.14     0.27     0.32     0.31    -0.67
+   -0.95    -1.53    -1.48    -0.20
+
+!-45
+   -1.18     0.08     2.35     4.21     5.38
+    5.39     4.38     2.46     1.12     0.11
+    0.01    -0.15    -0.80    -0.58     0.08
+    0.27    -0.05     0.38     0.25    -0.89
+   -1.58    -1.95    -1.98    -2.00
+
+!-30
+   -1.17     1.07     4.18     6.74     6.07
+    4.81     2.78     1.32     0.77    -0.01
+    0.28    -0.71     1.31     1.52     1.92
+    2.22     0.19     0.53     0.33    -1.60
+   -2.85    -3.55    -3.28    -2.66
+
+!-15
+    0.29     5.59     3.73     3.22     3.27
+    2.52     1.59     1.38     0.86     0.66
+    1.62     0.85     0.51     0.74     1.02
+    1.62    -0.34     0.18    -0.61    -2.56
+   -3.79    -3.81    -3.16    -1.75
+
+!0
+    2.83     0.79     0.32     0.48     0.63
+    0.98     1.24     1.67     1.65     2.52
+    1.61     0.78     0.12     0.07     0.12
+   -1.57    -1.21    -1.93    -2.60    -3.79
+   -3.93    -3.62    -2.68    -0.92
+
+!15
+   -0.78    -1.91    -2.05    -1.85    -1.05
+    0.18     1.68     2.22     1.36     2.45
+    1.44     0.68    -0.24    -0.54    -0.79
+   -2.18    -3.21    -4.35    -3.94    -3.91
+   -3.46    -2.77     1.76     0.31
+
+!30
+   -2.96    -3.48    -3.44    -2.40    -1.13
+    0.34     1.43     1.39     0.97     2.46
+    1.52     0.55    -0.41    -1.48    -3.58
+   -4.13    -4.56    -4.44    -3.58    -2.96
+   -1.96    -1.07    -1.60    -2.45
+
+!45
+   -4.02    -3.84    -3.37    -2.33    -0.98
+    0.36     0.81     0.75     0.50     1.90
+    0.77    -0.42    -3.29    -3.91    -4.52
+   -4.89    -3.85    -4.15    -2.67    -2.37
+   -2.86    -3.42    -3.67    -3.60
+
+!60
+   -3.35    -2.98    -2.32    -1.24    -0.26
+    0.72     0.67     0.44     2.40     1.63
+   -2.01    -3.31    -3.99    -4.53    -4.85
+   -3.77    -3.94    -3.89    -2.61    -3.51
+   -3.76    -3.64    -3.45    -3.34
+
+!75
+   -2.25    -1.64    -1.01     0.04     0.64
+    0.82     0.52    -0.01    -0.37    -1.19
+   -2.39    -3.38    -4.50    -5.59    -5.51
+   -4.94    -3.83    -3.84    -3.70    -4.15
+   -4.17    -3.73    -3.74    -2.62
+
+!90
+   -1.72    -1.18    -0.43     0.28     0.81
+    0.80     0.48    -0.34    -0.79    -1.77
+   -2.81    -3.80    -5.22    -6.28    -6.58
+   -5.64    -5.06    -4.02    -4.15    -4.47
+   -4.10    -3.77    -3.16    -2.65
+
+!105
+   -1.85    -1.09    -0.45     0.13     1.01
+    0.88     0.49    -0.22    -0.86    -1.68
+   -3.01    -4.13    -5.99    -6.86    -6.83
+   -5.85    -3.86    -4.86    -4.91    -4.72
+   -4.60    -4.09    -3.27    -2.41
+
+!120
+   -1.97    -1.12    -0.54    -0.15     0.76
+    1.04     0.76     0.31    -0.33    -1.87
+   -3.37    -5.01    -6.12    -7.05    -6.98
+   -3.70    -4.51    -5.09    -5.42    -4.85
+   -4.44    -4.00    -3.42    -2.75
+
+!135
+   -2.11    -1.17    -0.32    -0.01     0.32
+    1.09     0.94     0.63    -0.17    -1.83
+   -3.47    -4.95    -6.11    -1.92    -4.05
+   -5.00    -5.00    -4.84    -4.89    -4.30
+   -4.49    -4.44    -4.16    -3.18
+
+!150
+   -1.76    -0.40     0.02     0.36     0.63
+    1.26     1.36     0.95    -0.07    -1.48
+   -3.15     1.84    -1.76    -5.09    -5.74
+   -5.39    -4.78    -4.19    -4.12    -4.04
+   -4.13    -4.03    -4.03    -2.94
+
+!165
+   -0.81    -0.07     0.38     0.54     1.28
+    1.64     1.70     1.52     0.63    -1.09
+   -2.74    -0.74    -4.56    -6.41    -5.89
+   -5.14    -4.19    -3.67    -3.84    -3.56
+   -3.55    -3.25    -2.75    -1.81
+
+
+! alanine before proline map
+
+C    NH1  CT1  C    NH1  CT1  C    N     24
+
+! insertion 2
+!-180
+    0.13     0.77     0.97     1.25     2.12
+    2.72     2.09     1.79     0.78    -0.69
+    1.00    -2.20    -4.83    -4.82    -4.91
+   -3.59    -2.77    -2.78    -2.45    -2.35
+   -2.34    -1.52    -0.95    -0.04
+
+!-165
+   -0.13     1.38     1.58     1.87     2.40
+    2.49     2.44     1.93     1.09     0.64
+    0.26    -2.80    -4.01    -4.14    -3.42
+   -2.60    -2.30    -1.50    -1.10    -0.86
+   -0.64    -0.21    -1.08    -1.12
+
+!-150
+    0.08     1.42     1.62     2.05     2.65
+    2.72     2.32     1.99     1.56     2.46
+   -0.23    -1.82    -2.58    -3.01    -2.55
+   -1.89    -1.35    -0.73     0.07    -0.23
+   -0.77    -1.28    -1.29    -0.82
+
+!-135
+    0.93     1.52     2.24     2.55     3.11
+    2.92     2.46     2.19     2.06     1.85
+    0.12    -1.18    -2.00    -2.28    -1.96
+   -1.34    -0.93     0.02     0.31    -0.52
+   -1.15    -0.98    -0.57    -0.44
+
+!-120
+    1.36     1.96     2.70     3.04     3.70
+    3.56     2.64     2.77     2.72     1.63
+    0.71    -0.79    -2.12    -2.63    -1.80
+   -0.43    -0.06     0.44     0.91    -0.55
+   -0.97    -0.86    -0.25     0.45
+
+!-105
+    2.05     2.54     2.82     3.09     3.37
+    3.55     3.07     2.90     2.96     2.12
+    0.91    -0.82    -2.09    -2.24    -1.46
+    0.21     0.08     0.77     1.04    -0.12
+   -0.32    -0.16     0.31     0.73
+
+!-90
+    1.45     2.75     2.74     3.16     3.45
+    3.34     3.18     3.90     3.34     2.44
+    0.91    -0.61    -1.51    -1.62    -0.96
+   -0.02     0.42     0.91     0.46     0.15
+   -0.07     0.02     0.28     0.75
+
+!-75
+    1.38     3.35     2.35     3.06     3.81
+    3.70     3.58     4.21     3.54     1.69
+    0.10    -0.68    -0.12    -0.43    -0.60
+    0.23     0.42     0.30     0.55     0.19
+   -0.25    -0.19    -0.25     0.47
+
+!-60
+    0.24     1.23     1.72     3.17     4.21
+    4.39     4.28     3.67     2.27    -0.48
+   -0.41    -0.04    -0.36    -0.82    -0.17
+    0.14     0.27     0.32     0.31    -0.67
+   -0.95    -1.53    -1.48    -0.20
+
+!-45
+   -1.18     0.08     2.35     4.21     5.38
+    5.39     4.38     2.46     1.12     0.11
+    0.01    -0.15    -0.80    -0.58     0.08
+    0.27    -0.05     0.38     0.25    -0.89
+   -1.58    -1.95    -1.98    -2.00
+
+!-30
+   -1.17     1.07     4.18     6.74     6.07
+    4.81     2.78     1.32     0.77    -0.01
+    0.28    -0.71     1.31     1.52     1.92
+    2.22     0.19     0.53     0.33    -1.60
+   -2.85    -3.55    -3.28    -2.66
+
+!-15
+    0.29     5.59     3.73     3.22     3.27
+    2.52     1.59     1.38     0.86     0.66
+    1.62     0.85     0.51     0.74     1.02
+    1.62    -0.34     0.18    -0.61    -2.56
+   -3.79    -3.81    -3.16    -1.75
+
+!0
+    2.83     0.79     0.32     0.48     0.63
+    0.98     1.24     1.67     1.65     2.52
+    1.61     0.78     0.12     0.07     0.12
+   -1.57    -1.21    -1.93    -2.60    -3.79
+   -3.93    -3.62    -2.68    -0.92
+
+!15
+   -0.78    -1.91    -2.05    -1.85    -1.05
+    0.18     1.68     2.22     1.36     2.45
+    1.44     0.68    -0.24    -0.54    -0.79
+   -2.18    -3.21    -4.35    -3.94    -3.91
+   -3.46    -2.77     1.76     0.31
+
+!30
+   -2.96    -3.48    -3.44    -2.40    -1.13
+    0.34     1.43     1.39     0.97     2.46
+    1.52     0.55    -0.41    -1.48    -3.58
+   -4.13    -4.56    -4.44    -3.58    -2.96
+   -1.96    -1.07    -1.60    -2.45
+
+!45
+   -4.02    -3.84    -3.37    -2.33    -0.98
+    0.36     0.81     0.75     0.50     1.90
+    0.77    -0.42    -3.29    -3.91    -4.52
+   -4.89    -3.85    -4.15    -2.67    -2.37
+   -2.86    -3.42    -3.67    -3.60
+
+!60
+   -3.35    -2.98    -2.32    -1.24    -0.26
+    0.72     0.67     0.44     2.40     1.63
+   -2.01    -3.31    -3.99    -4.53    -4.85
+   -3.77    -3.94    -3.89    -2.61    -3.51
+   -3.76    -3.64    -3.45    -3.34
+
+!75
+   -2.25    -1.64    -1.01     0.04     0.64
+    0.82     0.52    -0.01    -0.37    -1.19
+   -2.39    -3.38    -4.50    -5.59    -5.51
+   -4.94    -3.83    -3.84    -3.70    -4.15
+   -4.17    -3.73    -3.74    -2.62
+
+!90
+   -1.72    -1.18    -0.43     0.28     0.81
+    0.80     0.48    -0.34    -0.79    -1.77
+   -2.81    -3.80    -5.22    -6.28    -6.58
+   -5.64    -5.06    -4.02    -4.15    -4.47
+   -4.10    -3.77    -3.16    -2.65
+
+!105
+   -1.85    -1.09    -0.45     0.13     1.01
+    0.88     0.49    -0.22    -0.86    -1.68
+   -3.01    -4.13    -5.99    -6.86    -6.83
+   -5.85    -3.86    -4.86    -4.91    -4.72
+   -4.60    -4.09    -3.27    -2.41
+
+!120
+   -1.97    -1.12    -0.54    -0.15     0.76
+    1.04     0.76     0.31    -0.33    -1.87
+   -3.37    -5.01    -6.12    -7.05    -6.98
+   -3.70    -4.51    -5.09    -5.42    -4.85
+   -4.44    -4.00    -3.42    -2.75
+
+!135
+   -2.11    -1.17    -0.32    -0.01     0.32
+    1.09     0.94     0.63    -0.17    -1.83
+   -3.47    -4.95    -6.11    -1.92    -4.05
+   -5.00    -5.00    -4.84    -4.89    -4.30
+   -4.49    -4.44    -4.16    -3.18
+
+!150
+   -1.76    -0.40     0.02     0.36     0.63
+    1.26     1.36     0.95    -0.07    -1.48
+   -3.15     1.84    -1.76    -5.09    -5.74
+   -5.39    -4.78    -4.19    -4.12    -4.04
+   -4.13    -4.03    -4.03    -2.94
+
+!165
+   -0.81    -0.07     0.38     0.54     1.28
+    1.64     1.70     1.52     0.63    -1.09
+   -2.74    -0.74    -4.56    -6.41    -5.89
+   -5.14    -4.19    -3.67    -3.84    -3.56
+   -3.55    -3.25    -2.75    -1.81
+
+
+! proline 
+! mp2/aug-cc-pVDZ//RIMP2/VTZ/VQZ CBS map
+C    N    CP1  C    N    CP1    C    NH1 24
+
+! phi = -180 
+     2.973500      3.348200      3.062900      2.113400      1.040500 
+     0.770600      0.785200      0.263300     -0.479000     -0.583000 
+    -0.463800     -0.292600      0.000000      0.259100      0.177100 
+    -0.151200     -0.173500      0.211700      0.348900     -0.135600 
+    -0.950000     -1.256600     -0.292800      1.560000 
+
+! phi = -165 
+     5.674100      6.011400      5.562700      4.467300      3.390800 
+     3.008800      2.848600      2.311200      1.661400      1.468400 
+     1.142700      1.437400      2.113200      2.799500      2.989100 
+     2.869000      3.016100      3.328500      3.232900      2.547600 
+     1.647200      1.422700      2.517100      4.339800 
+
+! phi = -150 
+     6.752800      6.973200      6.444300      5.389800      4.438600 
+     4.046000      3.832800      3.442400      3.303500      3.010000 
+     2.838100      3.162200      3.778300      4.362800      4.603600 
+     4.546200      4.702100      4.837200      4.549500      3.849600 
+     3.099200      3.031800      4.060200      5.624800 
+
+! phi = -135 
+     7.627800      8.153400      7.342500      5.893500      4.799200 
+     4.433400      4.551500      4.442800      2.222200      0.776300 
+     0.790000      2.152300      3.932900      5.274900      5.830800 
+     5.988600      5.588500      5.211000      4.918000      4.292100 
+     3.495500      3.449800      4.617700      6.311700 
+
+! phi = -120 
+     8.115600      8.477200      7.754300      6.585000      5.537900 
+     4.964300      4.929000      4.421200      2.336100      1.257800 
+     1.769300      3.359900      5.018000      6.055500      6.217600 
+     5.726100      5.512200      5.820200      5.716700      4.872300 
+     4.066800      4.094600      5.284900      6.931500 
+
+! phi = -105 
+     9.249700      9.483000      8.668500      7.525300      7.003200 
+     6.834600      6.822100      5.287600      3.320600      2.640300 
+     3.464800      5.100300      6.537600      6.885600      5.842000 
+     5.248700      5.540200      6.652400      7.196700      6.625400 
+     5.710100      5.581700      6.651500      8.192800 
+
+! phi = -90 
+     9.335600      9.208000      8.564600      8.010200      7.885100 
+     8.212200      8.737100      8.429100      7.306500      6.474200 
+     6.651300      7.484700      8.195300      8.295000      7.407200 
+     6.529900      6.242000      6.227500      6.347300      6.449700 
+     6.404700      6.579300      7.391700      8.570700 
+
+! phi = -75 
+    10.955200     11.455400     11.173300     10.428700     10.062400 
+    10.044500      9.279600      6.965100      5.361500      5.102700 
+     6.267600      7.871600      8.009800      7.104500      6.616400 
+     6.733700      7.504000      8.664700      9.282800      8.795900 
+     7.872500      7.612400      8.498100      9.894000 
+
+! phi = -60 
+     8.422900      8.529200      8.608500      9.306400     10.239400 
+    11.025900     11.510800      9.283500      7.566000      6.624600 
+     7.038700      8.222400      8.786400      8.512000      8.103500 
+     7.988200      8.192900      8.291000      8.055600      7.436800 
+     6.651800      6.317000      6.802500      7.746300 
+
+! phi = -45 
+     6.913200      7.937400      8.610800      9.316600      9.388500 
+     9.408400      8.828800      7.297900      5.456400      4.742700 
+     5.793100      7.118800      7.565400      7.598500      7.438700 
+     7.512500      7.878100      8.082200      7.642700      6.320500 
+     4.680400      3.830500      4.215800      5.435200 
+
+! phi = -30 
+     5.466700      7.116000      8.908800      8.347200      7.413500 
+     7.047000      6.031600      4.193100      2.674800      3.023700 
+     4.485300      5.451700      6.214900      6.422600      6.229300 
+     6.191100      6.488900      6.646400      5.833400      3.751300 
+     1.719800      1.064900      1.955800      3.860800 
+
+! phi = -15 
+     3.061500      5.603800     12.179500      6.295200      5.323400 
+     4.826500      3.705600      2.461500      2.291600      3.145900 
+     3.562100      4.443600      5.337500      5.728800      5.694800 
+     5.641600      5.943300      6.169000      4.759500      2.569400 
+     1.357100      1.669800      3.212300      5.031900 
+
+! phi = 0 
+     8.085900      8.051100      5.023600      3.450800      2.836100 
+     2.192500      1.566200      1.456300      2.039300      1.945200 
+     2.188400      2.921300      3.467500      3.543500      3.374500 
+     3.472300      4.069900      3.615600      2.082200      0.958600 
+     0.792600      1.494200      2.794900      4.853100 
+
+! phi = 15 
+     6.639500      5.177400      3.252300      1.952700      1.078400 
+     0.888300      1.505400      2.442300      2.178600      1.578600 
+     1.777400      2.395400      2.820200      2.795200      2.662400 
+     2.917100      2.562100      1.557900      1.322300      1.631400 
+     2.051200      2.555600      3.039100      4.915000 
+
+! phi = 30 
+     7.548800      5.095500      2.747000      0.955200      0.444500 
+     1.318700      2.733300      3.223200      2.565500      2.150900 
+     2.394400      2.939300      3.266000      3.210000      3.113400 
+     2.491300      0.978300      0.815300      1.522700      2.055600 
+     2.199900      2.327600      3.474200      7.977800 
+
+! phi = 45 
+     0.000000      0.000000      0.000000      0.000000      0.000000 
+     0.000000      0.000000      0.000000      0.000000      0.000000 
+     0.000000      0.000000      0.000000      0.000000      0.000000 
+     0.000000      0.000000      0.000000      0.000000      0.000000 
+     0.000000      0.000000      0.000000      0.000000 
+
+! phi = 60 
+     0.000000      0.000000      0.000000      0.000000      0.000000 
+     0.000000      0.000000      0.000000      0.000000      0.000000 
+     0.000000      0.000000      0.000000      0.000000      0.000000 
+     0.000000      0.000000      0.000000      0.000000      0.000000 
+     0.000000      0.000000      0.000000      0.000000 
+
+! phi = 75 
+     0.000000      0.000000      0.000000      0.000000      0.000000 
+     0.000000      0.000000      0.000000      0.000000      0.000000 
+     0.000000      0.000000      0.000000      0.000000      0.000000 
+     0.000000      0.000000      0.000000      0.000000      0.000000 
+     0.000000      0.000000      0.000000      0.000000 
+
+! phi = 90 
+     0.000000      0.000000      0.000000      0.000000      0.000000 
+     0.000000      0.000000      0.000000      0.000000      0.000000 
+     0.000000      0.000000      0.000000      0.000000      0.000000 
+     0.000000      0.000000      0.000000      0.000000      0.000000 
+     0.000000      0.000000      0.000000      0.000000 
+
+! phi = 105 
+     0.000000      0.000000      0.000000      0.000000      0.000000 
+     0.000000      0.000000      0.000000      0.000000      0.000000 
+     0.000000      0.000000      0.000000      0.000000      0.000000 
+     0.000000      0.000000      0.000000      0.000000      0.000000 
+     0.000000      0.000000      0.000000      0.000000 
+
+! phi = 120 
+     0.000000      0.000000      0.000000      0.000000      0.000000 
+     0.000000      0.000000      0.000000      0.000000      0.000000 
+     0.000000      0.000000      0.000000      0.000000      0.000000 
+     0.000000      0.000000      0.000000      0.000000      0.000000 
+     0.000000      0.000000      0.000000      0.000000 
+
+! phi = 135 
+     0.000000      0.000000      0.000000      0.000000      0.000000 
+     0.000000      0.000000      0.000000      0.000000      0.000000 
+     0.000000      0.000000      0.000000      0.000000      0.000000 
+     0.000000      0.000000      0.000000      0.000000      0.000000 
+     0.000000      0.000000      0.000000      0.000000 
+
+! phi = 150 
+     0.000000      0.000000      0.000000      0.000000      0.000000 
+     0.000000      0.000000      0.000000      0.000000      0.000000 
+     0.000000      0.000000      0.000000      0.000000      0.000000 
+     0.000000      0.000000      0.000000      0.000000      0.000000 
+     0.000000      0.000000      0.000000      0.000000 
+
+! phi = 165 
+     0.000000      0.000000      0.000000      0.000000      0.000000 
+     0.000000      0.000000      0.000000      0.000000      0.000000 
+     0.000000      0.000000      0.000000      0.000000      0.000000 
+     0.000000      0.000000      0.000000      0.000000      0.000000 
+     0.000000      0.000000      0.000000      0.000000 
+
+!2 adjacent prolines
+! mp2/aug-cc-pVDZ//RIMP2/VTZ/VQZ CBS map
+C    N    CP1  C    N    CP1    C    N 24
+
+! phi = -180 
+     2.973500      3.348200      3.062900      2.113400      1.040500 
+     0.770600      0.785200      0.263300     -0.479000     -0.583000 
+    -0.463800     -0.292600      0.000000      0.259100      0.177100 
+    -0.151200     -0.173500      0.211700      0.348900     -0.135600 
+    -0.950000     -1.256600     -0.292800      1.560000 
+
+! phi = -165 
+     5.674100      6.011400      5.562700      4.467300      3.390800 
+     3.008800      2.848600      2.311200      1.661400      1.468400 
+     1.142700      1.437400      2.113200      2.799500      2.989100 
+     2.869000      3.016100      3.328500      3.232900      2.547600 
+     1.647200      1.422700      2.517100      4.339800 
+
+! phi = -150 
+     6.752800      6.973200      6.444300      5.389800      4.438600 
+     4.046000      3.832800      3.442400      3.303500      3.010000 
+     2.838100      3.162200      3.778300      4.362800      4.603600 
+     4.546200      4.702100      4.837200      4.549500      3.849600 
+     3.099200      3.031800      4.060200      5.624800 
+
+! phi = -135 
+     7.627800      8.153400      7.342500      5.893500      4.799200 
+     4.433400      4.551500      4.442800      2.222200      0.776300 
+     0.790000      2.152300      3.932900      5.274900      5.830800 
+     5.988600      5.588500      5.211000      4.918000      4.292100 
+     3.495500      3.449800      4.617700      6.311700 
+
+! phi = -120 
+     8.115600      8.477200      7.754300      6.585000      5.537900 
+     4.964300      4.929000      4.421200      2.336100      1.257800 
+     1.769300      3.359900      5.018000      6.055500      6.217600 
+     5.726100      5.512200      5.820200      5.716700      4.872300 
+     4.066800      4.094600      5.284900      6.931500 
+
+! phi = -105 
+     9.249700      9.483000      8.668500      7.525300      7.003200 
+     6.834600      6.822100      5.287600      3.320600      2.640300 
+     3.464800      5.100300      6.537600      6.885600      5.842000 
+     5.248700      5.540200      6.652400      7.196700      6.625400 
+     5.710100      5.581700      6.651500      8.192800 
+
+! phi = -90 
+     9.335600      9.208000      8.564600      8.010200      7.885100 
+     8.212200      8.737100      8.429100      7.306500      6.474200 
+     6.651300      7.484700      8.195300      8.295000      7.407200 
+     6.529900      6.242000      6.227500      6.347300      6.449700 
+     6.404700      6.579300      7.391700      8.570700 
+
+! phi = -75 
+    10.955200     11.455400     11.173300     10.428700     10.062400 
+    10.044500      9.279600      6.965100      5.361500      5.102700 
+     6.267600      7.871600      8.009800      7.104500      6.616400 
+     6.733700      7.504000      8.664700      9.282800      8.795900 
+     7.872500      7.612400      8.498100      9.894000 
+
+! phi = -60 
+     8.422900      8.529200      8.608500      9.306400     10.239400 
+    11.025900     11.510800      9.283500      7.566000      6.624600 
+     7.038700      8.222400      8.786400      8.512000      8.103500 
+     7.988200      8.192900      8.291000      8.055600      7.436800 
+     6.651800      6.317000      6.802500      7.746300 
+
+! phi = -45 
+     6.913200      7.937400      8.610800      9.316600      9.388500 
+     9.408400      8.828800      7.297900      5.456400      4.742700 
+     5.793100      7.118800      7.565400      7.598500      7.438700 
+     7.512500      7.878100      8.082200      7.642700      6.320500 
+     4.680400      3.830500      4.215800      5.435200 
+
+! phi = -30 
+     5.466700      7.116000      8.908800      8.347200      7.413500 
+     7.047000      6.031600      4.193100      2.674800      3.023700 
+     4.485300      5.451700      6.214900      6.422600      6.229300 
+     6.191100      6.488900      6.646400      5.833400      3.751300 
+     1.719800      1.064900      1.955800      3.860800 
+
+! phi = -15 
+     3.061500      5.603800     12.179500      6.295200      5.323400 
+     4.826500      3.705600      2.461500      2.291600      3.145900 
+     3.562100      4.443600      5.337500      5.728800      5.694800 
+     5.641600      5.943300      6.169000      4.759500      2.569400 
+     1.357100      1.669800      3.212300      5.031900 
+
+! phi = 0 
+     8.085900      8.051100      5.023600      3.450800      2.836100 
+     2.192500      1.566200      1.456300      2.039300      1.945200 
+     2.188400      2.921300      3.467500      3.543500      3.374500 
+     3.472300      4.069900      3.615600      2.082200      0.958600 
+     0.792600      1.494200      2.794900      4.853100 
+
+! phi = 15 
+     6.639500      5.177400      3.252300      1.952700      1.078400 
+     0.888300      1.505400      2.442300      2.178600      1.578600 
+     1.777400      2.395400      2.820200      2.795200      2.662400 
+     2.917100      2.562100      1.557900      1.322300      1.631400 
+     2.051200      2.555600      3.039100      4.915000 
+
+! phi = 30 
+     7.548800      5.095500      2.747000      0.955200      0.444500 
+     1.318700      2.733300      3.223200      2.565500      2.150900 
+     2.394400      2.939300      3.266000      3.210000      3.113400 
+     2.491300      0.978300      0.815300      1.522700      2.055600 
+     2.199900      2.327600      3.474200      7.977800 
+
+! phi = 45 
+     0.000000      0.000000      0.000000      0.000000      0.000000 
+     0.000000      0.000000      0.000000      0.000000      0.000000 
+     0.000000      0.000000      0.000000      0.000000      0.000000 
+     0.000000      0.000000      0.000000      0.000000      0.000000 
+     0.000000      0.000000      0.000000      0.000000 
+
+! phi = 60 
+     0.000000      0.000000      0.000000      0.000000      0.000000 
+     0.000000      0.000000      0.000000      0.000000      0.000000 
+     0.000000      0.000000      0.000000      0.000000      0.000000 
+     0.000000      0.000000      0.000000      0.000000      0.000000 
+     0.000000      0.000000      0.000000      0.000000 
+
+! phi = 75 
+     0.000000      0.000000      0.000000      0.000000      0.000000 
+     0.000000      0.000000      0.000000      0.000000      0.000000 
+     0.000000      0.000000      0.000000      0.000000      0.000000 
+     0.000000      0.000000      0.000000      0.000000      0.000000 
+     0.000000      0.000000      0.000000      0.000000 
+
+! phi = 90 
+     0.000000      0.000000      0.000000      0.000000      0.000000 
+     0.000000      0.000000      0.000000      0.000000      0.000000 
+     0.000000      0.000000      0.000000      0.000000      0.000000 
+     0.000000      0.000000      0.000000      0.000000      0.000000 
+     0.000000      0.000000      0.000000      0.000000 
+
+! phi = 105 
+     0.000000      0.000000      0.000000      0.000000      0.000000 
+     0.000000      0.000000      0.000000      0.000000      0.000000 
+     0.000000      0.000000      0.000000      0.000000      0.000000 
+     0.000000      0.000000      0.000000      0.000000      0.000000 
+     0.000000      0.000000      0.000000      0.000000 
+
+! phi = 120 
+     0.000000      0.000000      0.000000      0.000000      0.000000 
+     0.000000      0.000000      0.000000      0.000000      0.000000 
+     0.000000      0.000000      0.000000      0.000000      0.000000 
+     0.000000      0.000000      0.000000      0.000000      0.000000 
+     0.000000      0.000000      0.000000      0.000000 
+
+! phi = 135 
+     0.000000      0.000000      0.000000      0.000000      0.000000 
+     0.000000      0.000000      0.000000      0.000000      0.000000 
+     0.000000      0.000000      0.000000      0.000000      0.000000 
+     0.000000      0.000000      0.000000      0.000000      0.000000 
+     0.000000      0.000000      0.000000      0.000000 
+
+! phi = 150 
+     0.000000      0.000000      0.000000      0.000000      0.000000 
+     0.000000      0.000000      0.000000      0.000000      0.000000 
+     0.000000      0.000000      0.000000      0.000000      0.000000 
+     0.000000      0.000000      0.000000      0.000000      0.000000 
+     0.000000      0.000000      0.000000      0.000000 
+
+! phi = 165 
+     0.000000      0.000000      0.000000      0.000000      0.000000 
+     0.000000      0.000000      0.000000      0.000000      0.000000 
+     0.000000      0.000000      0.000000      0.000000      0.000000 
+     0.000000      0.000000      0.000000      0.000000      0.000000 
+     0.000000      0.000000      0.000000      0.000000 
+
+! glycine map 
+! mp2/aug-cc-pVDZ//RIMP2/VTZ/VQZ CBS map
+C    NH1  CT2  C    NH1  CT2  C    NH1   24
+
+! phi = -180 
+     0.235350      0.182300      0.177200      0.396800      0.859400 
+     1.489700      2.092500      2.297700      1.808600      0.696200 
+    -0.563300     -1.432700     -1.015100      1.426300     -0.564300 
+     0.696200      1.808200      2.301700      2.092600      1.489100 
+     0.859500      0.396900      0.176900      0.182400 
+
+! phi = -165 
+     0.020100     -0.203800     -0.269700      0.014200      0.620800 
+     1.392400      2.046200      2.188200      1.683900      0.688500 
+    -0.373700     -0.703500      0.837800      3.704000     -0.730100 
+     0.594100      1.713100      2.205800      2.026400      1.529800 
+     1.027400      0.623800      0.348400      0.182800 
+
+! phi = -150 
+    -0.533600     -0.807400     -0.804600     -0.379800      0.365300 
+     1.168000      1.641000      1.618100      1.302200      0.615100 
+     0.065700      0.738500      2.959500     -2.036600     -0.934600 
+     0.407900      1.517000      1.984800      1.833100      1.435200 
+     0.995600      0.562200      0.150600     -0.209000 
+
+! phi = -135 
+    -1.208500     -1.429400     -1.319200     -0.817500     -0.112400 
+     0.454400      0.737600      0.879300      0.850100      0.670300 
+     0.943500     -2.651200     -2.829400     -2.199100     -1.065700 
+     0.279600      1.322000      1.668300      1.521300      1.193900 
+     0.765300      0.246000     -0.315500     -0.823200 
+
+! phi = -120 
+    -1.789100     -1.965500     -1.860700     -1.447900     -0.896500 
+    -0.401000     -0.015100      0.321300      0.634600      0.976300 
+    -1.977500     -2.883200     -2.848500     -2.137900     -0.960300 
+     0.308700      1.098100      1.245300      1.133600      0.881800 
+     0.448200     -0.153900     -0.823700     -1.404300 
+
+! phi = -105 
+    -2.246700     -2.487000     -2.473700     -2.135600     -1.577700 
+    -0.980600     -0.429100      0.144700      0.734000     -0.918300 
+    -2.299200     -2.882200     -2.668600     -1.847100     -0.719800 
+     0.107000      0.496000      0.553500      0.584300      0.494000 
+     0.098300     -0.529800     -1.237900     -1.840100 
+
+! phi = -90 
+    -2.851100     -3.181100     -3.199500     -2.785300     -2.054300 
+    -1.242900     -0.476500      0.288100     -0.045300     -1.470600 
+    -2.558800     -2.869400     -2.450300     -1.582200     -0.930800 
+    -0.426400     -0.022700      0.000000     -0.097400     -0.136100 
+    -0.439600     -1.038600     -1.741000     -2.373200 
+
+! phi = -75 
+    -3.961800     -4.268200     -4.109000     -3.364700     -2.252200 
+    -1.140400     -0.209800      0.487300     -0.746200     -2.127700 
+    -2.932100     -2.898500     -2.247900     -1.730400     -1.177200 
+    -0.448200      0.034900     -0.073300     -0.531600     -0.933300 
+    -1.360700     -2.009200     -2.745700     -3.424900 
+
+! phi = -60 
+    -5.408000     -5.355100     -4.640100     -3.283200     -1.710200 
+    -0.423800      0.354400     -0.103700     -1.577700     -2.828300 
+    -3.151200     -2.649200     -2.183000     -1.761200     -0.981700 
+    -0.174700      0.262600      0.039200     -0.663000     -1.530700 
+    -2.478200     -3.465600     -4.334200     -5.011200 
+
+! phi = -45 
+    -6.093200     -5.298400     -3.816620     -1.922530     -0.196160 
+     0.768200      0.568500     -0.831300     -2.343900     -3.037100 
+    -2.663700     -2.191100     -2.022900     -1.438500     -0.649000 
+     0.077000      0.441500      0.257500     -0.491100     -1.820600 
+    -3.473100     -4.895200     -5.790700     -6.205900 
+
+! phi = -30 
+    -5.258225     -3.675795     -1.631110      0.430085      1.496470 
+     0.318200     -0.555100     -1.695500     -2.434200     -2.192600 
+    -1.691300     -1.890000     -1.708500     -1.206300     -0.567400 
+     0.054300      0.497200      0.599600     -0.171000     -2.137600 
+    -4.237000     -5.584100     -6.135100     -6.067000 
+
+! phi = -15 
+    -3.161820     -0.902080      1.432450     -1.452885     -1.560780 
+    -1.665600     -1.783100     -1.755100     -1.329300     -0.731100 
+    -1.317000     -1.662800     -1.601200     -1.294900     -0.817300 
+    -0.197100      0.549500      0.850400     -0.689700     -2.819900 
+    -4.393000     -5.111500     -5.205690     -4.654785 
+
+! phi = 0 
+     0.034035     -2.349860     -3.412065     -3.620070     -3.450950 
+    -2.875650     -1.787800     -0.541250      0.410450     -0.372500 
+    -1.126850     -1.498450     -1.608700     -1.498450     -1.126850 
+    -0.372500      0.410450     -0.541250     -1.787800     -2.875650 
+    -3.450950     -3.620070     -3.412065     -2.349860 
+
+! phi = 15 
+    -3.162345     -4.654785     -5.205690     -5.111500     -4.393000 
+    -2.819900     -0.689700      0.850400      0.549500     -0.197100 
+    -0.817300     -1.294900     -1.601200     -1.662800     -1.317000 
+    -0.731100     -1.329300     -1.755100     -1.783100     -1.665600 
+    -1.560780     -1.452885      1.432450     -0.902080 
+
+! phi = 30 
+    -5.258220     -6.067000     -6.135100     -5.584100     -4.237000 
+    -2.137600     -0.171000      0.599600      0.497200      0.054300 
+    -0.567400     -1.206300     -1.708500     -1.890000     -1.691300 
+    -2.192600     -2.434200     -1.695500     -0.555100      0.318200 
+     1.496470      0.430085     -1.631110     -3.675795 
+
+! phi = 45 
+    -6.093300     -6.205900     -5.790700     -4.895200     -3.473100 
+    -1.820600     -0.491100      0.257500      0.441500      0.077000 
+    -0.649000     -1.438500     -2.022900     -2.191100     -2.663700 
+    -3.037100     -2.343900     -0.831300      0.568500      0.768200 
+    -0.196160     -1.922530     -3.816620     -5.298400 
+
+! phi = 60 
+    -5.407500     -5.011200     -4.334200     -3.465600     -2.478200 
+    -1.530700     -0.663000      0.039200      0.262600     -0.174700 
+    -0.981700     -1.761200     -2.183000     -2.649200     -3.151200 
+    -2.828300     -1.577700     -0.103700      0.354400     -0.423800 
+    -1.710200     -3.283200     -4.640100     -5.355100 
+
+! phi = 75 
+    -3.961900     -3.424900     -2.745700     -2.009200     -1.360700 
+    -0.933300     -0.531600     -0.073300      0.034900     -0.448200 
+    -1.177200     -1.730400     -2.247900     -2.898500     -2.932100 
+    -2.127700     -0.746200      0.487300     -0.209800     -1.140400 
+    -2.252200     -3.364700     -4.109000     -4.268200 
+
+! phi = 90 
+    -2.854500     -2.373200     -1.741000     -1.038600     -0.439600 
+    -0.136100     -0.097400      0.000000     -0.022700     -0.426400 
+    -0.930800     -1.582200     -2.450300     -2.869400     -2.558800 
+    -1.470600     -0.045300      0.288100     -0.476500     -1.242900 
+    -2.054300     -2.785300     -3.199500     -3.181100 
+
+! phi = 105 
+    -2.246400     -1.840100     -1.237900     -0.529800      0.098300 
+     0.494000      0.584300      0.553500      0.496000      0.107000 
+    -0.719800     -1.847100     -2.668600     -2.882200     -2.299200 
+    -0.918300      0.734000      0.144700     -0.429100     -0.980600 
+    -1.577700     -2.135600     -2.473700     -2.487000 
+
+! phi = 120 
+    -1.788800     -1.404300     -0.823700     -0.153900      0.448200 
+     0.881800      1.133600      1.245300      1.098100      0.308700 
+    -0.960300     -2.137900     -2.848500     -2.883200     -1.977500 
+     0.976300      0.634600      0.321300     -0.015100     -0.401000 
+    -0.896500     -1.447900     -1.860700     -1.965500 
+
+! phi = 135 
+    -1.208900     -0.823200     -0.315500      0.246000      0.765300 
+     1.193900      1.521300      1.668300      1.322000      0.279600 
+    -1.065700     -2.199100     -2.829400     -2.651200      0.943500 
+     0.670300      0.850100      0.879300      0.737600      0.454400 
+    -0.112400     -0.817500     -1.319200     -1.429400 
+
+! phi = 150 
+    -0.533400     -0.209000      0.150600      0.562200      0.995600 
+     1.435200      1.833100      1.984800      1.517000      0.407900 
+    -0.934600     -2.036600      2.959500      0.738500      0.065700 
+     0.615100      1.302200      1.618100      1.641000      1.168000 
+     0.365300     -0.379800     -0.804600     -0.807400 
+
+! phi = 165 
+     0.019900      0.182800      0.348400      0.623800      1.027400 
+     1.529800      2.026400      2.205800      1.713100      0.594100 
+    -0.730100      3.704000      0.837800     -0.703500     -0.373700 
+     0.688500      1.683900      2.188200      2.046200      1.392400 
+     0.620800      0.014200     -0.269700     -0.203800 
+
+! glycine before proline map: use glycine map
+! mp2/aug-cc-pVDZ//RIMP2/VTZ/VQZ CBS map
+C    NH1  CT2  C    NH1  CT2  C    N   24
+
+! phi = -180 
+     0.235350      0.182300      0.177200      0.396800      0.859400 
+     1.489700      2.092500      2.297700      1.808600      0.696200 
+    -0.563300     -1.432700     -1.015100      1.426300     -0.564300 
+     0.696200      1.808200      2.301700      2.092600      1.489100 
+     0.859500      0.396900      0.176900      0.182400 
+
+! phi = -165 
+     0.020100     -0.203800     -0.269700      0.014200      0.620800 
+     1.392400      2.046200      2.188200      1.683900      0.688500 
+    -0.373700     -0.703500      0.837800      3.704000     -0.730100 
+     0.594100      1.713100      2.205800      2.026400      1.529800 
+     1.027400      0.623800      0.348400      0.182800 
+
+! phi = -150 
+    -0.533600     -0.807400     -0.804600     -0.379800      0.365300 
+     1.168000      1.641000      1.618100      1.302200      0.615100 
+     0.065700      0.738500      2.959500     -2.036600     -0.934600 
+     0.407900      1.517000      1.984800      1.833100      1.435200 
+     0.995600      0.562200      0.150600     -0.209000 
+
+! phi = -135 
+    -1.208500     -1.429400     -1.319200     -0.817500     -0.112400 
+     0.454400      0.737600      0.879300      0.850100      0.670300 
+     0.943500     -2.651200     -2.829400     -2.199100     -1.065700 
+     0.279600      1.322000      1.668300      1.521300      1.193900 
+     0.765300      0.246000     -0.315500     -0.823200 
+
+! phi = -120 
+    -1.789100     -1.965500     -1.860700     -1.447900     -0.896500 
+    -0.401000     -0.015100      0.321300      0.634600      0.976300 
+    -1.977500     -2.883200     -2.848500     -2.137900     -0.960300 
+     0.308700      1.098100      1.245300      1.133600      0.881800 
+     0.448200     -0.153900     -0.823700     -1.404300 
+
+! phi = -105 
+    -2.246700     -2.487000     -2.473700     -2.135600     -1.577700 
+    -0.980600     -0.429100      0.144700      0.734000     -0.918300 
+    -2.299200     -2.882200     -2.668600     -1.847100     -0.719800 
+     0.107000      0.496000      0.553500      0.584300      0.494000 
+     0.098300     -0.529800     -1.237900     -1.840100 
+
+! phi = -90 
+    -2.851100     -3.181100     -3.199500     -2.785300     -2.054300 
+    -1.242900     -0.476500      0.288100     -0.045300     -1.470600 
+    -2.558800     -2.869400     -2.450300     -1.582200     -0.930800 
+    -0.426400     -0.022700      0.000000     -0.097400     -0.136100 
+    -0.439600     -1.038600     -1.741000     -2.373200 
+
+! phi = -75 
+    -3.961800     -4.268200     -4.109000     -3.364700     -2.252200 
+    -1.140400     -0.209800      0.487300     -0.746200     -2.127700 
+    -2.932100     -2.898500     -2.247900     -1.730400     -1.177200 
+    -0.448200      0.034900     -0.073300     -0.531600     -0.933300 
+    -1.360700     -2.009200     -2.745700     -3.424900 
+
+! phi = -60 
+    -5.408000     -5.355100     -4.640100     -3.283200     -1.710200 
+    -0.423800      0.354400     -0.103700     -1.577700     -2.828300 
+    -3.151200     -2.649200     -2.183000     -1.761200     -0.981700 
+    -0.174700      0.262600      0.039200     -0.663000     -1.530700 
+    -2.478200     -3.465600     -4.334200     -5.011200 
+
+! phi = -45 
+    -6.093200     -5.298400     -3.816620     -1.922530     -0.196160 
+     0.768200      0.568500     -0.831300     -2.343900     -3.037100 
+    -2.663700     -2.191100     -2.022900     -1.438500     -0.649000 
+     0.077000      0.441500      0.257500     -0.491100     -1.820600 
+    -3.473100     -4.895200     -5.790700     -6.205900 
+
+! phi = -30 
+    -5.258225     -3.675795     -1.631110      0.430085      1.496470 
+     0.318200     -0.555100     -1.695500     -2.434200     -2.192600 
+    -1.691300     -1.890000     -1.708500     -1.206300     -0.567400 
+     0.054300      0.497200      0.599600     -0.171000     -2.137600 
+    -4.237000     -5.584100     -6.135100     -6.067000 
+
+! phi = -15 
+    -3.161820     -0.902080      1.432450     -1.452885     -1.560780 
+    -1.665600     -1.783100     -1.755100     -1.329300     -0.731100 
+    -1.317000     -1.662800     -1.601200     -1.294900     -0.817300 
+    -0.197100      0.549500      0.850400     -0.689700     -2.819900 
+    -4.393000     -5.111500     -5.205690     -4.654785 
+
+! phi = 0 
+     0.034035     -2.349860     -3.412065     -3.620070     -3.450950 
+    -2.875650     -1.787800     -0.541250      0.410450     -0.372500 
+    -1.126850     -1.498450     -1.608700     -1.498450     -1.126850 
+    -0.372500      0.410450     -0.541250     -1.787800     -2.875650 
+    -3.450950     -3.620070     -3.412065     -2.349860 
+
+! phi = 15 
+    -3.162345     -4.654785     -5.205690     -5.111500     -4.393000 
+    -2.819900     -0.689700      0.850400      0.549500     -0.197100 
+    -0.817300     -1.294900     -1.601200     -1.662800     -1.317000 
+    -0.731100     -1.329300     -1.755100     -1.783100     -1.665600 
+    -1.560780     -1.452885      1.432450     -0.902080 
+
+! phi = 30 
+    -5.258220     -6.067000     -6.135100     -5.584100     -4.237000 
+    -2.137600     -0.171000      0.599600      0.497200      0.054300 
+    -0.567400     -1.206300     -1.708500     -1.890000     -1.691300 
+    -2.192600     -2.434200     -1.695500     -0.555100      0.318200 
+     1.496470      0.430085     -1.631110     -3.675795 
+
+! phi = 45 
+    -6.093300     -6.205900     -5.790700     -4.895200     -3.473100 
+    -1.820600     -0.491100      0.257500      0.441500      0.077000 
+    -0.649000     -1.438500     -2.022900     -2.191100     -2.663700 
+    -3.037100     -2.343900     -0.831300      0.568500      0.768200 
+    -0.196160     -1.922530     -3.816620     -5.298400 
+
+! phi = 60 
+    -5.407500     -5.011200     -4.334200     -3.465600     -2.478200 
+    -1.530700     -0.663000      0.039200      0.262600     -0.174700 
+    -0.981700     -1.761200     -2.183000     -2.649200     -3.151200 
+    -2.828300     -1.577700     -0.103700      0.354400     -0.423800 
+    -1.710200     -3.283200     -4.640100     -5.355100 
+
+! phi = 75 
+    -3.961900     -3.424900     -2.745700     -2.009200     -1.360700 
+    -0.933300     -0.531600     -0.073300      0.034900     -0.448200 
+    -1.177200     -1.730400     -2.247900     -2.898500     -2.932100 
+    -2.127700     -0.746200      0.487300     -0.209800     -1.140400 
+    -2.252200     -3.364700     -4.109000     -4.268200 
+
+! phi = 90 
+    -2.854500     -2.373200     -1.741000     -1.038600     -0.439600 
+    -0.136100     -0.097400      0.000000     -0.022700     -0.426400 
+    -0.930800     -1.582200     -2.450300     -2.869400     -2.558800 
+    -1.470600     -0.045300      0.288100     -0.476500     -1.242900 
+    -2.054300     -2.785300     -3.199500     -3.181100 
+
+! phi = 105 
+    -2.246400     -1.840100     -1.237900     -0.529800      0.098300 
+     0.494000      0.584300      0.553500      0.496000      0.107000 
+    -0.719800     -1.847100     -2.668600     -2.882200     -2.299200 
+    -0.918300      0.734000      0.144700     -0.429100     -0.980600 
+    -1.577700     -2.135600     -2.473700     -2.487000 
+
+! phi = 120 
+    -1.788800     -1.404300     -0.823700     -0.153900      0.448200 
+     0.881800      1.133600      1.245300      1.098100      0.308700 
+    -0.960300     -2.137900     -2.848500     -2.883200     -1.977500 
+     0.976300      0.634600      0.321300     -0.015100     -0.401000 
+    -0.896500     -1.447900     -1.860700     -1.965500 
+
+! phi = 135 
+    -1.208900     -0.823200     -0.315500      0.246000      0.765300 
+     1.193900      1.521300      1.668300      1.322000      0.279600 
+    -1.065700     -2.199100     -2.829400     -2.651200      0.943500 
+     0.670300      0.850100      0.879300      0.737600      0.454400 
+    -0.112400     -0.817500     -1.319200     -1.429400 
+
+! phi = 150 
+    -0.533400     -0.209000      0.150600      0.562200      0.995600 
+     1.435200      1.833100      1.984800      1.517000      0.407900 
+    -0.934600     -2.036600      2.959500      0.738500      0.065700 
+     0.615100      1.302200      1.618100      1.641000      1.168000 
+     0.365300     -0.379800     -0.804600     -0.807400 
+
+! phi = 165 
+     0.019900      0.182800      0.348400      0.623800      1.027400 
+     1.529800      2.026400      2.205800      1.713100      0.594100 
+    -0.730100      3.704000      0.837800     -0.703500     -0.373700 
+     0.688500      1.683900      2.188200      2.046200      1.392400 
+     0.620800      0.014200     -0.269700     -0.203800 
+
+NONBONDED nbxmod  5 atom cdiel fshift vatom vdistance vfswitch -
+cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 
+                !adm jr., 2013 correction
+!
+!V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6]
+!
+!epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j)
+!Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j
+!
+!atom  ignored    epsilon      Rmin/2   ignored   eps,1-4       Rmin/2,1-4
+!
+!carbons
+C      0.000000  -0.110000     2.000000 ! ALLOW   PEP POL ARO
+                ! NMA pure solvent, adm jr., 3/3/93
+CA     0.000000  -0.070000     1.992400 ! ALLOW   ARO
+                ! benzene (JES)
+CC     0.000000  -0.070000     2.000000 ! ALLOW   PEP POL ARO
+                ! adm jr. 3/3/92, acetic acid heat of solvation
+CD     0.000000  -0.070000     2.000000 ! ALLOW  POL
+                ! adm jr. 3/19/92, acetate a.i. and dH of solvation
+CE1    0.000000  -0.068000     2.090000 ! 
+		! for propene, yin/adm jr., 12/95
+CE2    0.000000  -0.064000     2.080000 ! 
+		! for ethene, yin/adm jr., 12/95
+CP1    0.000000  -0.020000     2.275000   0.000000  -0.010000     1.900000 ! ALLOW   ALI
+                ! alkane update, adm jr., 3/2/92
+CP2    0.000000  -0.055000     2.175000   0.000000  -0.010000     1.900000 ! ALLOW   ALI
+                ! alkane update, adm jr., 3/2/92
+CP3    0.000000  -0.055000     2.175000   0.000000  -0.010000     1.900000 ! ALLOW   ALI
+                ! alkane update, adm jr., 3/2/92
+CPH1   0.000000  -0.050000     1.800000 ! ALLOW ARO
+                ! adm jr., 10/23/91, imidazole solvation and sublimation
+CPH2   0.000000  -0.050000     1.800000 ! ALLOW ARO
+                ! adm jr., 10/23/91, imidazole solvation and sublimation
+CS     0.000000  -0.110000     2.200000 ! ALLOW SUL
+                ! methylthiolate to water and F.E. of solvation, adm jr. 6/1/92
+CPT    0.000000  -0.099000     1.860000 ! atm, indole vaporization 5/05
+CY     0.000000  -0.073000     1.990000 ! atm, indole vaporization 5/05
+CAI    0.000000  -0.073000     1.990000 ! atm, indole vaporization 5/05
+                ! TRP, JWK 08/29/89
+!new alkanes atoms types for conversion to new LJ parameters for c27
+CT       0.0       -0.0200    2.275 0.0 -0.01 1.9 ! 
+CT1      0.0       -0.0320    2.000 0.0 -0.01 1.9 ! alkane, 4/07, viv and adm jr.
+CT2      0.0       -0.0560    2.010 0.0 -0.01 1.9 ! alkane, 4/98, yin, adm jr.
+CT2A     0.0       -0.0560    2.010 0.0 -0.01 1.9 ! from CT2 (GLU, HSP), 05282010, zhu
+CT3      0.0       -0.0780    2.040 0.0 -0.01 1.9 ! alkane, 4/98, yin, adm jr.
+! hydrogens
+H      0.000000  -0.046000     0.224500 ! ALLOW PEP POL SUL ARO ALC
+                ! same as TIP3P hydrogen, adm jr., 7/20/89
+HA     0.000000  -0.022000     1.320000 ! ALLOW PEP ALI POL SUL ARO PRO ALC
+                ! methane/ethane a.i. and ethane pure solvent, adm jr, 2/3/92
+HB1    0.000000  -0.022000     1.320000 ! 
+                ! methane/ethane a.i. and ethane pure solvent, adm jr, 2/3/92
+HB2    0.000000  -0.028000     1.340000 ! 
+                ! Yin and MacKerell, adm jr., 5/30/02
+HE1    0.000000  -0.031000     1.250000 ! 
+		! for propene, yin/adm jr., 12/95
+HE2    0.000000  -0.026000     1.260000 ! 
+		! for ethene, yin/adm jr., 12/95
+!HB     0.000000  -0.022000     1.320000 ! ALLOW PEP ALI POL SUL ARO PRO ALC
+                ! methane/ethane a.i. and ethane pure solvent, adm jr, 2/3/92
+HC     0.000000  -0.046000     0.224500 ! ALLOW POL
+                ! new, small polar Hydrogen, see also adm jr. JG 8/27/89
+HP     0.000000  -0.030000     1.358200   0.000000  -0.030000     1.358200 ! ALLOW ARO
+                ! JES 8/25/89 values from Jorgensen fit to hydration energy
+HR1    0.000000  -0.046000     0.900000 ! ALLOW ARO
+                ! adm jr., 6/27/90, his
+HR2    0.000000  -0.046000     0.700000 ! ALLOW ARO
+                ! adm jr., 6/27/90, his
+HR3    0.000000  -0.007800     1.468000 ! ALLOW ARO
+                ! adm jr., 3/24/92, maintain old aliphatic H VDW params
+HS     0.000000  -0.100000     0.450000 ! ALLOW SUL
+                ! methanethiol pure solvent, adm jr., 6/22/92
+!new alkanes atoms types for conversion to new LJ parameters for c27 (see toppar_all22_prot_aliphatic_c27.str)
+HA1     0.0       -0.045     1.3400 ! alkane, viv and adm jr., 4/07
+HA2     0.0       -0.034     1.3400 ! alkane, viv and adm jr., 4/07
+HA3     0.0       -0.024     1.3400 ! alkane, yin and mackerell, 4/98
+!nitrogens
+N      0.000000  -0.200000     1.850000   0.000000  -0.000100     1.850000 ! ALLOW   PRO
+                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NC2    0.000000  -0.200000     1.850000 ! ALLOW   POL
+                ! JG 8/27/89; note: NH1 in ARG was changed to NC2.
+NH1    0.000000  -0.200000     1.850000   0.000000  -0.200000     1.550000 ! ALLOW   PEP POL ARO
+                ! This 1,4 vdW allows the C5 dipeptide minimum to exist.(LK)
+NH2    0.000000  -0.200000     1.850000 ! ALLOW   POL
+                ! adm jr.
+NH3    0.000000  -0.200000     1.850000 ! ALLOW   POL
+                ! adm jr.
+NP     0.000000  -0.200000     1.850000 ! ALLOW  PRO
+                ! N-terminal proline; from 6-31g* +ProNH2  RLD 9/28/90
+NR1    0.000000  -0.200000     1.850000 ! ALLOW ARO
+                ! His, adm jr., 9/4/89
+NR2    0.000000  -0.200000     1.850000 ! ALLOW ARO
+                ! His, adm jr., 9/4/89
+NR3    0.000000  -0.200000     1.850000 ! ALLOW ARO
+                ! His, adm jr., 9/4/89
+NY     0.000000  -0.200000     1.850000 ! atm, indole vaporization 5/05
+! oxygens
+O      0.000000  -0.120000     1.700000   0.000000  -0.120000     1.400000 ! ALLOW   PEP POL
+                ! This 1,4 vdW allows the C5 dipeptide minimum to exist.(LK)
+OB     0.000000  -0.120000     1.700000   0.000000  -0.120000     1.400000 ! ALLOW   PEP POL ARO
+                ! adm jr., 10/17/90, acetic acid carbonyl O
+OC     0.000000  -0.120000     1.700000 ! ALLOW   POL ION
+                ! JG 8/27/89
+OH1    0.000000  -0.152100     1.770000 ! ALLOW   ALC ARO
+                ! adm jr. 8/14/90, MeOH nonbond and solvent (same as TIP3P)
+OS     0.000000  -0.152100     1.770000 ! ALLOW   ALC ARO
+                ! adm jr. 9/17/90, avoid O* wildcard
+! sulfurs
+S      0.000000  -0.450000     2.000000 ! ALLOW   SUL ION
+                ! adm jr., 3/3/92, methanethiol/ethylmethylsulfide pure solvent
+SM     0.000000  -0.380000     1.975000 ! ALLOW  SUL  ION
+                ! adm jr., 3/3/92, dimethyldisulphide pure solvent
+SS     0.000000  -0.470000     2.200000 ! ALLOW  SUL
+                ! methylthiolate to water and F.E. of solvation, adm jr. 6/1/92
+NBFIX
+!              Emin         Rmin
+!            (kcal/mol)     (A)
+NC2    OC       -0.154919   3.637 !  From osmotic pressure calibration
+
+HBOND CUTHB 0.5  ! If you want to do hbond analysis (only), then use
+                 ! READ PARAM APPEND CARD
+                 ! to append hbond parameters from the file: par_hbond.inp
+
+END

tests/0-forcefields/toppar_all36_na_nad_ppi.str

@@ -0,0 +1,3988 @@
+* CHARMM36 All-Hydrogen Nucleic Acid Force Toppar Stream File
+* NAD+, NADH, ADP, ATP, PPI and related analogs
+* A.D. MacKerell, Jr., July 2001
+* stream following RTF and PARAM read of
+*
+
+!Update, 2015/1, nomenclature for NAD+ etc. consistent with PDB
+
+!Parent files that have to be read prior to streaming this file
+!top_all36_na.rtf
+!par_all36_na.prm
+
+!Testcase
+!test_all36_na_nad_ppi.inp
+
+!Reference
+!Pavelites, J.J., Bash, P.A., Gao, J., and MacKerell, Jr.,
+!A.D. A Molecular Mechanics Force Field for NAD+, NADH and the
+!Pyrophosphate Groups of Nucleotides, Journal of Computational
+!Chemistry, 1997, 18: 221-239.
+
+read rtf card append
+* NAD, PPI topology
+*
+31  1
+
+MASS  -1  HN3B       1.00800 H ! NAD+ aromatic hydrogen
+MASS  -1  CN1A      12.01100 C ! NAD+/NADH amide carbonyl carbon
+MASS  -1  CN3A      12.01100 C ! NAD+ aromatic carbon
+MASS  -1  CN3B      12.01100 C ! NAD+ aromatic carbon
+MASS  -1  CN3C      12.01100 C ! NADH aromatic carbon
+MASS  -1  P3        30.97400 P ! pyrophosphate phosphorus
+MASS  -1  P4        30.97400 P ! protonated pyrophosphate phosphorus
+
+RESI NIC         1.00  ! oxidized nicotinamide, jjp1/adm jr.
+                       ! checked for consistency with new NA params, adm jr., 9/98
+                       ! note that differences with respect to published results exist
+                       ! due to new NA params
+                       !
+                       !       H15
+GROUP                  !         \
+ATOM H1   HN2     0.45 !     H16-N14     H8
+ATOM N2   NN2    -0.52 !           \     |
+ATOM C3   CN3B    0.16 !            C12  C7
+ATOM H4   HN3B    0.19 !           // \ /  \\
+ATOM C5   CN3    -0.10 !         O13   C9   C5-H6
+ATOM H6   HN3B    0.16 !               ||   |
+ATOM C7   CN3A   -0.05 !           H11-C10  C3-H4
+ATOM H8   HN3B    0.16 !                \+ //
+ATOM C9   CN3     0.05 !                 N2
+ATOM C10  CN3B    0.18 !                 |
+ATOM H11  HN3B    0.16 !                 H1
+ATOM C12  CN1A    0.68 !
+ATOM O13  ON1    -0.40 !
+ATOM N14  NN1    -0.82 !
+ATOM H15  HN1     0.34 ! trans to O13
+ATOM H16  HN1     0.36 ! cis to O13
+BOND N2  H1   C3  H4   C3  C5   C5  H6
+BOND C7 H8   C7  C9   N2  C10
+BOND C10 H11  C9 C12  C12 N14  N14 H15  N14 H16
+DOUBLE C12 O13  C9 C10  C5 C7  N2 C3
+! amide impropers
+IMPR C12 N14 C9 O13   C12 C9  N14 O13
+IMPR N14 C12 H16 H15  N14 C12 H15 H16
+! ring hydrogen impropers
+IMPR N2   C10  C3   H1    C3   N2   C5   H4    C5   C3   C7   H6
+IMPR C7   C5   C9   H8    C10  C9   N2   H11
+! ic table for analysis
+IC N2   C3   C5   C7    0.0000  000.00  000.00  000.00  0.000
+IC C3   C5   C7   C9    0.0000  000.00  000.00  000.00  0.000
+IC C5   C7   C9   C10   0.0000  000.00  000.00  000.00  0.000
+IC C7   C9   C10  N2    0.0000  000.00  000.00  000.00  0.000
+IC C9   C10  N2   C3    0.0000  000.00  000.00  000.00  0.000
+IC C10  N2   C3   C5    0.0000  000.00  000.00  000.00  0.000
+IC C9   C10  N2   H1    0.0000  000.00  000.00  000.00  0.000
+IC C10  N2   C3   H4    0.0000  000.00  000.00  000.00  0.000
+IC N2   C3   C5   H6    0.0000  000.00  000.00  000.00  0.000
+IC C3   C5   C7   H8    0.0000  000.00  000.00  000.00  0.000
+IC C5   C7   C9   C12   0.0000  000.00  000.00  000.00  0.000
+IC N2   C10  C9   C12   0.0000  000.00  000.00  000.00  0.000
+IC C7   C9   C12  O13   0.0000  000.00  000.00  000.00  0.000
+IC C7   C9   C12  N14   0.0000  000.00  000.00  000.00  0.000
+IC O13  C12  N14  H15   0.0000  000.00  000.00  000.00  0.000
+IC O13  C12  N14  H16   0.0000  000.00  000.00  000.00  0.000
+patch first none last none
+
+RESI NICH         0.00 ! reduced nicotinamide, jjp1/adm jr.
+                       ! checked for consistency with new NA params, adm jr., 9/98
+                       ! note that differences with respect to published results exist
+                       ! due to new NA params
+                       ! HN3 to HN6 atom type switch to maintain proper vdw params, 9/98
+                       !
+                       !       H15
+GROUP                  !         \
+ATOM H1   HN2     0.42 !     H16-N14   H8  H17
+ATOM N2   NN2    -0.69 !           \    \  /
+ATOM C3   CN3C   -0.06 !            C12  C7
+ATOM H4   HN6     0.17 !           /  \ /  \
+ATOM C5   CN3    -0.18 !         O13   C9   C5-H6
+ATOM H6   HN6     0.14 !               ||   ||
+ATOM C7   CN8    -0.28 !           H11-C10  C3-H4
+ATOM H8   HN8     0.09 !                \  /
+ATOM H17  HN8     0.09 !                 N2
+ATOM C10  CN3C   -0.10 !                 |
+ATOM H11  HN6     0.14 !                 H1
+ATOM C9   CN3     0.36 !
+ATOM C12  CN1A    0.55 !
+ATOM O13  ON1    -0.51 !
+ATOM N14  NN1    -0.72 !
+ATOM H15  HN1     0.26 ! trans to O13
+ATOM H16  HN1     0.32 ! cis to O13
+
+BOND N2  H1   N2 C3   C3  H4   C5  H6
+BOND C5  C7   C7 H8   C7  H17  C7  C9   N2  C10
+BOND C10 H11  C9 C12  C12 N14  N14 H15  N14 H16
+DOUBLE C12 O13   C9 C10   C3  C5
+! amide impropers
+IMPR C12 N14 C9 O13   C12 C9  N14 O13
+IMPR N14 C12 H16 H15  N14 C12 H15 H16
+! ring hydrogen impropers
+IMPR N2   C10  C3   H1    C3   N2   C5   H4    C5   C3   C7   H6
+IMPR C10  C9   N2   H11
+! ic table for analysis
+IC N2   C3   C5   C7    0.0000  000.00  000.00  000.00  0.000
+IC C3   C5   C7   C9    0.0000  000.00  000.00  000.00  0.000
+IC C5   C7   C9   C10   0.0000  000.00  000.00  000.00  0.000
+IC C7   C9   C10  N2    0.0000  000.00  000.00  000.00  0.000
+IC C9   C10  N2   C3    0.0000  000.00  000.00  000.00  0.000
+IC C10  N2   C3   C5    0.0000  000.00  000.00  000.00  0.000
+IC C9   C10  N2   H1    0.0000  000.00  000.00  000.00  0.000
+IC C10  N2   C3   H4    0.0000  000.00  000.00  000.00  0.000
+IC N2   C3   C5   H6    0.0000  000.00  000.00  000.00  0.000
+IC C3   C5   C7   H8    0.0000  000.00  000.00  000.00  0.000
+IC C3   C5   C7   H17   0.0000  000.00  000.00  000.00  0.000
+IC C5   C7   C9   C12   0.0000  000.00  000.00  000.00  0.000
+IC N2   C10  C9   C12   0.0000  000.00  000.00  000.00  0.000
+IC C7   C9   C12  O13   0.0000  000.00  000.00  000.00  0.000
+IC C7   C9   C12  N14   0.0000  000.00  000.00  000.00  0.000
+IC O13  C12  N14  H15   0.0000  000.00  000.00  000.00  0.000
+IC O13  C12  N14  H16   0.0000  000.00  000.00  000.00  0.000
+patch first none last none
+
+RESI PPI1        -3.00   ! Inorganic phosphate, jjp1/adm jr.
+GROUP                    !
+ATOM C1   CN9    -0.17   !
+ATOM O11  ON2    -0.62   !
+ATOM P1   P       1.50   !                 H11
+ATOM O12  ON2    -0.74   !                  |
+ATOM O13  ON3    -0.82   !            H13--C1--H12
+ATOM O14  ON3    -0.82   !                  |
+                         !                 O11
+ATOM P2   P3      1.10   !                  |
+ATOM O22  ON3    -0.90   !            O14==P1==O13  (-)
+ATOM O23  ON3    -0.90   !                 |
+ATOM O24  ON3    -0.90   !                 O12
+                         !                 |
+ATOM H11  HN9     0.09   !        (-) O24==P2==O23  (-)
+ATOM H12  HN9     0.09   !                 ||
+ATOM H13  HN9     0.09   !                 O22
+
+BOND P1  O11   P1  O12   P1  O13   P1  O14   O11  C1
+BOND C1  H11   C1  H12   C1  H13
+BOND O12 P2    P2  O22   P2  O23   P2  O24
+! IC Table
+IC C1   O11  P1   O12  0.0000    000.00    180.0     000.00    0.0000
+IC O11  P1   O12  P2   0.0000    000.00    180.0     000.00    0.0000
+IC P1   O12  P2   O22  0.0000    000.00    180.0     000.00    0.0000
+IC C1   O11  P1   O13  0.0000    000.00     60.0     000.00    0.0000
+IC C1   O11  P1   O14  0.0000    000.00    -60.0     000.00    0.0000
+IC P1   O12  P2   O23  0.0000    000.00     60.0     000.00    0.0000
+IC P1   O12  P2   O24  0.0000    000.00    -60.0     000.00    0.0000
+IC P1   O11  C1   H11  0.0000    000.00    180.0     000.00    0.0000
+IC P1   O11  C1   H12  0.0000    000.00     60.0     000.00    0.0000
+IC P1   O11  C1   H13  0.0000    000.00    -60.0     000.00    0.0000
+PATC  FIRS NONE LAST NONE
+
+RESI PPI2        -2.00   ! Inorganic phosphate, protonated, adm jr.
+                         ! terminal P charges based on neutral  
+GROUP                    ! methylphosphate
+ATOM C1   CN9    -0.17   !
+ATOM O11  ON2    -0.62   !
+ATOM P1   P       1.46   !                 H11
+ATOM O12  ON2    -0.63   !                  |
+ATOM O13  ON3    -0.83   !            H13--C1--H12
+ATOM O14  ON3    -0.83   !                  |
+                         !                 O11
+ATOM P2   P4      1.34   !                  |
+ATOM O22  ON4    -0.72   !            O14==P1==O13  (-)
+ATOM H22  HN4     0.45   !                 |
+ATOM O23  ON3    -0.86   !                 |
+ATOM O24  ON3    -0.86   !                 O12
+                         !                 |
+ATOM H11  HN9     0.09   !        (-) O24==P2==O23  (-)
+ATOM H12  HN9     0.09   !                 | 
+ATOM H13  HN9     0.09   !                 O22
+                         !                   \
+                         !                   H22
+
+BOND P1  O11   P1  O12   P1  O13   P1  O14   O11  C1
+BOND C1  H11   C1  H12   C1  H13
+BOND O12 P2    P2  O22   P2  O23   P2  O24   O22  H22
+! IC Table
+IC C1   O11  P1   O12  0.0000    000.00    180.0     000.00    0.0000
+IC O11  P1   O12  P2   0.0000    000.00    180.0     000.00    0.0000
+IC P1   O12  P2   O22  0.0000    000.00    180.0     000.00    0.0000
+IC C1   O11  P1   O13  0.0000    000.00     60.0     000.00    0.0000
+IC C1   O11  P1   O14  0.0000    000.00    -60.0     000.00    0.0000
+IC P1   O12  P2   O23  0.0000    000.00     60.0     000.00    0.0000
+IC P1   O12  P2   O24  0.0000    000.00    -60.0     000.00    0.0000
+IC P1   O11  C1   H11  0.0000    000.00    180.0     000.00    0.0000
+IC P1   O11  C1   H12  0.0000    000.00     60.0     000.00    0.0000
+IC P1   O11  C1   H13  0.0000    000.00    -60.0     000.00    0.0000
+IC O12  P2   O22  H22  0.0000    000.00    180.0     000.00    0.0000
+PATC  FIRS NONE LAST NONE
+
+!adenine nucleotides
+RESI AMP         -2.00  ! adenosine monophosphate, jjp1/adm jr.
+                        ! atom names correspond to pdb nomenclature
+GROUP
+ATOM C4'  CN7     0.16  !                       H61  H62
+ATOM H4'  HN7     0.09  !                         \  /
+ATOM O4'  ON6B   -0.50  !                          N6
+ATOM C1'  CN7B    0.16  !                          |
+ATOM H1'  HN7     0.09  !                          C6
+GROUP                   !                        //  \
+ATOM C5   CN5     0.28  !                        N1   C5--N7\\
+ATOM N7   NN4    -0.71  !                        |    ||     C8-H8
+ATOM C8   CN4     0.34  !                        C2   C4--N9/
+ATOM H8   HN3     0.12  !                       / \\ /     \
+ATOM N9   NN2    -0.05  !                     H2   N3       \
+                        !                                    \
+ATOM N1   NN3A   -0.74  !                                     \
+ATOM C2   CN4     0.50  !                                      \
+ATOM H2   HN3     0.13  !                  O1A    H5' H4'  O4'  \
+ATOM N3   NN3A   -0.75  !                   |      |    \ /   \  \
+ATOM C4   CN5     0.43  !              O3A=PA-O5'-C5'---C4'    C1'
+ATOM C6   CN2     0.46  !                   |      |     \     / \
+                        !                  O2A    H5''   C3'--C2' H1'
+ATOM N6   NN1    -0.77  !                               / \   / \
+ATOM H61  HN1     0.38  !                            O3' H3' O2' H2''
+ATOM H62  HN1     0.38  !                             |       |
+GROUP                   !                            H3T     H2'
+ATOM C2'  CN7B    0.14  !
+ATOM H2'' HN7     0.09
+ATOM O2'  ON5    -0.66
+ATOM H2'  HN5     0.43
+GROUP
+ATOM C3'  CN7     0.14
+ATOM H3'  HN7     0.09
+ATOM O3'  ON5    -0.66
+ATOM H3T  HN5     0.43
+GROUP
+ATOM C5'  CN8B   -0.18
+ATOM H5'  HN8     0.09
+ATOM H5'' HN8     0.09
+GROUP
+ATOM O5'  ON2    -0.40
+ATOM PA   P       1.10
+ATOM O1A  ON3    -0.90
+ATOM O2A  ON3    -0.90
+ATOM O3A  ON3    -0.90
+
+BOND PA   O1A       PA   O2A       PA   O3A       PA    O5'      O3'  H3T
+BOND O5'  C5'       C5'  C4'       C4'  O4'       C4'  C3'       O4'  C1'
+BOND C1'  N9        C1'  C2'       N9   C4        N9   C8        C4   N3
+BOND C2   N1        C6   N6
+BOND N6   H61       N6   H62       C6   C5        C5   N7
+BOND C2'  C3'       C2'  O2'       O2'  H2'       C3'  O3'
+BOND C1'  H1'       C2'  H2''      C3'  H3'       C4'  H4'       C5'  H5'
+BOND C5'  H5''      C8   H8        C2   H2
+DOUBLE N1   C6    N3   C2    C4   C5        N7   C8
+IMPR N6   C6   H61  H62       C6   N1   C5   N6        
+DONO H61  N6
+DONO H62  N6
+DONO H2'  O2'
+ACCE N3
+ACCE N7
+ACCE N1
+ACCE O1A  PA
+ACCE O2A  PA
+ACCE O3A  PA
+ACCE O2'
+ACCE O3'
+ACCE O4'
+ACCE O5'
+
+ IC    C5'     O5'     PA      O1A         1.4449  121.33   73.87  103.48   1.4828
+ IC    C5'     O5'     PA      O2A         1.4449  121.33  -46.00  105.57   1.4776
+ IC    O1A     O2A     *PA     O3A         1.4828  113.83 -132.36  114.06   1.4776
+ IC    PA      O5'     C5'     C4'         1.5840  121.33 -147.38  113.85   1.5508
+ IC    O5'     C5'     C4'     C3'         1.4449  113.85  128.15  110.17   1.5416
+ IC    C5'     C4'     C3'     O3'         1.5508  110.17  151.98  114.50   1.4413
+ IC    H3T     O3'     C3'     C4'         0.9638  105.27  160.52  114.50   1.5416
+ IC    O4'     C3'     *C4'    C5'         1.4701  103.10 -121.12  110.17   1.5508
+ IC    C2'     C4'     *C3'    O3'         1.5240  101.86 -123.48  114.50   1.4413
+ IC    C4'     C3'     C2'     C1'         1.5416  101.86  -38.77  101.03   1.5059
+ IC    C3'     C2'     C1'     N9          1.5240  101.03  155.09  111.78   1.4716
+ IC    O4'     C1'     N9      C4          1.4137  114.18 -154.31  121.73   1.3703
+ IC    C1'     C4      *N9     C8          1.4716  121.73  178.72  105.87   1.3855
+ IC    C4      N9      C8      N7          1.3703  105.87    4.44  112.40   1.3266
+ IC    C8      N9      C4      C5          1.3855  105.87   -3.48  106.32   1.3792
+ IC    C8      N7      C5      C6          1.3266  104.45  179.66  132.25   1.4124
+ IC    N7      C5      C6      N1          1.3786  132.25 -179.60  117.95   1.3597
+ IC    C5      C6      N1      C2          1.4124  117.95   -0.70  118.00   1.3353
+ IC    N9      C5      *C4     N3          1.3703  106.32 -179.31  126.63   1.3526
+ IC    C5      N1      *C6     N6          1.4124  117.95 -179.56  118.80   1.3481
+ IC    N1      C6      N6      H61         1.3597  118.80   -3.01  118.66   0.9923
+ IC    H61     C6      *N6     H62         0.9923  118.66 -174.71  119.12   0.9995
+ IC    C5      N1      *C6     N6          1.4124  117.95 -179.56  118.80   1.3481
+ IC    N1      C6      N6      H61         1.3597  118.80   -3.01  118.66   0.9923
+ IC    H61     C6      *N6     H62         0.9923  118.66 -174.71  119.12   0.9995
+ IC    N9      N7      *C8     H8          1.3855  112.40 -179.62  125.31   1.0957
+ IC    N1      N3      *C2     H2          1.3353  129.78  179.62  114.59   1.0943
+ IC    C1'     C3'     *C2'    O2'         1.5059  101.03 -118.47  112.30   1.4247
+ IC    H2'     O2'     C2'     C3'         0.9720  107.05  156.19  112.30   1.5240
+ IC    O4'     C2'     *C1'    H1'         1.4137  108.71 -112.42  108.76   1.1146
+ IC    C1'     C3'     *C2'    H2''        1.5059  101.03  117.01  109.50   1.1181
+ IC    C2'     C4'     *C3'    H3'         1.5240  101.86  115.18  108.62   1.1109
+ IC    C3'     O4'     *C4'    H4'         1.5416  103.10 -116.67  109.24   1.1099
+ IC    C4'     O5'     *C5'    H5'         1.5508  113.85 -122.02  108.16   1.1124
+ IC    C4'     O5'     *C5'    H5''        1.5508  113.85  122.40  110.00   1.1166
+PATC  FIRS NONE LAST NONE
+
+
+RESI ADP         -3.00  ! adenosine diphosphate, jjp1/adm jr.
+                        ! atom names correspond to pdb nomenclature
+GROUP
+ATOM C4'  CN7     0.16  !                       H61  H62
+ATOM H4'  HN7     0.09  !                         \  /
+ATOM O4'  ON6B   -0.50  !                          N6
+ATOM C1'  CN7B    0.16  !                          |
+ATOM H1'  HN7     0.09  !                          C6
+GROUP                   !                        //  \
+ATOM C5   CN5     0.28  !                        N1   C5--N7\\
+ATOM N7   NN4    -0.71  !                        |    ||     C8-H8
+ATOM C8   CN4     0.34  !                        C2   C4--N9/
+ATOM H8   HN3     0.12  !                       / \\ /     \
+ATOM N9   NN2    -0.05  !                     H2   N3       \
+                        !                                    \
+ATOM N1   NN3A   -0.74  !                                     \
+ATOM C2   CN4     0.50  !                                      \
+ATOM H2   HN3     0.13  !           O3B    O1A    H5' H4'  O4'  \
+ATOM N3   NN3A   -0.75  !           |       |      |    \ /   \  \
+ATOM C4   CN5     0.43  !      O1B=PB-O3A--PA-O5'-C5'---C4'    C1'
+ATOM C6   CN2     0.46  !           |       |      |     \     / \
+                        !           O2B    O2A    H5''   C3'--C2' H1'
+ATOM N6   NN1    -0.77  !                               / \   / \
+ATOM H61  HN1     0.38  !                            O3' H3' O2' H2''
+ATOM H62  HN1     0.38  !                             |       |
+GROUP                   !                            H3T     H2'
+ATOM C2'  CN7B    0.14  !
+ATOM H2'' HN7     0.09
+ATOM O2'  ON5    -0.66
+ATOM H2'  HN5     0.43
+GROUP
+ATOM C3'  CN7     0.14
+ATOM H3'  HN7     0.09
+ATOM O3'  ON5    -0.66
+ATOM H3T  HN5     0.43
+GROUP
+ATOM C5'  CN8B   -0.08
+ATOM H5'  HN8     0.09
+ATOM H5'' HN8     0.09
+ATOM O5'  ON2    -0.62
+ATOM PA   P       1.50
+ATOM O1A  ON3    -0.82
+ATOM O2A  ON3    -0.82
+ATOM O3A  ON2    -0.74
+ATOM PB   P3      1.10
+ATOM O1B  ON3    -0.90
+ATOM O2B  ON3    -0.90
+ATOM O3B  ON3    -0.90
+
+BOND PB   O3A       PB   O1B       PB    O2B      PB   O3B       O3A  PA
+BOND PA   O1A       PA   O2A       PA    O5'      O3'  H3T
+BOND O5'  C5'       C5'  C4'       C4'  O4'       C4'  C3'       O4'  C1'
+BOND C1'  N9        C1'  C2'       N9   C4        N9   C8        C4   N3
+BOND C2   N1        C6   N6
+BOND N6   H61       N6   H62       C6   C5        C5   N7
+BOND C2'  C3'       C2'  O2'       O2'  H2'       C3'  O3'
+BOND C1'  H1'       C2'  H2''      C3'  H3'       C4'  H4'       C5'  H5'
+BOND C5'  H5''      C8   H8        C2   H2
+DOUBLE N1   C6    N3   C2    C4   C5        N7   C8
+IMPR N6   C6   H61  H62       C6   N1   C5   N6        
+DONO H61  N6
+DONO H62  N6
+DONO H2'  O2'
+ACCE N3
+ACCE N7
+ACCE N1
+ACCE O1A  PA
+ACCE O2A  PA
+ACCE O2'
+ACCE O3'
+ACCE O4'
+ACCE O5'
+ACCE O3A
+ACCE O3B
+ACCE O2B
+ACCE O1B
+
+ IC    C5'     O5'     PA      O1A         1.4410  122.32   87.94  100.49   1.4886
+ IC    C5'     O5'     PA      O2A         1.4410  122.32  -34.46  103.58   1.4860
+ IC    O1A     O2A     *PA     O3A         1.4886  117.99 -144.34  113.98   1.5239
+ IC    O5'     PA      O3A     PB          1.5958   98.37 -161.33  117.20   1.6142
+ IC    PA      O3A     PB      O1B         1.5239  117.20  -40.60  110.60   1.5279
+ IC    O3A     PB      *O1B    O2B         2.5838   35.79 -113.37   34.28   2.5253
+ IC    O3A     PB      *O1B    O3B         2.5838   35.79  119.13   32.99   2.5605
+ IC    PA      O5'     C5'     C4'         1.5958  122.32  -51.67  114.79   1.5447
+ IC    O5'     C5'     C4'     C3'         1.4410  114.79  -58.82  120.15   1.5575
+ IC    C5'     C4'     C3'     O3'         1.5447  120.15   24.57  114.35   1.4341
+ IC    H3T     O3'     C3'     C4'         0.9993  106.88   49.50  114.35   1.5575
+ IC    O4'     C3'     *C4'    C5'         1.4692  104.72 -123.02  120.15   1.5447
+ IC    C2'     C4'     *C3'    O3'         1.5185  103.84  123.29  114.35   1.4341
+ IC    C4'     C3'     C2'     C1'         1.5575  103.84  -34.69  100.67   1.5216
+ IC    C3'     C2'     C1'     N9          1.5185  100.67  159.08  113.67   1.4641
+ IC    O4'     C1'     N9      C4          1.4113  111.63 -130.55  127.26   1.3686
+ IC    C1'     C4      *N9     C8          1.4641  127.26  179.24  106.16   1.3741
+ IC    C4      N9      C8      N7          1.3686  106.16    0.49  113.56   1.3167
+ IC    C8      N9      C4      C5          1.3741  106.16   -0.36  105.63   1.3838
+ IC    C8      N7      C5      C6          1.3167  103.56 -179.38  131.99   1.4088
+ IC    N7      C5      C6      N1          1.3861  131.99  179.37  118.17   1.3553
+ IC    C5      C6      N1      C2          1.4088  118.17    0.12  117.88   1.3365
+ IC    N9      C5      *C4     N3          1.3686  105.63 -179.47  126.53   1.3462
+ IC    C5      N1      *C6     N6          1.4088  118.17  179.95  118.70   1.3458
+ IC    N1      C6      N6      H61         1.3553  118.70    0.02  117.62   0.9928
+ IC    H61     C6      *N6     H62         0.9928  117.62 -177.97  120.15   0.9969
+ IC    C5      N1      *C6     N6          1.4088  118.17  179.95  118.70   1.3458
+ IC    N1      C6      N6      H61         1.3553  118.70    0.02  117.62   0.9928
+ IC    H61     C6      *N6     H62         0.9928  117.62 -177.97  120.15   0.9969
+ IC    N9      N7      *C8     H8          1.3741  113.56 -179.64  125.94   1.0936
+ IC    N1      N3      *C2     H2          1.3365  129.74  179.76  115.01   1.0933
+ IC    C1'     C3'     *C2'    O2'         1.5216  100.67  120.50  109.82   1.4183
+ IC    H2'     O2'     C2'     C3'         0.9782  102.50   14.41  109.82   1.5185
+ IC    O4'     C2'     *C1'    H1'         1.4113  108.03 -113.14  108.10   1.1140
+ IC    C1'     C3'     *C2'    H2''        1.5216  100.67 -117.81  110.45   1.1106
+ IC    C2'     C4'     *C3'    H3'         1.5185  103.84 -116.26  105.90   1.1117
+ IC    C3'     O4'     *C4'    H4'         1.5575  104.72 -113.29  107.42   1.1138
+ IC    C4'     O5'     *C5'    H5'         1.5447  114.79 -121.61  108.15   1.1098
+ IC    C4'     O5'     *C5'    H5''        1.5447  114.79  121.78  108.81   1.1138
+PATC  FIRS NONE LAST NONE
+
+RESI ATP         -4.00  !adenosine triphosphate , jjp1/adm jr.
+                        !atom names correspond to pdb nomenclature
+                        !
+GROUP
+ATOM C4'  CN7     0.16  !                       H61  H62
+ATOM H4'  HN7     0.09  !                         \  /
+ATOM O4'  ON6B   -0.50  !                          N6
+ATOM C1'  CN7B    0.16  !                          |
+ATOM H1'  HN7     0.09  !                          C6
+GROUP                   !                        //  \
+ATOM C5   CN5     0.28  !                        N1   C5--N7\\
+ATOM N7   NN4    -0.71  !                        |    ||     C8-H8
+ATOM C8   CN4     0.34  !                        C2   C4--N9/
+ATOM H8   HN3     0.12  !                       / \\ /     \
+ATOM N9   NN2    -0.05  !                     H2   N3       \
+                        !                                    \
+ATOM N1   NN3A   -0.74  !                                     \
+ATOM C2   CN4     0.50  !                                      \
+ATOM H2   HN3     0.13  ! (-)O3G   O2B     O1A    H5' H4'  O4'  \
+ATOM N3   NN3A   -0.75  !    |      |       |      |    \ /   \  \
+ATOM C4   CN5     0.43  !O1G=PG-O3B-PB-O3A-PA-O5'-C5'---C4'    C1'
+ATOM C6   CN2     0.46  !    |      |       |      |     \     / \
+                        ! (-)O2G (-)O1B (-)O2A    H5''   C3'--C2' H1'
+ATOM N6   NN1    -0.77  !                               / \   / \
+ATOM H61  HN1     0.38  !                            O3' H3' O2' H2''
+ATOM H62  HN1     0.38  !                             |       |
+GROUP                   !                            H3T     H2'
+ATOM C2'  CN7B    0.14  !
+ATOM H2'' HN7     0.09
+ATOM O2'  ON5    -0.66
+ATOM H2'  HN5     0.43
+GROUP
+ATOM C3'  CN7     0.14
+ATOM H3'  HN7     0.09
+ATOM O3'  ON5    -0.66
+ATOM H3T  HN5     0.43
+GROUP
+ATOM C5'  CN8B   -0.08
+ATOM H5'  HN8     0.09
+ATOM H5'' HN8     0.09
+ATOM O5'  ON2    -0.62
+ATOM PA   P       1.50
+ATOM O1A  ON3    -0.82
+ATOM O2A  ON3    -0.82
+ATOM O3A  ON2    -0.74
+ATOM PB   P3      1.50
+ATOM O1B  ON3    -0.82
+ATOM O2B  ON3    -0.82
+ATOM O3B  ON2    -0.86 ! charge adjusted to yield total triP of -4.0
+ATOM PG   P3      1.10
+ATOM O1G  ON3    -0.90
+ATOM O2G  ON3    -0.90
+ATOM O3G  ON3    -0.90
+
+BOND O5'  C5'       O5'  PA        PA   O1A       PA   O2A       PA   O3A
+BOND O3A  PB        PB   O1B       PB   O2B       PB   O3B       O3B  PG
+BOND PG   O1G       PG   O2G       PG   O3G
+BOND C5'  C4'       C4'  O4'       C4'  C3'       O4'  C1'
+BOND C1'  N9        C1'  C2'       N9   C4        N9   C8        C4   N3
+BOND C2   N1        C6   N6
+BOND N6   H61       N6   H62       C6   C5        C5   N7
+BOND C2'  C3'       C2'  O2'       O2'  H2'       C3'  O3'       O3'  H3T
+BOND C1'  H1'       C2'  H2''      C3'  H3'       C4'  H4'       C5'  H5'
+BOND C5'  H5''      C8   H8        C2   H2
+DOUBLE N1   C6    N3   C2    C4   C5        N7   C8
+IMPR N6   C6   H61  H62       C6   N1   C5   N6       
+DONO H61  N6
+DONO H62  N6
+DONO H2'  O2'
+ACCE N3
+ACCE N7
+ACCE N1
+ACCE O1A  PA
+ACCE O2A  PA
+ACCE O2'
+ACCE O3'
+ACCE O4'
+ACCE O5'
+ACCE O3A
+ACCE O2B
+ACCE O1B
+ACCE O3B
+ACCE O3G
+ACCE O2G
+ACCE O2G
+
+ IC    C5'     O5'     PA      O1A         1.4378  121.47   77.19  100.91   1.4899
+ IC    C5'     O5'     PA      O2A         1.4378  121.47  -44.89  102.27   1.4823
+ IC    O1A     O2A     *PA     O3A         1.4899  117.99 -149.47  116.28   1.5095
+ IC    O5'     PA      O3A     PB          1.5970   94.16 -172.73  101.71   1.6154
+ IC    PA      O3A     PB      O1B         1.5095  101.71   72.81  111.02   1.5359
+ IC    O3A     PB      *O1B    O2B         2.5978   35.48 -133.09   31.39   2.6245
+ IC    O3A     PB      *O1B    O3B         2.5978   35.48  104.92   37.93   2.6047
+ IC    O3A     PB      O3B     PG          1.6154   96.78 -173.49  154.12   1.6853
+ IC    PA      O3B     PG      O1G         3.7941  178.28 -151.96  107.36   1.5287
+ IC    O3B     PG      *O1G    O2G         2.5914   38.37 -116.07   33.82   2.5436
+ IC    O3B     PG      *O1G    O3G         2.5914   38.37  116.49   33.72   2.5459
+ IC    PA      O5'     C5'     C4'         1.5970  121.47  -80.85  111.25   1.5321
+ IC    O5'     C5'     C4'     C3'         1.4378  111.25  -31.77  117.04   1.5487
+ IC    O5'     C5'     C4'     C3'         1.4378  111.25  -31.77  117.04   1.5487
+ IC    C5'     C4'     C3'     O3'         1.5321  117.04  114.00  111.81   1.4379
+ IC    H3T     O3'     C3'     C4'         1.0005  103.99  -64.58  111.81   1.5487
+ IC    O4'     C3'     *C4'    C5'         1.4622  104.95 -122.79  117.04   1.5321
+ IC    C2'     C4'     *C3'    O3'         1.5314  104.67 -124.46  111.81   1.4379
+ IC    C4'     C3'     C2'     C1'         1.5487  104.67  -23.03  101.91   1.5055
+ IC    C3'     C2'     C1'     N9          1.5314  101.91  158.43  111.95   1.4582
+ IC    O4'     C1'     N9      C4          1.4051  110.48 -119.72  127.77   1.3720
+ IC    C1'     C4      *N9     C8          1.4582  127.77 -179.09  106.11   1.3733
+ IC    C4      N9      C8      N7          1.3720  106.11   -0.75  113.74   1.3140
+ IC    C8      N9      C4      C5          1.3733  106.11    0.64  105.48   1.3837
+ IC    C8      N7      C5      C6          1.3140  103.52  179.77  131.85   1.4097
+ IC    N7      C5      C6      N1          1.3877  131.85 -179.91  118.18   1.3551
+ IC    C5      C6      N1      C2          1.4097  118.18    0.04  117.81   1.3370
+ IC    N9      C5      *C4     N3          1.3720  105.48 -179.86  126.34   1.3449
+ IC    C5      N1      *C6     N6          1.4097  118.18  179.89  118.87   1.3458
+ IC    N1      C6      N6      H61         1.3551  118.87   -0.85  117.73   0.9931
+ IC    H61     C6      *N6     H62         0.9931  117.73 -179.14  119.98   0.9966
+ IC    C5      N1      *C6     N6          1.4097  118.18  179.89  118.87   1.3458
+ IC    N1      C6      N6      H61         1.3551  118.87   -0.85  117.73   0.9931
+ IC    H61     C6      *N6     H62         0.9931  117.73 -179.14  119.98   0.9966
+ IC    N9      N7      *C8     H8          1.3733  113.74 -179.49  125.37   1.0933
+ IC    N1      N3      *C2     H2          1.3370  129.70 -179.80  114.84   1.0933
+ IC    C1'     C3'     *C2'    O2'         1.5055  101.91 -119.05  111.28   1.4120
+ IC    H2'     O2'     C2'     C3'         0.9769  102.12    8.83  111.28   1.5314
+ IC    O4'     C2'     *C1'    H1'         1.4051  105.32 -114.88  110.01   1.1152
+ IC    C1'     C3'     *C2'    H2''        1.5055  101.91  118.84  108.68   1.1120
+ IC    C2'     C4'     *C3'    H3'         1.5314  104.67  115.81  108.72   1.1136
+ IC    C3'     O4'     *C4'    H4'         1.5487  104.95 -114.27  108.43   1.1139
+ IC    C4'     O5'     *C5'    H5'         1.5321  111.25 -119.46  107.24   1.1108
+ IC    C4'     O5'     *C5'    H5''        1.5321  111.25  123.64  111.88   1.1145
+PATC  FIRS NONE LAST NONE
+
+!guanine nucleotides
+RESI GMP         -2.00  ! guanine monophosphate, adm jr.
+                        ! atom names correspond to pdb nomenclature
+GROUP
+ATOM C4'  CN7     0.16  !                      O6
+ATOM H4'  HN7     0.09  !                      ||
+ATOM O4'  ON6B   -0.50  !                      C6
+ATOM C1'  CN7B    0.16  !                     /  \
+ATOM H1'  HN7     0.09  !                 H1-N1   C5--N7\\
+GROUP                   !                    |    ||     C8-H8
+ATOM N9   NN2B   -0.02  !                    C2   C4--N9/
+ATOM C4   CN5     0.26  !                   / \\ /      \
+ATOM N2   NN1    -0.68  !             H21-N2   N3        \
+ATOM H21  HN1     0.32  !                 |               \
+ATOM H22  HN1     0.35  !                H22               \
+ATOM N3   NN3G   -0.74  !                                   \
+ATOM C2   CN2     0.75  !        O3B    O1A    H5' H4'  O4'  \
+ATOM N1   NN2G   -0.34  !        |       |      |    \ /   \  \
+ATOM H1   HN2     0.26  !   O1B=PB-O3A--PA-O5'-C5'---C4'    C1'
+ATOM C6   CN1     0.54  !        |       |      |     \     / \
+ATOM O6   ON1    -0.51  !        O2B    O2A    H5''   C3'--C2' H1'
+ATOM C5   CN5G    0.00  !                            / \   / \
+ATOM N7   NN4    -0.60  !                         O3' H3' O2' H2''
+ATOM C8   CN4     0.25  !                          |       |
+ATOM H8   HN3     0.16  !                         H3T     H2'
+GROUP                 
+ATOM C2'  CN7B    0.14
+ATOM H2'' HN7     0.09
+ATOM O2'  ON5    -0.66
+ATOM H2'  HN5     0.43
+GROUP
+ATOM C3'  CN7     0.14
+ATOM H3'  HN7     0.09
+ATOM O3'  ON5    -0.66
+ATOM H3T  HN5     0.43
+GROUP
+ATOM C5'  CN8B   -0.18
+ATOM H5'  HN8     0.09
+ATOM H5'' HN8     0.09
+GROUP
+ATOM O5'  ON2    -0.40
+ATOM PA   P       1.10
+ATOM O1A  ON3    -0.90
+ATOM O2A  ON3    -0.90
+ATOM O3A  ON3    -0.90
+
+BOND N9   C4        N9   C8        C4   N3        N3   C2
+BOND C2   N1        N1   C6        C6   C5        C5   N7
+BOND C4   C5        N7   C8        C6   O6        C8   H8
+BOND C2   N2        N2   H21       N2   H22       N1   H1
+BOND C1'  N9        C1'  C2'       
+BOND PA   O1A       PA   O2A       PA   O3A       PA   O5'       O3'  H3T
+BOND O5'  C5'       C5'  C4'       C4'  O4'       C4'  C3'       O4'  C1'
+BOND C2'  C3'       C2'  O2'       O2'  H2'       C3'  O3'
+BOND C1'  H1'       C2'  H2''      C3'  H3'       C4'  H4'       C5'  H5'
+BOND C5'  H5''     
+
+IMPR C2   N3   N1   N2        C6   N1   C5   O6        N2   H21  C2   H22
+
+DONO H21  N2            
+DONO H22  N2   
+DONO H1   N1   
+DONO H2'  O2'
+ACCE O6   C6         
+ACCE N3
+ACCE N7
+ACCE O1A  PA
+ACCE O2A  PA
+ACCE O3A  PA
+ACCE O2'
+ACCE O3'
+ACCE O4'
+ACCE O5'
+
+ IC    C5'     O5'     PA      O1A         1.4449  117.42   52.17  105.04   1.4828
+ IC    C5'     O5'     PA      O2A         1.4449  117.42  -67.15  104.81   1.4806
+ IC    O1A     O2A     *PA     O3A         1.4828  113.00 -131.19  113.56   1.4790
+ IC    PA      O5'     C5'     C4'         1.5977  117.42  162.15  110.69   1.5276
+ IC    O5'     C5'     C4'     C3'         1.4449  110.69 -168.25  111.34   1.5446
+ IC    C5'     C4'     C3'     O3'         1.5276  111.34  144.97  115.23   1.4384
+ IC    H3T     O3'     C3'     C4'         0.9628  104.75  161.01  115.23   1.5446
+ IC    O4'     C3'     *C4'    C5'         1.4655  104.84 -120.73  111.34   1.5276
+ IC    C2'     C4'     *C3'    O3'         1.5224  102.02 -121.78  115.23   1.4384
+ IC    C4'     C3'     C2'     C1'         1.5446  102.02  -39.49   99.95   1.5059
+ IC    C3'     C2'     C1'     N9          1.5224   99.95  163.39  112.13   1.4653
+ IC    O4'     C1'     N9      C4          1.4081  112.64 -161.94  125.06   1.3695
+ IC    C1'     C4      *N9     C8          1.4653  125.06  179.61  106.74   1.3780
+ IC    C4      N9      C8      N7          1.3695  106.74    1.12  112.45   1.3168
+ IC    C8      N9      C4      C5          1.3780  106.74   -1.48  105.61   1.3806
+ IC    N9      C5      *C4     N3          1.3695  105.61  179.30  128.48   1.3512
+ IC    C5      C4      N3      C2          1.3806  128.48   -5.38  112.09   1.3200
+ IC    C4      N3      C2      N1          1.3512  112.09    3.91  123.88   1.3723
+ IC    N1      N3      *C2     N2          1.3723  123.88  179.31  119.43   1.3225
+ IC    N3      C2      N2      H21         1.3200  119.43  175.82  123.65   0.9906
+ IC    H21     C2      *N2     H22         0.9906  123.65 -173.52  114.75   0.9960
+ IC    N3      C2      N1      C6          1.3200  123.88   -1.31  125.17   1.3919
+ IC    C6      C2      *N1     H1          1.3919  125.17 -178.04  119.92   0.9977
+ IC    C5      N1      *C6     O6          1.4225  111.56 -179.99  119.10   1.2332
+ IC    N9      N7      *C8     H8          1.3780  112.45 -179.50  126.25   1.0962
+ IC    C1'     C3'     *C2'    O2'         1.5059   99.95 -118.94  112.61   1.4256
+ IC    H2'     O2'     C2'     C3'         0.9721  107.31  151.43  112.61   1.5224
+ IC    O4'     C2'     *C1'    H1'         1.4081  106.93 -113.28  109.47   1.1132
+ IC    C1'     C3'     *C2'    H2''        1.5059   99.95  116.92  109.70   1.1151
+ IC    C2'     C4'     *C3'    H3'         1.5224  102.02  115.92  107.85   1.1103
+ IC    C3'     O4'     *C4'    H4'         1.5446  104.84 -117.41  110.00   1.1117
+ IC    C4'     O5'     *C5'    H5'         1.5276  110.69 -119.42  109.72   1.1174
+ IC    C4'     O5'     *C5'    H5''        1.5276  110.69  122.86  109.05   1.1107
+PATC  FIRS NONE LAST NONE
+
+RESI GDP         -3.00  ! guanine diphosphate, adm jr.
+                        ! atom names correspond to pdb nomenclature
+GROUP
+ATOM C4'  CN7     0.16  !                      O6
+ATOM H4'  HN7     0.09  !                      ||
+ATOM O4'  ON6B   -0.50  !                      C6
+ATOM C1'  CN7B    0.16  !                     /  \
+ATOM H1'  HN7     0.09  !                 H1-N1   C5--N7\\
+GROUP                   !                    |    ||     C8-H8
+ATOM N9   NN2B   -0.02  !                    C2   C4--N9/
+ATOM C4   CN5     0.26  !                   / \\ /      \
+ATOM N2   NN1    -0.68  !             H21-N2   N3        \
+ATOM H21  HN1     0.32  !                 |               \
+ATOM H22  HN1     0.35  !                H22               \
+ATOM N3   NN3G   -0.74  !                                   \
+ATOM C2   CN2     0.75  !        O3B    O1A    H5' H4'  O4'  \
+ATOM N1   NN2G   -0.34  !        |       |      |    \ /   \  \
+ATOM H1   HN2     0.26  !   O1B=PB-O3A--PA-O5'-C5'---C4'    C1'
+ATOM C6   CN1     0.54  !        |       |      |     \     / \
+ATOM O6   ON1    -0.51  !        O2B    O2A    H5''   C3'--C2' H1'
+ATOM C5   CN5G    0.00  !                            / \   / \
+ATOM N7   NN4    -0.60  !                         O3' H3' O2' H2''
+ATOM C8   CN4     0.25  !                          |       |
+ATOM H8   HN3     0.16  !                         H3T     H2'
+GROUP
+ATOM C2'  CN7B    0.14
+ATOM H2'' HN7     0.09
+ATOM O2'  ON5    -0.66
+ATOM H2'  HN5     0.43
+GROUP
+ATOM C3'  CN7     0.14
+ATOM H3'  HN7     0.09
+ATOM O3'  ON5    -0.66
+ATOM H3T  HN5     0.43
+GROUP
+ATOM C5'  CN8B   -0.08
+ATOM H5'  HN8     0.09
+ATOM H5'' HN8     0.09
+ATOM O5'  ON2    -0.62
+ATOM PA   P       1.50
+ATOM O1A  ON3    -0.82
+ATOM O2A  ON3    -0.82
+ATOM O3A  ON2    -0.74
+ATOM PB   P3      1.10
+ATOM O1B  ON3    -0.90
+ATOM O2B  ON3    -0.90
+ATOM O3B  ON3    -0.90
+
+BOND N9   C4        N9   C8        C4   N3        N3   C2
+BOND C2   N1        N1   C6        C6   C5        C5   N7
+BOND C4   C5        N7   C8        C6   O6        C8   H8
+BOND C2   N2        N2   H21       N2   H22       N1   H1
+BOND C1'  N9        C1'  C2'       
+BOND PB   O3A       PB   O1B       PB    O2B      PB   O3B       O3A  PA
+BOND PA   O1A       PA   O2A       PA    O5'      O3'  H3T
+BOND O5'  C5'       C5'  C4'       C4'  O4'       C4'  C3'       O4'  C1'
+BOND C2'  C3'       C2'  O2'       O2'  H2'       C3'  O3'
+BOND C1'  H1'       C2'  H2''      C3'  H3'       C4'  H4'       C5'  H5'
+BOND C5'  H5''
+
+IMPR C2   N3   N1   N2        C6   N1   C5   O6        N2   H21  C2   H22
+
+DONO H21  N2            
+DONO H22  N2   
+DONO H1   N1   
+DONO H2'  O2'
+ACCE O6   C6         
+ACCE N3
+ACCE N7
+ACCE O1A  PA
+ACCE O2A  PA
+ACCE O2'
+ACCE O3'
+ACCE O4'
+ACCE O5'
+ACCE O3A
+ACCE O3B
+ACCE O2B
+ACCE O1B
+
+ IC    C5'     O5'     PA      O1A         1.4413  122.93   91.71  100.28   1.4877
+ IC    C5'     O5'     PA      O2A         1.4413  122.93  -30.68  103.81   1.4867
+ IC    O1A     O2A     *PA     O3A         1.4877  117.98 -144.37  113.97   1.5234
+ IC    O5'     PA      O3A     PB          1.5946   98.34 -162.17  116.89   1.6138
+ IC    PA      O3A     PB      O1B         1.5234  116.89  -41.55  110.65   1.5281
+ IC    O3A     PB      *O1B    O2B         2.5844   35.75 -113.28   34.27   2.5257
+ IC    O3A     PB      *O1B    O3B         2.5844   35.75  119.32   33.00   2.5600
+ IC    PA      O5'     C5'     C4'         1.5946  122.93  -50.51  114.80   1.5441
+ IC    O5'     C5'     C4'     C3'         1.4413  114.80  -52.35  122.03   1.5606
+ IC    C5'     C4'     C3'     O3'         1.5441  122.03    8.61  113.75   1.4344
+ IC    H3T     O3'     C3'     C4'         0.9971  105.35   57.55  113.75   1.5606
+ IC    O4'     C3'     *C4'    C5'         1.4660  105.23 -126.40  122.03   1.5441
+ IC    C2'     C4'     *C3'    O3'         1.5255  104.77  124.76  113.75   1.4344
+ IC    C4'     C3'     C2'     C1'         1.5606  104.77  -28.98  100.20   1.5185
+ IC    C3'     C2'     C1'     N9          1.5255  100.20  165.88  114.82   1.4718
+ IC    O4'     C1'     N9      C4          1.4065  112.89 -112.42  126.14   1.3705
+ IC    C1'     C4      *N9     C8          1.4718  126.14 -179.09  106.47   1.3755
+ IC    C4      N9      C8      N7          1.3705  106.47   -0.36  113.07   1.3168
+ IC    C8      N9      C4      C5          1.3755  106.47    0.03  105.56   1.3833
+ IC    N9      C5      *C4     N3          1.3705  105.56  179.81  128.27   1.3494
+ IC    C5      C4      N3      C2          1.3833  128.27   -3.62  112.43   1.3156
+ IC    C4      N3      C2      N1          1.3494  112.43    3.08  123.80   1.3729
+ IC    N1      N3      *C2     N2          1.3729  123.80  179.83  119.72   1.3235
+ IC    N3      C2      N2      H21         1.3156  119.72    3.65  114.36   0.9968
+ IC    H21     C2      *N2     H22         0.9968  114.36  165.67  123.15   0.9891
+ IC    N3      C2      N1      C6          1.3156  123.80   -1.16  125.17   1.3916
+ IC    C6      C2      *N1     H1          1.3916  125.17 -180.00  119.89   0.9970
+ IC    C5      N1      *C6     O6          1.4212  111.57 -179.85  119.32   1.2334
+ IC    N9      N7      *C8     H8          1.3755  113.07  179.83  125.93   1.0925
+ IC    C1'     C3'     *C2'    O2'         1.5185  100.20  120.66  109.78   1.4177
+ IC    H2'     O2'     C2'     C3'         0.9775  101.98   11.65  109.78   1.5255
+ IC    O4'     C2'     *C1'    H1'         1.4065  106.83 -111.81  107.72   1.1143
+ IC    C1'     C3'     *C2'    H2''        1.5185  100.20 -117.60  110.39   1.1104
+ IC    C2'     C4'     *C3'    H3'         1.5255  104.77 -116.17  105.28   1.1124
+ IC    C3'     O4'     *C4'    H4'         1.5606  105.23 -111.13  105.99   1.1140
+ IC    C4'     O5'     *C5'    H5'         1.5441  114.80 -121.03  108.08   1.1104
+ IC    C4'     O5'     *C5'    H5''        1.5441  114.80  122.15  109.04   1.1132
+PATC  FIRS NONE LAST NONE
+
+RESI GTP         -4.00  !guanine triphosphate , adm jr.
+                        !atom names correspond to pdb nomenclature
+                        !
+ATOM C4'  CN7     0.16  !                      O6
+ATOM H4'  HN7     0.09  !                      ||
+ATOM O4'  ON6B   -0.50  !                      C6
+ATOM C1'  CN7B    0.16  !                     /  \
+ATOM H1'  HN7     0.09  !                 H1-N1   C5--N7\\
+GROUP                   !                    |    ||     C8-H8
+ATOM N9   NN2B   -0.02  !                    C2   C4--N9/
+ATOM C4   CN5     0.26  !                   / \\ /      \
+ATOM N2   NN1    -0.68  !             H21-N2   N3        \
+ATOM H21  HN1     0.32  !                 |               \
+ATOM H22  HN1     0.35  !                H22               \
+ATOM N3   NN3G   -0.74  !                                   \
+ATOM C2   CN2     0.75  !        O3B    O1A    H5' H4'  O4'  \
+ATOM N1   NN2G   -0.34  !        |       |      |    \ /   \  \
+ATOM H1   HN2     0.26  !   O1B=PB-O3A--PA-O5'-C5'---C4'    C1'
+ATOM C6   CN1     0.54  !        |       |      |     \     / \
+ATOM O6   ON1    -0.51  !        O2B    O2A    H5''   C3'--C2' H1'
+ATOM C5   CN5G    0.00  !                            / \   / \
+ATOM N7   NN4    -0.60  !                         O3' H3' O2' H2''
+ATOM C8   CN4     0.25  !                          |       |
+ATOM H8   HN3     0.16  !                         H3T     H2'
+GROUP
+ATOM C2'  CN7B    0.14
+ATOM H2'' HN7     0.09
+ATOM O2'  ON5    -0.66
+ATOM H2'  HN5     0.43
+GROUP
+ATOM C3'  CN7     0.14
+ATOM H3'  HN7     0.09
+ATOM O3'  ON5    -0.66
+ATOM H3T  HN5     0.43
+GROUP
+ATOM C5'  CN8B   -0.08
+ATOM H5'  HN8     0.09
+ATOM H5'' HN8     0.09
+ATOM O5'  ON2    -0.62
+ATOM PA   P       1.50
+ATOM O1A  ON3    -0.82
+ATOM O2A  ON3    -0.82
+ATOM O3A  ON2    -0.74
+ATOM PB   P3      1.50
+ATOM O1B  ON3    -0.82
+ATOM O2B  ON3    -0.82
+ATOM O3B  ON2    -0.86 ! charge adjusted to yield total triP of -4.0
+ATOM PG   P3      1.10
+ATOM O1G  ON3    -0.90
+ATOM O2G  ON3    -0.90
+ATOM O3G  ON3    -0.90
+
+BOND N9   C4        N9   C8        C4   N3        N3   C2
+BOND C2   N1        N1   C6        C6   C5        C5   N7
+BOND C4   C5        N7   C8        C6   O6        C8   H8
+BOND C2   N2        N2   H21       N2   H22       N1   H1
+BOND C1'  N9        C1'  C2'       
+BOND O5'  C5'       O5'  PA        PA   O1A       PA   O2A       PA   O3A
+BOND O3A  PB        PB   O1B       PB   O2B       PB   O3B       O3B  PG
+BOND PG   O1G       PG   O2G       PG   O3G
+BOND C5'  C4'       C4'  O4'       C4'  C3'       O4'  C1'
+BOND C2'  C3'       C2'  O2'       O2'  H2'       C3'  O3'       O3'  H3T
+BOND C1'  H1'       C2'  H2''      C3'  H3'       C4'  H4'       C5'  H5'
+BOND C5'  H5''
+
+IMPR C2   N3   N1   N2        C6   N1   C5   O6        N2   H21  C2   H22
+
+DONO H21  N2            
+DONO H22  N2   
+DONO H1   N1   
+DONO H2'  O2'
+ACCE O6   C6         
+ACCE N3
+ACCE N7
+ACCE O1A  PA
+ACCE O2A  PA
+ACCE O2'
+ACCE O3'
+ACCE O4'
+ACCE O5'
+ACCE O3A
+ACCE O2B
+ACCE O1B
+ACCE O3B
+ACCE O3G
+ACCE O2G
+ACCE O2G
+
+ IC    C5'     O5'     PA      O1A         1.4386  121.55   77.89  100.89   1.4893
+ IC    C5'     O5'     PA      O2A         1.4386  121.55  -44.16  102.34   1.4826
+ IC    O1A     O2A     *PA     O3A         1.4893  117.94 -149.15  116.36   1.5099
+ IC    O5'     PA      O3A     PB          1.5972   94.38 -173.25  101.74   1.6158
+ IC    PA      O3A     PB      O1B         1.5099  101.74   71.90  111.32   1.5358
+ IC    O3A     PB      *O1B    O2B         2.6028   35.33 -132.99   31.41   2.6238
+ IC    O3A     PB      *O1B    O3B         2.6028   35.33  105.17   37.87   2.6059
+ IC    O3A     PB      O3B     PG          1.6158   96.85 -169.20  153.75   1.6849
+ IC    PA      O3B     PG      O1G         3.7962  176.66 -118.03  107.34   1.5288
+ IC    O3B     PG      *O1G    O2G         2.5907   38.37 -115.96   33.86   2.5425
+ IC    O3B     PG      *O1G    O3G         2.5907   38.37  116.61   33.69   2.5467
+ IC    PA      O5'     C5'     C4'         1.5972  121.55  -79.94  111.03   1.5309
+ IC    O5'     C5'     C4'     C3'         1.4386  111.03  -34.44  116.91   1.5495
+ IC    O5'     C5'     C4'     C3'         1.4386  111.03  -34.44  116.91   1.5495
+ IC    C5'     C4'     C3'     O3'         1.5309  116.91  113.16  111.77   1.4390
+ IC    H3T     O3'     C3'     C4'         1.0011  104.38  -62.53  111.77   1.5495
+ IC    O4'     C3'     *C4'    C5'         1.4621  104.76 -123.13  116.91   1.5309
+ IC    C2'     C4'     *C3'    O3'         1.5333  104.58 -124.03  111.77   1.4390
+ IC    C4'     C3'     C2'     C1'         1.5495  104.58  -23.65  101.32   1.5036
+ IC    C3'     C2'     C1'     N9          1.5333  101.32  162.27  112.43   1.4657
+ IC    O4'     C1'     N9      C4          1.4076  111.90 -129.15  126.74   1.3696
+ IC    C1'     C4      *N9     C8          1.4657  126.74  179.56  106.58   1.3750
+ IC    C4      N9      C8      N7          1.3696  106.58   -0.26  113.09   1.3154
+ IC    C8      N9      C4      C5          1.3750  106.58    0.48  105.46   1.3840
+ IC    N9      C5      *C4     N3          1.3696  105.46 -179.39  128.28   1.3485
+ IC    C5      C4      N3      C2          1.3840  128.28    2.26  112.50   1.3124
+ IC    C4      N3      C2      N1          1.3485  112.50   -1.89  123.91   1.3730
+ IC    N1      N3      *C2     N2          1.3730  123.91 -179.85  119.33   1.3219
+ IC    N3      C2      N2      H21         1.3124  119.33 -174.37  124.20   0.9897
+ IC    H21     C2      *N2     H22         0.9897  124.20  172.33  113.43   0.9968
+ IC    N3      C2      N1      C6          1.3124  123.91    0.72  125.11   1.3919
+ IC    C6      C2      *N1     H1          1.3919  125.11  179.82  119.77   0.9968
+ IC    C5      N1      *C6     O6          1.4216  111.58  179.91  119.39   1.2342
+ IC    N9      N7      *C8     H8          1.3750  113.09 -179.04  125.80   1.0922
+ IC    C1'     C3'     *C2'    O2'         1.5036  101.32 -118.99  110.95   1.4134
+ IC    H2'     O2'     C2'     C3'         0.9766  101.89    9.44  110.95   1.5333
+ IC    O4'     C2'     *C1'    H1'         1.4076  104.92 -114.02  109.46   1.1150
+ IC    C1'     C3'     *C2'    H2''        1.5036  101.32  118.43  109.28   1.1120
+ IC    C2'     C4'     *C3'    H3'         1.5333  104.58  116.08  108.56   1.1134
+ IC    C3'     O4'     *C4'    H4'         1.5495  104.76 -114.13  108.29   1.1140
+ IC    C4'     O5'     *C5'    H5'         1.5309  111.03 -119.42  107.43   1.1107
+ IC    C4'     O5'     *C5'    H5''        1.5309  111.03  123.45  111.83   1.1145
+PATC  FIRS NONE LAST NONE
+
+!cytosine nucleotides
+RESI CMP         -2.00  ! cytosine monophosphate, adm jr.
+                        ! atom names correspond to pdb nomenclature
+GROUP
+ATOM C4'  CN7     0.16  !                              H42  H41
+ATOM H4'  HN7     0.09  !                                \  /    
+ATOM O4'  ON6B   -0.50  !                                 N4
+ATOM C1'  CN7B    0.16  !                                 |
+ATOM H1'  HN7     0.09  !                                 C4
+GROUP                   !                                /  \\
+ATOM N1   NN2    -0.13  !                            H5-C5   N3
+ATOM C6   CN3     0.05  !                               ||   |
+ATOM H6   HN3     0.17  !                            H6-C6   C2
+ATOM C5   CN3    -0.13  !                                \  / \\
+ATOM H5   HN3     0.07  !                                 N1   O2
+ATOM C2   CN1     0.52  !                                  \
+ATOM O2   ON1C   -0.49  !                                   \
+ATOM N3   NN3    -0.66  !               O1A    H5' H4'  O4'  \
+ATOM C4   CN2     0.65  !                |      |    \ /   \  \
+ATOM N4   NN1    -0.75  !          O3A--PA-O5'-C5'---C4'    C1'
+ATOM H41  HN1     0.37  !                |      |     \     / \  
+ATOM H42  HN1     0.33  !               O2A    H5''   C3'--C2' H1'  
+GROUP                   !                            / \   / \
+ATOM C2'  CN7B    0.14  !                         O3' H3' O2' H2''
+ATOM H2'' HN7     0.09  !                          |       |
+ATOM O2'  ON5    -0.66  !                         H3T     H2'
+ATOM H2'  HN5     0.43
+GROUP
+ATOM C3'  CN7     0.14
+ATOM H3'  HN7     0.09
+ATOM O3'  ON5    -0.66
+ATOM H3T  HN5     0.43
+GROUP
+ATOM C5'  CN8B   -0.18
+ATOM H5'  HN8     0.09
+ATOM H5'' HN8     0.09
+GROUP
+ATOM O5'  ON2    -0.40
+ATOM PA   P       1.10
+ATOM O1A  ON3    -0.90
+ATOM O2A  ON3    -0.90
+ATOM O3A  ON3    -0.90
+
+BOND N1   C2        C2   N3        N3   C4        C4   C5
+BOND C5   C6        N1   C6
+BOND C4   N4        N4   H41       N4   H42
+BOND C2   O2        C5   H5        C6   H6
+BOND C1'  N1        C1'  C2'       
+BOND PA   O1A       PA   O2A       PA   O3A       PA   O5'       O3'  H3T
+BOND O5'  C5'       C5'  C4'       C4'  O4'       C4'  C3'       O4'  C1'
+BOND C2'  C3'       C2'  O2'       O2'  H2'       C3'  O3'
+BOND C1'  H1'       C2'  H2''      C3'  H3'       C4'  H4'       C5'  H5'
+BOND C5'  H5''     
+
+IMPR C2   N1   N3   O2        C4   N3   C5   N4
+IMPR N4   C4   H41  H42      
+
+DONO H2'  O2'
+DONO H41  N4   
+DONO H42  N4   
+ACCE O2   C2
+ACCE N3     
+ACCE O1A  PA
+ACCE O2A  PA
+ACCE O3A  PA
+ACCE O2'
+ACCE O3'
+ACCE O4'
+ACCE O5'
+
+ IC    C5'     O5'     PA      O1A         1.4355  125.73   29.84  105.66   1.4793
+ IC    C5'     O5'     PA      O2A         1.4355  125.73  -91.13  105.46   1.4775
+ IC    O1A     O2A     *PA     O3A         1.4793  113.93 -131.58  113.82   1.4809
+ IC    PA      O5'     C5'     C4'         1.5817  125.73 -106.56  114.58   1.5485
+ IC    O5'     C5'     C4'     C3'         1.4355  114.58   82.54  114.21   1.5385
+ IC    C5'     C4'     C3'     O3'         1.5485  114.21  139.15  113.65   1.4400
+ IC    H3T     O3'     C3'     C4'         0.9657  102.79  157.45  113.65   1.5385
+ IC    O4'     C3'     *C4'    C5'         1.4688  105.40 -125.30  114.21   1.5485
+ IC    C2'     C4'     *C3'    O3'         1.5240  103.66 -122.40  113.65   1.4400
+ IC    C4'     C3'     C2'     C1'         1.5385  103.66  -33.47  101.88   1.5143
+ IC    C3'     C2'     C1'     N1          1.5240  101.88  154.47  110.60   1.4866
+ IC    O4'     C1'     N1      C2          1.4277  113.60 -151.06  121.54   1.3966
+ IC    C1'     C2      *N1     C6          1.4866  121.54  167.48  119.36   1.3726
+ IC    C2      N1      C6      C5          1.3966  119.36    7.13  121.63   1.3363
+ IC    C6      N1      C2      N3          1.3726  119.36  -10.00  119.51   1.3602
+ IC    N1      N3      *C2     O2          1.3966  119.51 -178.93  121.39   1.2434
+ IC    N1      C2      N3      C4          1.3966  119.51    8.49  119.33   1.3427
+ IC    C5      N3      *C4     N4          1.4190  122.04  178.61  118.12   1.3332
+ IC    N3      C4      N4      H41         1.3427  118.12   -6.92  114.61   0.9924
+ IC    H41     C4      *N4     H42         0.9924  114.61 -157.30  119.69   0.9937
+ IC    C6      C4      *C5     H5          1.3363  117.43  176.45  120.96   1.0882
+ IC    N1      C5      *C6     H6          1.3726  121.63 -178.59  121.78   1.0892
+ IC    C1'     C3'     *C2'    O2'         1.5143  101.88 -119.06  112.57   1.4272
+ IC    H2'     O2'     C2'     C3'         0.9654  106.91  171.65  112.57   1.5240
+ IC    O4'     C2'     *C1'    H1'         1.4277  108.35 -113.18  108.73   1.1143
+ IC    C1'     C3'     *C2'    H2''        1.5143  101.88  117.56  108.68   1.1163
+ IC    C2'     C4'     *C3'    H3'         1.5240  103.66  115.28  107.93   1.1146
+ IC    C3'     O4'     *C4'    H4'         1.5385  105.40 -113.98  108.05   1.1106
+ IC    C4'     O5'     *C5'    H5'         1.5485  114.58 -119.26  107.06   1.1096
+ IC    C4'     O5'     *C5'    H5''        1.5485  114.58  124.53  111.01   1.1140
+PATC  FIRS NONE LAST NONE
+
+RESI CDP         -3.00  ! cytosine diphosphate, adm jr.
+                        ! atom names correspond to pdb nomenclature
+
+ATOM C4'  CN7     0.16  !                              H42  H41
+ATOM H4'  HN7     0.09  !                                \  /    
+ATOM O4'  ON6B   -0.50  !                                 N4
+ATOM C1'  CN7B    0.16  !                                 |
+ATOM H1'  HN7     0.09  !                                 C4
+GROUP                   !                                /  \\
+ATOM N1   NN2    -0.13  !                            H5-C5   N3
+ATOM C6   CN3     0.05  !                               ||   |
+ATOM H6   HN3     0.17  !                            H6-C6   C2
+ATOM C5   CN3    -0.13  !                                \  / \\
+ATOM H5   HN3     0.07  !                                 N1   O2
+ATOM C2   CN1     0.52  !                                  \
+ATOM O2   ON1C   -0.49  !                                   \
+ATOM N3   NN3    -0.66  !        O3B    O1A    H5' H4'  O4'  \
+ATOM C4   CN2     0.65  !        |       |      |    \ /   \  \
+ATOM N4   NN1    -0.75  !   O1B=PB-O3A--PA-O5'-C5'---C4'    C1'
+ATOM H41  HN1     0.37  !        |       |      |     \     / \  
+ATOM H42  HN1     0.33  !        O2B    O2A    H5''   C3'--C2' H1'  
+GROUP                   !                            / \   / \
+ATOM C2'  CN7B    0.14  !                         O3' H3' O2' H2''
+ATOM H2'' HN7     0.09  !                          |       |
+ATOM O2'  ON5    -0.66  !                         H3T     H2'
+ATOM H2'  HN5     0.43
+GROUP
+ATOM C3'  CN7     0.14
+ATOM H3'  HN7     0.09
+ATOM O3'  ON5    -0.66
+ATOM H3T  HN5     0.43
+GROUP
+ATOM C5'  CN8B   -0.08
+ATOM H5'  HN8     0.09
+ATOM H5'' HN8     0.09
+ATOM O5'  ON2    -0.62
+ATOM PA   P       1.50
+ATOM O1A  ON3    -0.82
+ATOM O2A  ON3    -0.82
+ATOM O3A  ON2    -0.74
+ATOM PB   P3      1.10
+ATOM O1B  ON3    -0.90
+ATOM O2B  ON3    -0.90
+ATOM O3B  ON3    -0.90
+
+BOND N1   C2        C2   N3        N3   C4        C4   C5
+BOND C5   C6        N1   C6
+BOND C4   N4        N4   H41       N4   H42
+BOND C2   O2        C5   H5        C6   H6
+BOND C1'  N1        C1'  C2'       
+BOND PB   O3A       PB   O1B       PB    O2B      PB   O3B       O3A  PA
+BOND PA   O1A       PA   O2A       PA    O5'      O3'  H3T
+BOND O5'  C5'       C5'  C4'       C4'  O4'       C4'  C3'       O4'  C1'
+BOND C2'  C3'       C2'  O2'       O2'  H2'       C3'  O3'
+BOND C1'  H1'       C2'  H2''      C3'  H3'       C4'  H4'       C5'  H5'
+BOND C5'  H5''
+
+IMPR C2   N1   N3   O2        C4   N3   C5   N4
+IMPR N4   C4   H41  H42      
+
+DONO H2'  O2'
+DONO H41  N4   
+DONO H42  N4   
+ACCE O2   C2
+ACCE N3     
+ACCE O1A  PA
+ACCE O2A  PA
+ACCE O2'
+ACCE O3'
+ACCE O4'
+ACCE O5'
+ACCE O3A
+ACCE O3B
+ACCE O2B
+ACCE O1B
+
+ IC    C5'     O5'     PA      O1A         1.4425  120.73 -171.23  102.18   1.4828
+ IC    C5'     O5'     PA      O2A         1.4425  120.73   66.15  100.85   1.4861
+ IC    O1A     O2A     *PA     O3A         1.4828  118.54 -146.08  114.13   1.5266
+ IC    O5'     PA      O3A     PB          1.5949   97.60 -165.85  119.57   1.6105
+ IC    PA      O3A     PB      O1B         1.5266  119.57  -43.22  109.89   1.5262
+ IC    O3A     PB      *O1B    O2B         2.5681   36.14 -112.68   34.17   2.5275
+ IC    O3A     PB      *O1B    O3B         2.5681   36.14  119.09   32.92   2.5612
+ IC    PA      O5'     C5'     C4'         1.5949  120.73 -154.23  112.44   1.5457
+ IC    O5'     C5'     C4'     C3'         1.4425  112.44   45.68  117.83   1.5501
+ IC    C5'     C4'     C3'     O3'         1.5457  117.83  -32.52  117.14   1.4300
+ IC    H3T     O3'     C3'     C4'         0.9882  105.85   24.62  117.14   1.5501
+ IC    O4'     C3'     *C4'    C5'         1.4625  105.13 -124.89  117.83   1.5457
+ IC    C2'     C4'     *C3'    O3'         1.5127  103.43  120.51  117.14   1.4300
+ IC    C4'     C3'     C2'     C1'         1.5501  103.43   34.51  101.64   1.5272
+ IC    C3'     C2'     C1'     N1          1.5127  101.64   94.90  112.49   1.4975
+ IC    O4'     C1'     N1      C2          1.4246  112.69 -159.47  121.37   1.3985
+ IC    C1'     C2      *N1     C6          1.4975  121.37  175.71  119.50   1.3804
+ IC    C2      N1      C6      C5          1.3985  119.50    2.69  121.63   1.3352
+ IC    C6      N1      C2      N3          1.3804  119.50   -3.85  119.51   1.3617
+ IC    N1      N3      *C2     O2          1.3985  119.51  179.76  121.33   1.2430
+ IC    N1      C2      N3      C4          1.3985  119.51    2.83  119.69   1.3444
+ IC    C5      N3      *C4     N4          1.4196  121.99 -179.61  118.24   1.3337
+ IC    N3      C4      N4      H41         1.3444  118.24   -2.06  116.78   0.9910
+ IC    H41     C4      *N4     H42         0.9910  116.78 -175.36  120.63   0.9957
+ IC    C6      C4      *C5     H5          1.3352  117.58  179.72  120.95   1.0898
+ IC    N1      C5      *C6     H6          1.3804  121.63 -178.41  121.71   1.0928
+ IC    C1'     C3'     *C2'    O2'         1.5272  101.64 -119.10  110.23   1.4207
+ IC    H2'     O2'     C2'     C3'         0.9588  108.13  -87.19  110.23   1.5127
+ IC    O4'     C2'     *C1'    H1'         1.4246  108.02 -113.99  108.53   1.1132
+ IC    C1'     C3'     *C2'    H2''        1.5272  101.64  118.36  111.16   1.1128
+ IC    C2'     C4'     *C3'    H3'         1.5127  103.43 -117.68  107.15   1.1105
+ IC    C3'     O4'     *C4'    H4'         1.5501  105.13 -113.16  105.27   1.1104
+ IC    C4'     O5'     *C5'    H5'         1.5457  112.44 -121.82  108.90   1.1132
+ IC    C4'     O5'     *C5'    H5''        1.5457  112.44  120.84  110.82   1.1175
+PATC  FIRS NONE LAST NONE
+
+RESI CTP         -4.00  !cytosine triphosphate , adm jr.
+                        !atom names correspond to pdb nomenclature
+                        !
+ATOM C4'  CN7     0.16  !                              H42  H41
+ATOM H4'  HN7     0.09  !                                \  /    
+ATOM O4'  ON6B   -0.50  !                                 N4
+ATOM C1'  CN7B    0.16  !                                 |
+ATOM H1'  HN7     0.09  !                                 C4
+GROUP                   !                                /  \\
+ATOM N1   NN2    -0.13  !                            H5-C5   N3
+ATOM C6   CN3     0.05  !                               ||   |
+ATOM H6   HN3     0.17  !                            H6-C6   C2
+ATOM C5   CN3    -0.13  !                                \  / \\
+ATOM H5   HN3     0.07  !                                 N1   O2
+ATOM C2   CN1     0.52  !                                  \
+ATOM O2   ON1C   -0.49  !                                   \
+ATOM N3   NN3    -0.66  !        O3B    O1A    H5' H4'  O4'  \
+ATOM C4   CN2     0.65  !        |       |      |    \ /   \  \
+ATOM N4   NN1    -0.75  !   O1B=PB-O3A--PA-O5'-C5'---C4'    C1'
+ATOM H41  HN1     0.37  !        |       |      |     \     / \  
+ATOM H42  HN1     0.33  !        O2B    O2A    H5''   C3'--C2' H1'  
+GROUP                   !                            / \   / \
+ATOM C2'  CN7B    0.14  !                         O3' H3' O2' H2''
+ATOM H2'' HN7     0.09  !                          |       |
+ATOM O2'  ON5    -0.66  !                         H3T     H2'
+ATOM H2'  HN5     0.43
+GROUP
+ATOM C3'  CN7     0.14
+ATOM H3'  HN7     0.09
+ATOM O3'  ON5    -0.66
+ATOM H3T  HN5     0.43
+GROUP
+ATOM C5'  CN8B   -0.08
+ATOM H5'  HN8     0.09
+ATOM H5'' HN8     0.09
+ATOM O5'  ON2    -0.62
+ATOM PA   P       1.50
+ATOM O1A  ON3    -0.82
+ATOM O2A  ON3    -0.82
+ATOM O3A  ON2    -0.74
+ATOM PB   P3      1.50
+ATOM O1B  ON3    -0.82
+ATOM O2B  ON3    -0.82
+ATOM O3B  ON2    -0.86 ! charge adjusted to yield total triP of -4.0
+ATOM PG   P3      1.10
+ATOM O1G  ON3    -0.90
+ATOM O2G  ON3    -0.90
+ATOM O3G  ON3    -0.90
+
+BOND N1   C2        C2   N3        N3   C4        C4   C5
+BOND C5   C6        N1   C6
+BOND C4   N4        N4   H41       N4   H42
+BOND C2   O2        C5   H5        C6   H6
+BOND C1'  N1        C1'  C2'       
+BOND O5'  C5'       O5'  PA        PA   O1A       PA   O2A       PA   O3A
+BOND O3A  PB        PB   O1B       PB   O2B       PB   O3B       O3B  PG
+BOND PG   O1G       PG   O2G       PG   O3G
+BOND C5'  C4'       C4'  O4'       C4'  C3'       O4'  C1'
+BOND C2'  C3'       C2'  O2'       O2'  H2'       C3'  O3'       O3'  H3T
+BOND C1'  H1'       C2'  H2''      C3'  H3'       C4'  H4'       C5'  H5'
+BOND C5'  H5''
+
+IMPR C2   N1   N3   O2        C4   N3   C5   N4
+IMPR N4   C4   H41  H42      
+
+DONO H2'  O2'
+DONO H41  N4   
+DONO H42  N4   
+ACCE O2   C2
+ACCE N3     
+ACCE O1A  PA
+ACCE O2A  PA
+ACCE O2'
+ACCE O3'
+ACCE O4'
+ACCE O5'
+ACCE O3A
+ACCE O2B
+ACCE O1B
+ACCE O3B
+ACCE O3G
+ACCE O2G
+ACCE O2G
+
+ IC    C5'     O5'     PA      O1A         1.4374  124.19    9.59  104.00   1.4923
+ IC    C5'     O5'     PA      O2A         1.4374  124.19 -114.42  104.65   1.4799
+ IC    O1A     O2A     *PA     O3A         1.4923  117.63 -145.47  113.13   1.5080
+ IC    O5'     PA      O3A     PB          1.5913   92.94 -156.20  107.64   1.5985
+ IC    PA      O3A     PB      O1B         1.5080  107.64   80.47  107.43   1.5316
+ IC    O3A     PB      *O1B    O2B         2.5234   37.18 -130.54   31.00   2.6293
+ IC    O3A     PB      *O1B    O3B         2.5234   37.18  103.63   37.65   2.6119
+ IC    O3A     PB      O3B     PG          1.5985   96.76 -173.66  156.81   1.6792
+ IC    PA      O3B     PG      O1G         3.8251  173.26 -135.48  106.83   1.5253
+ IC    O3B     PG      *O1G    O2G         2.5748   38.62 -119.21   33.03   2.5553
+ IC    O3B     PG      *O1G    O3G         2.5748   38.62  112.99   35.25   2.4958
+ IC    PA      O5'     C5'     C4'         1.5913  124.19  -89.15  114.76   1.5460
+ IC    O5'     C5'     C4'     C3'         1.4374  114.76   53.17  118.79   1.5327
+ IC    O5'     C5'     C4'     C3'         1.4374  114.76   53.17  118.79   1.5327
+ IC    C5'     C4'     C3'     O3'         1.5460  118.79   69.96  109.76   1.4345
+ IC    H3T     O3'     C3'     C4'         0.9919  101.28  -87.58  109.76   1.5327
+ IC    O4'     C3'     *C4'    C5'         1.4600  103.99 -127.40  118.79   1.5460
+ IC    C2'     C4'     *C3'    O3'         1.5077  100.80 -122.49  109.76   1.4345
+ IC    C4'     C3'     C2'     C1'         1.5327  100.80   43.97   99.50   1.5247
+ IC    C3'     C2'     C1'     N1          1.5077   99.50   89.23  109.95   1.4935
+ IC    O4'     C1'     N1      C2          1.4364  113.05 -159.72  119.96   1.3986
+ IC    C1'     C2      *N1     C6          1.4935  119.96  174.01  119.68   1.3780
+ IC    C2      N1      C6      C5          1.3986  119.68    2.03  121.33   1.3337
+ IC    C6      N1      C2      N3          1.3780  119.68   -1.80  119.80   1.3569
+ IC    N1      N3      *C2     O2          1.3986  119.80 -179.96  121.55   1.2448
+ IC    N1      C2      N3      C4          1.3986  119.80    4.60  119.43   1.3537
+ IC    C5      N3      *C4     N4          1.4218  121.37  178.95  119.72   1.3264
+ IC    N3      C4      N4      H41         1.3537  119.72  -51.72  111.09   0.9906
+ IC    H41     C4      *N4     H42         0.9906  111.09 -118.26  112.11   1.0266
+ IC    C6      C4      *C5     H5          1.3337  117.92  172.01  120.22   1.0891
+ IC    N1      C5      *C6     H6          1.3780  121.33  179.06  120.93   1.0958
+ IC    C1'     C3'     *C2'    O2'         1.5247   99.50 -119.79  110.03   1.4190
+ IC    H2'     O2'     C2'     C3'         0.9679  101.70  -36.76  110.03   1.5077
+ IC    O4'     C2'     *C1'    H1'         1.4364  107.34 -115.45  109.29   1.1119
+ IC    C1'     C3'     *C2'    H2''        1.5247   99.50  117.77  110.99   1.1124
+ IC    C2'     C4'     *C3'    H3'         1.5077  100.80  115.80  109.37   1.1105
+ IC    C3'     O4'     *C4'    H4'         1.5327  103.99 -111.63  105.45   1.1095
+ IC    C4'     O5'     *C5'    H5'         1.5460  114.76 -120.46  108.07   1.1105
+ IC    C4'     O5'     *C5'    H5''        1.5460  114.76  122.97  110.78   1.1139
+PATC  FIRS NONE LAST NONE
+
+!thymine nucleotides
+RESI TMP         -2.00  ! thymine monophosphate, adm jr.
+                        ! atom names correspond to pdb nomenclature
+GROUP                   !
+ATOM C4'  CN7     0.16  !                              
+ATOM H4'  HN7     0.09  !                              
+ATOM O4'  ON6B   -0.50  !                          H51    O4
+ATOM C1'  CN7B    0.16  !                           |     ||
+ATOM H1'  HN7     0.09  !                       H52-C5M   C4    H3
+GROUP                   !                           |  \ /  \  /
+ATOM N1   NN2B   -0.34  !                          H53  C5   N3
+ATOM C6   CN3     0.17  !                               ||   |
+ATOM H6   HN3     0.17  !                            H6-C6   C2
+ATOM C2   CN1T    0.51  !                                \  / \\
+ATOM O2   ON1    -0.41  !                                 N1   O2
+ATOM N3   NN2U   -0.46  !                                  \
+ATOM H3   HN2     0.36  !                                   \
+ATOM C4   CN1     0.50  !               O1A    H5' H4'  O4'  \
+ATOM O4   ON1    -0.45  !                |      |    \ /   \  \
+ATOM C5   CN3T   -0.15  !          O3A--PA-O5'-C5'---C4'    C1'
+ATOM C5M  CN9    -0.11  !                |      |     \     / \  
+ATOM H51  HN9     0.07  !               O2A    H5''   C3'--C2' H1'  
+ATOM H52  HN9     0.07  !                            / \   / \
+ATOM H53  HN9     0.07  !                         O3' H3' O2' H2''
+GROUP                   !                          |       |
+ATOM C2'  CN7B    0.14  !                         H3T     H2'
+ATOM H2'' HN7     0.09
+ATOM O2'  ON5    -0.66
+ATOM H2'  HN5     0.43
+GROUP
+ATOM C3'  CN7     0.14
+ATOM H3'  HN7     0.09
+ATOM O3'  ON5    -0.66
+ATOM H3T  HN5     0.43
+GROUP
+ATOM C5'  CN8B   -0.18
+ATOM H5'  HN8     0.09
+ATOM H5'' HN8     0.09
+GROUP
+ATOM O5'  ON2    -0.40
+ATOM PA   P       1.10
+ATOM O1A  ON3    -0.90
+ATOM O2A  ON3    -0.90
+ATOM O3A  ON3    -0.90
+
+BOND N1   C2        C2   N3        N3   C4        C4   C5
+BOND C5   C6        N1   C6
+BOND C2   O2        C4   O4        N3   H3        C6   H6        
+BOND C5   C5M       C5M  H51       C5M  H52       C5M  H53
+BOND C1'  N1        C1'  C2'       
+BOND PA   O1A       PA   O2A       PA   O3A       PA   O5'       O3'  H3T
+BOND O5'  C5'       C5'  C4'       C4'  O4'       C4'  C3'       O4'  C1'
+BOND C2'  C3'       C2'  O2'       O2'  H2'       C3'  O3'
+BOND C1'  H1'       C2'  H2''      C3'  H3'       C4'  H4'       C5'  H5'
+BOND C5'  H5''     
+
+IMPR C2   N1   N3   O2        C4   N3   C5   O4        C5   C4   C6   C5M
+
+DONO H3   N3
+DONO H2'  O2'
+ACCE O2   C2
+ACCE O4   C4
+ACCE O1A  PA
+ACCE O2A  PA
+ACCE O3A  PA
+ACCE O2'
+ACCE O3'
+ACCE O4'
+ACCE O5'
+
+ IC    C5'     O5'     PA      O1A         1.4400  125.37  137.83  103.50   1.4812
+ IC    C5'     O5'     PA      O2A         1.4400  125.37   19.22  105.83   1.4793
+ IC    O1A     O2A     *PA     O3A         1.4812  112.59 -131.81  114.29   1.4766
+ IC    PA      O5'     C5'     C4'         1.5863  125.37 -107.59  114.23   1.5482
+ IC    O5'     C5'     C4'     C3'         1.4400  114.23   68.41  114.41   1.5398
+ IC    C5'     C4'     C3'     O3'         1.5482  114.41  143.93  114.36   1.4402
+ IC    H3T     O3'     C3'     C4'         0.9640  103.41  159.98  114.36   1.5398
+ IC    O4'     C3'     *C4'    C5'         1.4658  105.05 -123.89  114.41   1.5482
+ IC    C2'     C4'     *C3'    O3'         1.5217  102.68 -122.25  114.36   1.4402
+ IC    C4'     C3'     C2'     C1'         1.5398  102.68  -36.86  101.04   1.5223
+ IC    C3'     C2'     C1'     N1          1.5217  101.04  154.90  113.33   1.4848
+ IC    O4'     C1'     N1      C2          1.4189  110.62 -103.32  119.64   1.3741
+ IC    C1'     C2      *N1     C6          1.4848  119.64 -175.07  121.11   1.3805
+ IC    C2      N1      C6      C5          1.3741  121.11   -5.22  123.51   1.3386
+ IC    C6      N1      C2      N3          1.3805  121.11    3.50  114.62   1.3735
+ IC    N1      N3      *C2     O2          1.3741  114.62 -179.71  121.72   1.2273
+ IC    N1      C2      N3      C4          1.3741  114.62   -2.55  127.21   1.3812
+ IC    C5      N3      *C4     O4          1.4408  115.13  179.57  119.15   1.2323
+ IC    C2      C4      *N3     H3          1.3735  127.21  175.47  117.05   0.9962
+ IC    C4      C6      *C5     C5M         1.4408  118.17  171.46  120.65   1.4965
+ IC    N1      C5      *C6     H6          1.3805  123.51 -176.23  120.19   1.0910
+ IC    C6      C5      C5M     H51         1.3386  120.65   37.09  110.64   1.1161
+ IC    C5      H51     *C5M    H52         1.4965  110.64  120.93  107.19   1.1127
+ IC    H51     H52     *C5M    H53         1.1161  107.19 -116.03  108.61   1.1110
+ IC    C1'     C3'     *C2'    O2'         1.5223  101.04 -120.82  113.11   1.4248
+ IC    H2'     O2'     C2'     C3'         0.9628  105.68 -140.74  113.11   1.5217
+ IC    O4'     C2'     *C1'    H1'         1.4189  107.84 -112.80  107.54   1.1154
+ IC    C1'     C3'     *C2'    H2''        1.5223  101.04  117.63  108.19   1.1094
+ IC    C2'     C4'     *C3'    H3'         1.5217  102.68  115.26  107.66   1.1144
+ IC    C3'     O4'     *C4'    H4'         1.5398  105.05 -114.57  108.17   1.1101
+ IC    C4'     O5'     *C5'    H5'         1.5482  114.23 -119.64  107.43   1.1103
+ IC    C4'     O5'     *C5'    H5''        1.5482  114.23  123.75  111.18   1.1146
+PATC  FIRS NONE LAST NONE
+
+RESI TDP         -3.00  ! thymine diphosphate, adm jr.
+                        ! atom names correspond to pdb nomenclature
+
+GROUP                   !
+ATOM C4'  CN7     0.16  !                              
+ATOM H4'  HN7     0.09  !                              
+ATOM O4'  ON6B   -0.50  !                          H51    O4
+ATOM C1'  CN7B    0.16  !                           |     ||
+ATOM H1'  HN7     0.09  !                       H52-C5M   C4    H3
+GROUP                   !                           |  \ /  \  /
+ATOM N1   NN2B   -0.34  !                          H53  C5   N3
+ATOM C6   CN3     0.17  !                               ||   |
+ATOM H6   HN3     0.17  !                            H6-C6   C2
+ATOM C2   CN1T    0.51  !                                \  / \\
+ATOM O2   ON1    -0.41  !                                 N1   O2
+ATOM N3   NN2U   -0.46  !                                  \
+ATOM H3   HN2     0.36  !                                   \
+ATOM C4   CN1     0.50  !        O3B    O1A    H5' H4'  O4'  \
+ATOM O4   ON1    -0.45  !        |       |      |    \ /   \  \
+ATOM C5   CN3T   -0.15  !   O1B=PB-O3A--PA-O5'-C5'---C4'    C1'
+ATOM C5M  CN9    -0.11  !        |       |      |     \     / \
+ATOM H51  HN9     0.07  !        O2B    O2A    H5''   C3'--C2' H1'
+ATOM H52  HN9     0.07  !                            / \   / \
+ATOM H53  HN9     0.07  !                         O3' H3' O2' H2''
+GROUP                   !                          |       |
+ATOM C2'  CN7B    0.14  !                         H3T     H2'
+ATOM H2'' HN7     0.09
+ATOM O2'  ON5    -0.66
+ATOM H2'  HN5     0.43
+GROUP
+ATOM C3'  CN7     0.14
+ATOM H3'  HN7     0.09
+ATOM O3'  ON5    -0.66
+ATOM H3T  HN5     0.43
+GROUP
+ATOM C5'  CN8B   -0.08
+ATOM H5'  HN8     0.09
+ATOM H5'' HN8     0.09
+ATOM O5'  ON2    -0.62
+ATOM PA   P       1.50
+ATOM O1A  ON3    -0.82
+ATOM O2A  ON3    -0.82
+ATOM O3A  ON2    -0.74
+ATOM PB   P3      1.10
+ATOM O1B  ON3    -0.90
+ATOM O2B  ON3    -0.90
+ATOM O3B  ON3    -0.90
+
+BOND N1   C2        C2   N3        N3   C4        C4   C5
+BOND C5   C6        N1   C6
+BOND C2   O2        C4   O4        N3   H3        C6   H6        
+BOND C5   C5M       C5M  H51       C5M  H52       C5M  H53
+BOND C1'  N1        C1'  C2'       
+BOND PB   O3A       PB   O1B       PB    O2B      PB   O3B       O3A  PA
+BOND PA   O1A       PA   O2A       PA    O5'      O3'  H3T
+BOND O5'  C5'       C5'  C4'       C4'  O4'       C4'  C3'       O4'  C1'
+BOND C2'  C3'       C2'  O2'       O2'  H2'       C3'  O3'
+BOND C1'  H1'       C2'  H2''      C3'  H3'       C4'  H4'       C5'  H5'
+BOND C5'  H5''
+
+IMPR C2   N1   N3   O2        C4   N3   C5   O4        C5   C4   C6   C5M
+
+DONO H3   N3
+DONO H2'  O2'
+ACCE O2   C2
+ACCE O4   C4
+ACCE O1A  PA
+ACCE O2A  PA
+ACCE O3A  PA
+ACCE O2'
+ACCE O3'
+ACCE O4'
+ACCE O5'
+ACCE O3A
+ACCE O3B
+ACCE O2B
+ACCE O1B
+
+ IC    C5'     O5'     PA      O1A         1.4455  118.72  178.82  102.92   1.4827
+ IC    C5'     O5'     PA      O2A         1.4455  118.72   55.43  102.27   1.4864
+ IC    O1A     O2A     *PA     O3A         1.4827  118.46 -143.46  114.83   1.5249
+ IC    O5'     PA      O3A     PB          1.6018   97.48 -176.70  126.12   1.6123
+ IC    PA      O3A     PB      O1B         1.5249  126.12  -18.77  109.94   1.5251
+ IC    O3A     PB      *O1B    O2B         2.5696   36.15 -114.07   33.74   2.5396
+ IC    O3A     PB      *O1B    O3B         2.5696   36.15  116.77   33.21   2.5528
+ IC    PA      O5'     C5'     C4'         1.6018  118.72  -94.65  112.53   1.5424
+ IC    O5'     C5'     C4'     C3'         1.4455  112.53  -12.09  119.74   1.5559
+ IC    C5'     C4'     C3'     O3'         1.5424  119.74  -30.51  116.31   1.4330
+ IC    H3T     O3'     C3'     C4'         0.9848  103.20   51.10  116.31   1.5559
+ IC    O4'     C3'     *C4'    C5'         1.4677  105.16 -123.76  119.74   1.5424
+ IC    C2'     C4'     *C3'    O3'         1.5140  102.76  120.50  116.31   1.4330
+ IC    C4'     C3'     C2'     C1'         1.5559  102.76   34.89  102.13   1.5267
+ IC    C3'     C2'     C1'     N1          1.5140  102.13   91.37  112.87   1.4944
+ IC    O4'     C1'     N1      C2          1.4165  111.23 -144.95  119.12   1.3725
+ IC    C1'     C2      *N1     C6          1.4944  119.12  179.24  120.91   1.3836
+ IC    C2      N1      C6      C5          1.3725  120.91   -0.93  123.77   1.3377
+ IC    C6      N1      C2      N3          1.3836  120.91   -1.10  114.76   1.3735
+ IC    N1      N3      *C2     O2          1.3725  114.76  179.57  121.97   1.2269
+ IC    N1      C2      N3      C4          1.3725  114.76    0.33  127.20   1.3815
+ IC    C5      N3      *C4     O4          1.4399  115.20 -179.93  119.31   1.2312
+ IC    C2      C4      *N3     H3          1.3735  127.20  179.19  117.03   0.9968
+ IC    C4      C6      *C5     C5M         1.4399  118.04  173.19  121.29   1.4971
+ IC    N1      C5      *C6     H6          1.3836  123.77  178.29  120.97   1.0948
+ IC    C6      C5      C5M     H51         1.3377  121.29   32.69  110.96   1.1155
+ IC    C5      H51     *C5M    H52         1.4971  110.96  121.38  107.65   1.1125
+ IC    H51     H52     *C5M    H53         1.1155  107.65 -115.95  108.29   1.1123
+ IC    C1'     C3'     *C2'    O2'         1.5267  102.13 -117.96  110.34   1.4182
+ IC    H2'     O2'     C2'     C3'         0.9640  107.13   43.83  110.34   1.5140
+ IC    O4'     C2'     *C1'    H1'         1.4165  107.51 -113.71  108.81   1.1146
+ IC    C1'     C3'     *C2'    H2''        1.5267  102.13  119.61  111.22   1.1110
+ IC    C2'     C4'     *C3'    H3'         1.5140  102.76 -117.99  107.30   1.1139
+ IC    C3'     O4'     *C4'    H4'         1.5559  105.16 -113.01  107.94   1.1119
+ IC    C4'     O5'     *C5'    H5'         1.5424  112.53 -120.89  107.50   1.1103
+ IC    C4'     O5'     *C5'    H5''        1.5424  112.53  123.23  112.75   1.1186
+PATC  FIRS NONE LAST NONE
+
+RESI TTP         -4.00  ! thymine triphosphate, adm jr.
+                        ! atom names correspond to pdb nomenclature
+                        !
+GROUP                   !
+ATOM C4'  CN7     0.16  !                              
+ATOM H4'  HN7     0.09  !                              
+ATOM O4'  ON6B   -0.50  !                          H51    O4
+ATOM C1'  CN7B    0.16  !                           |     ||
+ATOM H1'  HN7     0.09  !                       H52-C5M   C4    H3
+GROUP                   !                           |  \ /  \  /
+ATOM N1   NN2B   -0.34  !                          H53  C5   N3
+ATOM C6   CN3     0.17  !                               ||   |
+ATOM H6   HN3     0.17  !                            H6-C6   C2
+ATOM C2   CN1T    0.51  !                                \  / \\
+ATOM O2   ON1    -0.41  !                                 N1   O2
+ATOM N3   NN2U   -0.46  !                                  \
+ATOM H3   HN2     0.36  !                                   \
+ATOM C4   CN1     0.50  !        O3B    O1A    H5' H4'  O4'  \
+ATOM O4   ON1    -0.45  !        |       |      |    \ /   \  \
+ATOM C5   CN3T   -0.15  !   O1B=PB-O3A--PA-O5'-C5'---C4'    C1'
+ATOM C5M  CN9    -0.11  !        |       |      |     \     / \
+ATOM H51  HN9     0.07  !        O2B    O2A    H5''   C3'--C2' H1'
+ATOM H52  HN9     0.07  !                            / \   / \
+ATOM H53  HN9     0.07  !                         O3' H3' O2' H2''
+GROUP                   !                          |       |
+ATOM C2'  CN7B    0.14  !                         H3T     H2'
+ATOM H2'' HN7     0.09
+ATOM O2'  ON5    -0.66
+ATOM H2'  HN5     0.43
+GROUP
+ATOM C3'  CN7     0.14
+ATOM H3'  HN7     0.09
+ATOM O3'  ON5    -0.66
+ATOM H3T  HN5     0.43
+GROUP
+ATOM C5'  CN8B   -0.08
+ATOM H5'  HN8     0.09
+ATOM H5'' HN8     0.09
+ATOM O5'  ON2    -0.62
+ATOM PA   P       1.50
+ATOM O1A  ON3    -0.82
+ATOM O2A  ON3    -0.82
+ATOM O3A  ON2    -0.74
+ATOM PB   P3      1.50
+ATOM O1B  ON3    -0.82
+ATOM O2B  ON3    -0.82
+ATOM O3B  ON2    -0.86 ! charge adjusted to yield total triP of -4.0
+ATOM PG   P3      1.10
+ATOM O1G  ON3    -0.90
+ATOM O2G  ON3    -0.90
+ATOM O3G  ON3    -0.90
+
+BOND N1   C2        C2   N3        N3   C4        C4   C5
+BOND C5   C6        N1   C6
+BOND C2   O2        C4   O4        N3   H3        C6   H6        
+BOND C5   C5M       C5M  H51       C5M  H52       C5M  H53
+BOND C1'  N1        C1'  C2'       
+BOND O5'  C5'       O5'  PA        PA   O1A       PA   O2A       PA   O3A
+BOND O3A  PB        PB   O1B       PB   O2B       PB   O3B       O3B  PG
+BOND PG   O1G       PG   O2G       PG   O3G
+BOND C5'  C4'       C4'  O4'       C4'  C3'       O4'  C1'
+BOND C2'  C3'       C2'  O2'       O2'  H2'       C3'  O3'       O3'  H3T
+BOND C1'  H1'       C2'  H2''      C3'  H3'       C4'  H4'       C5'  H5'
+BOND C5'  H5''
+
+IMPR C2   N1   N3   O2        C4   N3   C5   O4        C5   C4   C6   C5M
+
+DONO H3   N3
+DONO H2'  O2'
+ACCE O2   C2
+ACCE O4   C4
+ACCE O1A  PA
+ACCE O2A  PA
+ACCE O3A  PA
+ACCE O2'
+ACCE O3'
+ACCE O4'
+ACCE O5'
+ACCE O3A
+ACCE O2B
+ACCE O1B
+ACCE O3B
+ACCE O3G
+ACCE O2G
+ACCE O2G
+
+ IC    C5'     O5'     PA      O1A         1.4401  123.09   16.55  102.93   1.4933
+ IC    C5'     O5'     PA      O2A         1.4401  123.09 -107.14  103.98   1.4803
+ IC    O1A     O2A     *PA     O3A         1.4933  118.07 -146.90  113.77   1.5140
+ IC    O5'     PA      O3A     PB          1.5925   93.17 -158.62  104.64   1.6083
+ IC    PA      O3A     PB      O1B         1.5140  104.64   79.95  107.61   1.5335
+ IC    O3A     PB      *O1B    O2B         2.5359   37.19 -131.19   31.13   2.6313
+ IC    O3A     PB      *O1B    O3B         2.5359   37.19  104.58   37.08   2.6197
+ IC    O3A     PB      O3B     PG          1.6083   97.23 -147.19  153.72   1.6788
+ IC    PA      O3B     PG      O1G         3.8073  169.46 -135.11  107.23   1.5280
+ IC    O3B     PG      *O1G    O2G         2.5832   38.37 -115.26   33.76   2.5441
+ IC    O3B     PG      *O1G    O3G         2.5832   38.37  116.43   33.28   2.5561
+ IC    PA      O5'     C5'     C4'         1.5925  123.09  -95.33  113.20   1.5426
+ IC    O5'     C5'     C4'     C3'         1.4401  113.20   41.03  118.58   1.5380
+ IC    O5'     C5'     C4'     C3'         1.4401  113.20   41.03  118.58   1.5380
+ IC    C5'     C4'     C3'     O3'         1.5426  118.58   78.12  109.57   1.4380
+ IC    H3T     O3'     C3'     C4'         0.9928  102.84  -86.68  109.57   1.5380
+ IC    O4'     C3'     *C4'    C5'         1.4580  104.71 -124.25  118.58   1.5426
+ IC    C2'     C4'     *C3'    O3'         1.5167  102.03 -122.41  109.57   1.4380
+ IC    C4'     C3'     C2'     C1'         1.5380  102.03   35.92  101.65   1.5275
+ IC    C3'     C2'     C1'     N1          1.5167  101.65   97.44  112.77   1.4901
+ IC    O4'     C1'     N1      C2          1.4164  110.59 -125.32  118.29   1.3771
+ IC    C1'     C2      *N1     C6          1.4901  118.29  179.10  120.54   1.3963
+ IC    C2      N1      C6      C5          1.3771  120.54    0.81  123.15   1.3377
+ IC    C6      N1      C2      N3          1.3963  120.54   -2.65  114.92   1.3665
+ IC    N1      N3      *C2     O2          1.3771  114.92  179.31  121.44   1.2292
+ IC    N1      C2      N3      C4          1.3771  114.92   -2.57  127.52   1.3790
+ IC    C5      N3      *C4     O4          1.4408  114.71 -177.54  118.30   1.2292
+ IC    C2      C4      *N3     H3          1.3665  127.52  174.49  115.81   0.9947
+ IC    C4      C6      *C5     C5M         1.4408  118.41  173.37  121.54   1.4945
+ IC    N1      C5      *C6     H6          1.3963  123.15 -175.27  118.98   1.0993
+ IC    C6      C5      C5M     H51         1.3377  121.54  -86.48  111.81   1.1122
+ IC    C5      H51     *C5M    H52         1.4945  111.81  124.82  109.28   1.1162
+ IC    H51     H52     *C5M    H53         1.1122  109.28 -114.95  105.93   1.1172
+ IC    C1'     C3'     *C2'    O2'         1.5275  101.65 -119.10  110.11   1.4172
+ IC    H2'     O2'     C2'     C3'         0.9713  101.08  -29.97  110.11   1.5167
+ IC    O4'     C2'     *C1'    H1'         1.4164  108.58 -113.02  107.93   1.1147
+ IC    C1'     C3'     *C2'    H2''        1.5275  101.65  118.88  110.18   1.1121
+ IC    C2'     C4'     *C3'    H3'         1.5167  102.03  116.25  109.94   1.1106
+ IC    C3'     O4'     *C4'    H4'         1.5380  104.71 -112.76  105.69   1.1100
+ IC    C4'     O5'     *C5'    H5'         1.5426  113.20 -120.33  108.24   1.1112
+ IC    C4'     O5'     *C5'    H5''        1.5426  113.20  122.84  111.42   1.1153
+PATC  FIRS NONE LAST NONE
+
+!uracil nucleotides
+RESI UMP         -2.00  ! uracil monophosphate, adm jr.
+                        ! atom names correspond to pdb nomenclature
+GROUP                   !
+ATOM C4'  CN7     0.16  !                              
+ATOM H4'  HN7     0.09  !                              
+ATOM O4'  ON6B   -0.50  !                                 O4
+ATOM C1'  CN7B    0.16  !                                 ||
+ATOM H1'  HN7     0.09  !                                 C4    H3
+GROUP                   !                                /  \  /
+ATOM N1   NN2B   -0.34  !                            H5-C5   N3
+ATOM C6   CN3     0.20  !                               ||   |
+ATOM H6   HN3     0.14  !                            H6-C6   C2
+ATOM C2   CN1T    0.55  !                                \  / \\
+ATOM O2   ON1    -0.45  !                                 N1   O2
+ATOM N3   NN2U   -0.46  !                                  \
+ATOM H3   HN2     0.36  !                                   \
+ATOM C4   CN1     0.53  !               O1A    H5' H4'  O4'  \
+ATOM O4   ON1    -0.48  !                |      |    \ /   \  \
+ATOM C5   CN3    -0.15  !          O3A--PA-O5'-C5'---C4'    C1'
+ATOM H5   HN3     0.10  !                |      |     \     / \  
+GROUP                   !               O2A    H5''   C3'--C2' H1'  
+ATOM C2'  CN7B    0.14  !                            / \   / \
+ATOM H2'' HN7     0.09  !                         O3' H3' O2' H2''
+ATOM O2'  ON5    -0.66  !                          |       |
+ATOM H2'  HN5     0.43  !                         H3T     H2'
+GROUP                 
+ATOM C3'  CN7     0.14
+ATOM H3'  HN7     0.09
+ATOM O3'  ON5    -0.66
+ATOM H3T  HN5     0.43
+GROUP
+ATOM C5'  CN8B   -0.18
+ATOM H5'  HN8     0.09
+ATOM H5'' HN8     0.09
+GROUP
+ATOM O5'  ON2    -0.40
+ATOM PA   P       1.10
+ATOM O1A  ON3    -0.90
+ATOM O2A  ON3    -0.90
+ATOM O3A  ON3    -0.90
+
+BOND N1   C2        C2   N3        N3   C4        C4   C5
+BOND C5   C6        N1   C6        N3   H3
+BOND C2   O2        C4   O4        C5   H5        C6   H6        
+BOND C1'  N1        C1'  C2'       
+BOND PA   O1A       PA   O2A       PA   O3A       PA   O5'       O3'  H3T
+BOND O5'  C5'       C5'  C4'       C4'  O4'       C4'  C3'       O4'  C1'
+BOND C2'  C3'       C2'  O2'       O2'  H2'       C3'  O3'
+BOND C1'  H1'       C2'  H2''      C3'  H3'       C4'  H4'       C5'  H5'
+BOND C5'  H5''     
+
+IMPR C2   N1   N3   O2        C4   N3   C5   O4
+
+DONO H3   N3   
+DONO H2'  O2'
+ACCE O2   C2
+ACCE O4   C4
+ACCE O1A  PA
+ACCE O2A  PA
+ACCE O3A  PA
+ACCE O2'
+ACCE O3'
+ACCE O4'
+ACCE O5'
+
+ IC    C5'     O5'     PA      O1A         1.4386  125.37   30.84  105.62   1.4796
+ IC    C5'     O5'     PA      O2A         1.4386  125.37  -90.57  105.92   1.4765
+ IC    O1A     O2A     *PA     O3A         1.4796  114.13 -131.09  114.21   1.4812
+ IC    PA      O5'     C5'     C4'         1.5867  125.37 -107.44  114.55   1.5499
+ IC    O5'     C5'     C4'     C3'         1.4386  114.55   73.74  113.74   1.5378
+ IC    C5'     C4'     C3'     O3'         1.5499  113.74  143.96  114.47   1.4402
+ IC    H3T     O3'     C3'     C4'         0.9641  103.40  157.99  114.47   1.5378
+ IC    O4'     C3'     *C4'    C5'         1.4689  104.93 -124.30  113.74   1.5499
+ IC    C2'     C4'     *C3'    O3'         1.5200  102.40 -122.09  114.47   1.4402
+ IC    C4'     C3'     C2'     C1'         1.5378  102.40  -38.48  100.83   1.5198
+ IC    C3'     C2'     C1'     N1          1.5200  100.83  156.79  112.75   1.4834
+ IC    O4'     C1'     N1      C2          1.4213  110.92 -114.25  120.00   1.3727
+ IC    C1'     C2      *N1     C6          1.4834  120.00 -178.72  121.10   1.3782
+ IC    C2      N1      C6      C5          1.3727  121.10   -1.47  122.78   1.3422
+ IC    C6      N1      C2      N3          1.3782  121.10    1.33  114.81   1.3720
+ IC    N1      N3      *C2     O2          1.3727  114.81 -179.71  121.46   1.2270
+ IC    N1      C2      N3      C4          1.3727  114.81   -0.62  127.53   1.3791
+ IC    C5      N3      *C4     O4          1.4318  114.39 -179.77  119.32   1.2301
+ IC    C2      C4      *N3     H3          1.3720  127.53  179.65  117.07   0.9957
+ IC    C4      C6      *C5     H5          1.4318  119.38  179.73  120.76   1.0878
+ IC    N1      C5      *C6     H6          1.3782  122.78 -178.04  121.26   1.0873
+ IC    C1'     C3'     *C2'    O2'         1.5198  100.83 -121.43  112.64   1.4237
+ IC    H2'     O2'     C2'     C3'         0.9640  105.10 -120.35  112.64   1.5200
+ IC    O4'     C2'     *C1'    H1'         1.4213  107.25 -112.85  107.97   1.1150
+ IC    C1'     C3'     *C2'    H2''        1.5198  100.83  116.88  108.80   1.1107
+ IC    C2'     C4'     *C3'    H3'         1.5200  102.40  115.44  107.82   1.1136
+ IC    C3'     O4'     *C4'    H4'         1.5378  104.93 -114.45  108.43   1.1100
+ IC    C4'     O5'     *C5'    H5'         1.5499  114.55 -119.70  107.28   1.1099
+ IC    C4'     O5'     *C5'    H5''        1.5499  114.55  123.87  110.91   1.1143
+PATC  FIRS NONE LAST NONE
+
+RESI UDP         -3.00  ! uracil diphosphate, adm jr.
+                        ! atom names correspond to pdb nomenclature
+
+GROUP                   !
+ATOM C4'  CN7     0.16  !                              
+ATOM H4'  HN7     0.09  !                              
+ATOM O4'  ON6B   -0.50  !                                 O4
+ATOM C1'  CN7B    0.16  !                                 ||
+ATOM H1'  HN7     0.09  !                                 C4    H3
+GROUP                   !                                /  \  /
+ATOM N1   NN2B   -0.34  !                            H5-C5   N3
+ATOM C6   CN3     0.20  !                               ||   |
+ATOM H6   HN3     0.14  !                            H6-C6   C2
+ATOM C2   CN1T    0.55  !                                \  / \\
+ATOM O2   ON1    -0.45  !                                 N1   O2
+ATOM N3   NN2U   -0.46  !                                  \
+ATOM H3   HN2     0.36  !                                   \
+ATOM C4   CN1     0.53  !               O1A    H5' H4'  O4'  \
+ATOM O4   ON1    -0.48  !                |      |    \ /   \  \
+ATOM C5   CN3    -0.15  !          O3A--PA-O5'-C5'---C4'    C1'
+ATOM H5   HN3     0.10  !                |      |     \     / \  
+GROUP                   !               O2A    H5''   C3'--C2' H1'  
+ATOM C2'  CN7B    0.14  !                            / \   / \
+ATOM H2'' HN7     0.09  !                         O3' H3' O2' H2''
+ATOM O2'  ON5    -0.66  !                          |       |
+ATOM H2'  HN5     0.43  !                         H3T     H2'
+GROUP
+ATOM C3'  CN7     0.14
+ATOM H3'  HN7     0.09
+ATOM O3'  ON5    -0.66
+ATOM H3T  HN5     0.43
+GROUP
+ATOM C5'  CN8B   -0.08
+ATOM H5'  HN8     0.09
+ATOM H5'' HN8     0.09
+ATOM O5'  ON2    -0.62
+ATOM PA   P       1.50
+ATOM O1A  ON3    -0.82
+ATOM O2A  ON3    -0.82
+ATOM O3A  ON2    -0.74
+ATOM PB   P3      1.10
+ATOM O1B  ON3    -0.90
+ATOM O2B  ON3    -0.90
+ATOM O3B  ON3    -0.90
+
+BOND N1   C2        C2   N3        N3   C4        C4   C5
+BOND C5   C6        N1   C6        N3   H3
+BOND C2   O2        C4   O4        C5   H5        C6   H6        
+BOND C1'  N1        C1'  C2'       
+BOND PB   O3A       PB   O1B       PB    O2B      PB   O3B       O3A  PA
+BOND PA   O1A       PA   O2A       PA    O5'      O3'  H3T
+BOND O5'  C5'       C5'  C4'       C4'  O4'       C4'  C3'       O4'  C1'
+BOND C2'  C3'       C2'  O2'       O2'  H2'       C3'  O3'
+BOND C1'  H1'       C2'  H2''      C3'  H3'       C4'  H4'       C5'  H5'
+BOND C5'  H5''
+
+IMPR C2   N1   N3   O2        C4   N3   C5   O4
+
+DONO H3   N3   
+DONO H2'  O2'
+ACCE O2   C2
+ACCE O4   C4
+ACCE O1A  PA
+ACCE O2A  PA
+ACCE O3A  PA
+ACCE O2'
+ACCE O3'
+ACCE O4'
+ACCE O5'
+ACCE O3A
+ACCE O3B
+ACCE O2B
+ACCE O1B
+
+ IC    C5'     O5'     PA      O1A         1.4452  119.36  179.48  102.79   1.4826
+ IC    C5'     O5'     PA      O2A         1.4452  119.36   56.33  102.34   1.4877
+ IC    O1A     O2A     *PA     O3A         1.4826  118.27 -143.92  114.07   1.5245
+ IC    O5'     PA      O3A     PB          1.6044   97.44 -169.69  121.80   1.6100
+ IC    PA      O3A     PB      O1B         1.5245  121.80  -34.02  110.11   1.5260
+ IC    O3A     PB      *O1B    O2B         2.5710   36.02 -113.19   34.02   2.5317
+ IC    O3A     PB      *O1B    O3B         2.5710   36.02  118.21   32.97   2.5592
+ IC    PA      O5'     C5'     C4'         1.6044  119.36  -88.66  111.34   1.5371
+ IC    O5'     C5'     C4'     C3'         1.4452  111.34  -23.34  117.61   1.5455
+ IC    C5'     C4'     C3'     O3'         1.5371  117.61  -33.43  114.93   1.4337
+ IC    H3T     O3'     C3'     C4'         0.9846  102.14   54.81  114.93   1.5455
+ IC    O4'     C3'     *C4'    C5'         1.4644  104.98 -123.57  117.61   1.5371
+ IC    C2'     C4'     *C3'    O3'         1.5125  102.66  121.49  114.93   1.4337
+ IC    C4'     C3'     C2'     C1'         1.5455  102.66   34.63  102.26   1.5293
+ IC    C3'     C2'     C1'     N1          1.5125  102.26   95.97  112.35   1.4894
+ IC    O4'     C1'     N1      C2          1.4185  111.08 -145.64  119.10   1.3727
+ IC    C1'     C2      *N1     C6          1.4894  119.10  177.16  120.97   1.3801
+ IC    C2      N1      C6      C5          1.3727  120.97    1.27  122.77   1.3425
+ IC    C6      N1      C2      N3          1.3801  120.97   -2.01  114.96   1.3711
+ IC    N1      N3      *C2     O2          1.3727  114.96 -179.99  121.59   1.2266
+ IC    N1      C2      N3      C4          1.3727  114.96    1.86  127.49   1.3787
+ IC    C5      N3      *C4     O4          1.4327  114.41 -179.82  119.58   1.2291
+ IC    C2      C4      *N3     H3          1.3711  127.49 -177.70  117.20   0.9968
+ IC    C4      C6      *C5     H5          1.4327  119.37 -179.83  121.52   1.0872
+ IC    N1      C5      *C6     H6          1.3801  122.77 -179.58  122.06   1.0949
+ IC    C1'     C3'     *C2'    O2'         1.5293  102.26 -118.27  110.08   1.4181
+ IC    H2'     O2'     C2'     C3'         0.9661  107.60   32.30  110.08   1.5125
+ IC    O4'     C2'     *C1'    H1'         1.4185  108.13 -113.95  108.75   1.1149
+ IC    C1'     C3'     *C2'    H2''        1.5293  102.26  119.74  111.10   1.1107
+ IC    C2'     C4'     *C3'    H3'         1.5125  102.66 -117.67  107.54   1.1142
+ IC    C3'     O4'     *C4'    H4'         1.5455  104.98 -113.44  108.49   1.1124
+ IC    C4'     O5'     *C5'    H5'         1.5371  111.34 -120.03  107.51   1.1101
+ IC    C4'     O5'     *C5'    H5''        1.5371  111.34  123.36  112.67   1.1172
+PATC  FIRS NONE LAST NONE
+
+RESI UTP         -4.00  ! uracil triphosphate, adm jr.
+                        ! atom names correspond to pdb nomenclature
+                        !
+GROUP                   !
+ATOM C4'  CN7     0.16  !                              
+ATOM H4'  HN7     0.09  !                              
+ATOM O4'  ON6B   -0.50  !                                 O4
+ATOM C1'  CN7B    0.16  !                                 ||
+ATOM H1'  HN7     0.09  !                                 C4    H3
+GROUP                   !                                /  \  /
+ATOM N1   NN2B   -0.34  !                            H5-C5   N3
+ATOM C6   CN3     0.20  !                               ||   |
+ATOM H6   HN3     0.14  !                            H6-C6   C2
+ATOM C2   CN1T    0.55  !                                \  / \\
+ATOM O2   ON1    -0.45  !                                 N1   O2
+ATOM N3   NN2U   -0.46  !                                  \
+ATOM H3   HN2     0.36  !                                   \
+ATOM C4   CN1     0.53  !               O1A    H5' H4'  O4'  \
+ATOM O4   ON1    -0.48  !                |      |    \ /   \  \
+ATOM C5   CN3    -0.15  !          O3A--PA-O5'-C5'---C4'    C1'
+ATOM H5   HN3     0.10  !                |      |     \     / \  
+GROUP                   !               O2A    H5''   C3'--C2' H1'  
+ATOM C2'  CN7B    0.14  !                            / \   / \
+ATOM H2'' HN7     0.09  !                         O3' H3' O2' H2''
+ATOM O2'  ON5    -0.66  !                          |       |
+ATOM H2'  HN5     0.43  !                         H3T     H2'
+GROUP
+ATOM C3'  CN7     0.14
+ATOM H3'  HN7     0.09
+ATOM O3'  ON5    -0.66
+ATOM H3T  HN5     0.43
+GROUP
+ATOM C5'  CN8B   -0.08
+ATOM H5'  HN8     0.09
+ATOM H5'' HN8     0.09
+ATOM O5'  ON2    -0.62
+ATOM PA   P       1.50
+ATOM O1A  ON3    -0.82
+ATOM O2A  ON3    -0.82
+ATOM O3A  ON2    -0.74
+ATOM PB   P3      1.50
+ATOM O1B  ON3    -0.82
+ATOM O2B  ON3    -0.82
+ATOM O3B  ON2    -0.86 ! charge adjusted to yield total triP of -4.0
+ATOM PG   P3      1.10
+ATOM O1G  ON3    -0.90
+ATOM O2G  ON3    -0.90
+ATOM O3G  ON3    -0.90
+
+BOND N1   C2        C2   N3        N3   C4        C4   C5
+BOND C5   C6        N1   C6        N3   H3
+BOND C2   O2        C4   O4        C5   H5        C6   H6        
+BOND C1'  N1        C1'  C2'       
+BOND O5'  C5'       O5'  PA        PA   O1A       PA   O2A       PA   O3A
+BOND O3A  PB        PB   O1B       PB   O2B       PB   O3B       O3B  PG
+BOND PG   O1G       PG   O2G       PG   O3G
+BOND C5'  C4'       C4'  O4'       C4'  C3'       O4'  C1'
+BOND C2'  C3'       C2'  O2'       O2'  H2'       C3'  O3'       O3'  H3T
+BOND C1'  H1'       C2'  H2''      C3'  H3'       C4'  H4'       C5'  H5'
+BOND C5'  H5''
+
+IMPR C2   N1   N3   O2        C4   N3   C5   O4
+
+DONO H3   N3   
+DONO H2'  O2'
+ACCE O2   C2
+ACCE O4   C4
+ACCE O1A  PA
+ACCE O2A  PA
+ACCE O3A  PA
+ACCE O2'
+ACCE O3'
+ACCE O4'
+ACCE O5'
+ACCE O3A
+ACCE O2B
+ACCE O1B
+ACCE O3B
+ACCE O3G
+ACCE O2G
+ACCE O2G
+
+ IC    C5'     O5'     PA      O1A         1.4436  123.18   -4.19  104.07   1.4896
+ IC    C5'     O5'     PA      O2A         1.4436  123.18 -128.27  105.09   1.4796
+ IC    O1A     O2A     *PA     O3A         1.4896  117.48 -144.86  112.24   1.5060
+ IC    O5'     PA      O3A     PB          1.5927   93.29 -154.64  107.67   1.5942
+ IC    PA      O3A     PB      O1B         1.5060  107.67   68.87  110.34   1.5347
+ IC    O3A     PB      *O1B    O2B         2.5686   35.59 -129.92   31.09   2.6307
+ IC    O3A     PB      *O1B    O3B         2.5686   35.59  104.59   36.93   2.6213
+ IC    O3A     PB      O3B     PG          1.5942   96.09 -119.52  151.10   1.6742
+ IC    PA      O3B     PG      O1G         3.8152  152.27 -123.23  106.71   1.5270
+ IC    O3B     PG      *O1G    O2G         2.5699   38.61 -114.53   33.79   2.5404
+ IC    O3B     PG      *O1G    O3G         2.5699   38.61  116.98   33.14   2.5609
+ IC    PA      O5'     C5'     C4'         1.5927  123.18  -89.06  115.64   1.5507
+ IC    O5'     C5'     C4'     C3'         1.4436  115.64   49.18  119.96   1.5360
+ IC    O5'     C5'     C4'     C3'         1.4436  115.64   49.18  119.96   1.5360
+ IC    C5'     C4'     C3'     O3'         1.5507  119.96   74.41  110.78   1.4388
+ IC    H3T     O3'     C3'     C4'         0.9867  102.53 -104.57  110.78   1.5360
+ IC    O4'     C3'     *C4'    C5'         1.4601  104.58 -126.54  119.96   1.5507
+ IC    C2'     C4'     *C3'    O3'         1.5122  101.75 -122.80  110.78   1.4388
+ IC    C4'     C3'     C2'     C1'         1.5360  101.75   39.19  100.86   1.5243
+ IC    C3'     C2'     C1'     N1          1.5122  100.86   92.81  111.95   1.4916
+ IC    O4'     C1'     N1      C2          1.4265  111.16 -147.40  118.55   1.3742
+ IC    C1'     C2      *N1     C6          1.4916  118.55  172.02  119.98   1.3897
+ IC    C2      N1      C6      C5          1.3742  119.98   10.83  122.70   1.3455
+ IC    C6      N1      C2      N3          1.3897  119.98  -10.49  115.19   1.3703
+ IC    N1      N3      *C2     O2          1.3742  115.19  175.89  121.40   1.2306
+ IC    N1      C2      N3      C4          1.3742  115.19    3.36  127.40   1.3788
+ IC    C5      N3      *C4     O4          1.4296  114.47 -173.68  118.19   1.2356
+ IC    C2      C4      *N3     H3          1.3703  127.40 -160.74  114.36   0.9907
+ IC    C4      C6      *C5     H5          1.4296  119.28 -179.18  121.12   1.0872
+ IC    N1      C5      *C6     H6          1.3897  122.70 -177.32  120.53   1.0892
+ IC    C1'     C3'     *C2'    O2'         1.5243  100.86 -119.14  109.80   1.4201
+ IC    H2'     O2'     C2'     C3'         0.9693  100.49  -35.37  109.80   1.5122
+ IC    O4'     C2'     *C1'    H1'         1.4265  108.04 -114.27  108.39   1.1130
+ IC    C1'     C3'     *C2'    H2''        1.5243  100.86  117.99  110.14   1.1147
+ IC    C2'     C4'     *C3'    H3'         1.5122  101.75  114.23  109.76   1.1048
+ IC    C3'     O4'     *C4'    H4'         1.5360  104.58 -111.39  105.32   1.1094
+ IC    C4'     O5'     *C5'    H5'         1.5507  115.64 -120.26  107.77   1.1109
+ IC    C4'     O5'     *C5'    H5''        1.5507  115.64  123.55  110.93   1.1137
+PATC  FIRS NONE LAST NONE
+
+
+PRES 5DP         -3.00  ! patch to create 5' diphosphate on nucleotides, jjp1/adm jr.
+                        ! as in ADP, use in generate statement
+GROUP
+ATOM C5'  CN8    -0.08
+ATOM H5'  HN8     0.09
+ATOM H5'' HN8     0.09
+ATOM O5'  ON2    -0.62
+ATOM P    P       1.50
+ATOM O1P  ON3    -0.82
+ATOM O2P  ON3    -0.82
+ATOM O13  ON2    -0.74
+ATOM P2   P3      1.10
+ATOM O21  ON3    -0.90
+ATOM O22  ON3    -0.90
+ATOM O23  ON3    -0.90
+
+BOND P    O13       O13   P2       
+BOND P2   O21       P2    O22      P2   O23
+ACCE O13
+ACCE O21
+ACCE O22
+ACCE O23
+IC C5'  O5'  P    O13    0.0000  000.00  180.0   000.00   0.0000
+IC O5'  P    O13  P2     0.0000  000.00  180.0   000.00   0.0000
+IC P    O13  P2   O21    0.0000  000.00  180.0   000.00   0.0000
+IC P    O13  P2   O22    0.0000  000.00   60.0   000.00   0.0000
+IC P    O13  P2   O23    0.0000  000.00  -60.0   000.00   0.0000
+PATC  FIRS NONE LAST NONE
+
+!atom nomenclature consisent with PDB, 2015
+
+RESI NAD         -1.00  ! oxidized nicotinamide adenine dinucleotide, jjp1/adm jr.
+                        ! atom names correspond to pdb nomenclature
+                        ! checked for consistency with new NA params, adm jr., 9/98
+                        ! note that differences with respect to published results exist
+                        ! due to new NA params
+GROUP                   !
+ATOM C4B  CN7     0.16  !                H61A  H62A
+ATOM H4B  HN7     0.09  !                   \  /
+ATOM O4B  ON6B   -0.50  !                   N6A
+ATOM C1B  CN7B    0.16  !                    |
+ATOM H1B  HN7     0.09  !                   C6A
+GROUP                   !                  //  \
+ATOM C5A  CN5     0.28  !                 N1A  C5A--N7A\\
+ATOM N7A  NN4    -0.71  !                  |    ||     C8A-H8A
+ATOM C8A  CN4     0.34  !                 C2A  C4A--N9A/
+ATOM H8A  HN3     0.12  !                 / \\ /     \
+ATOM N9A  NN2    -0.05  !              H2A  N3A       \
+                        !                              \
+ATOM N1A  NN3A   -0.74  !                               \
+ATOM C2A  CN4     0.50  !                                \
+ATOM H2A  HN3     0.13  !    O1N     O1A    H52AH4B  O4B  \
+ATOM N3A  NN3A   -0.75  !     |       |      |    \ /   \  \
+ATOM C4A  CN5     0.43  ! O5D PN-O3--PA-O5B -C5B -C4B    C1B 
+ATOM C6A  CN2     0.46  ! \   |       |      |     \     / \
+                        !  \ O2N     O2A    H51A C3B -C2B  H1B 
+ATOM N6A  NN1    -0.77  !   \                     / \   / \
+ATOM H61A HN1     0.38  !    \                O3B  H3B O2B H2B 
+ATOM H62A HN1     0.38  !     \                 |       |
+GROUP                   !      \              HO3A     HO2A
+ATOM C2B  CN7B    0.14  !       \                        H71N
+ATOM H2B  HN7     0.09  !        \                          \ 
+ATOM O2B  ON5    -0.66  !         \                    H72N-N7N    N41N
+ATOM HO2A HN5     0.43  !          \                          \     |
+GROUP                   !           \                         C7N  C4N
+ATOM C3B  CN7     0.14  !            \                        / \  /  \
+ATOM H3B  HN7     0.09  !             \                    O7N  C3N  C5N-H5N
+ATOM O3B  ON5    -0.66  !              \                          |    |
+ATOM HO3A HN5     0.43  !               \ H51N H4D O4D       H2N-C2N C6N-HN6
+GROUP                   !                \ |    \ /   \            \+ /   
+ATOM C5B  CN8B   -0.08  !                 C5D --C4D    C1D ---------N1N
+ATOM H51A HN8     0.09  !                  |     \     / \
+ATOM H52A HN8     0.09  !                 H52N   C3D -C2D H1D 
+ATOM PA   P       1.50  !                       / \   / \
+ATOM O1A  ON3    -0.82  !                   O3D  H3D O2D H2D 
+ATOM O2A  ON3    -0.82  !                    |       |
+ATOM O5B  ON2    -0.62  !                   HO3N    HO2N
+ATOM O3   ON2    -0.68
+ATOM PN   P       1.50
+ATOM O1N  ON3    -0.82
+ATOM O2N  ON3    -0.82
+ATOM O5D  ON2    -0.62
+ATOM C5D  CN8B   -0.08
+ATOM H51N HN8     0.09
+ATOM H52N HN8     0.09 
+GROUP                  
+ATOM C2D  CN7B    0.14 
+ATOM H2D  HN7     0.09 
+ATOM O2D  ON5    -0.66
+ATOM HO2N HN5     0.43
+GROUP
+ATOM C3D  CN7     0.14
+ATOM H3D  HN7     0.09
+ATOM O3D  ON5    -0.66
+ATOM HO3N HN5     0.43
+GROUP
+ATOM C1D  CN7B    0.16
+ATOM H1D  HN7     0.09
+ATOM C4D  CN7     0.16
+ATOM H4D  HN7     0.09
+ATOM O4D  ON6B   -0.50
+GROUP                  
+ATOM N1N  NN2    -0.07
+ATOM C6N  CN3B    0.16
+ATOM HN6  HN3B    0.19
+ATOM C5N  CN3    -0.10
+ATOM H5N  HN3B    0.16
+ATOM C4N  CN3A   -0.05
+ATOM H41N HN3B    0.16 !H4N in official nomenclature
+ATOM C3N  CN3     0.05 
+ATOM C2N  CN3B    0.18
+ATOM H2N  HN3B    0.16
+ATOM C7N  CN1A    0.68 
+ATOM O7N  ON1    -0.40 
+ATOM N7N  NN1    -0.82
+ATOM H71N HN1     0.34  ! trans to amide O
+ATOM H72N HN1     0.36  ! cis to amide O
+
+BOND N1A  C2A       N3A  C4A       C5A  C6A
+BOND C6A  N6A       C5A  N7A       C8A  N9A
+BOND N9A  C4A       C2A  H2A       N6A  H61A      N6A  H62A      C8A  H8A
+DOUBLE C6A  N1A       C2A  N3A       C4A  C5A      N7A  C8A
+BOND N9A  C1B       C1B  C2B       C2B  C3B       C3B  C4B       C4B  O4B 
+BOND O4B  C1B       C1B  H1B       C2B  O2B       O2B  HO2A      C2B  H2B 
+BOND C3B  H3B       C3B  O3B       O3B  HO3A      C4B  H4B       C4B  C5B 
+BOND C5B  H52A      C5B  H51A      C5B  O5B       O5B  PA        PA   O1A
+BOND PA   O2A       PA   O3        O3   PN        PN   O1N       PN   O2N
+BOND PN   O5D       O5D  C5D       C5D  H51N      C5D  H52N      C5D  C4D 
+BOND C4D  O4D       O4D  C1D       C1D  C2D       C2D  C3D       C3D  C4D 
+BOND C1D  H1D       C2D  H2D       C2D  O2D       O2D  HO2N      C3D  H3D 
+BOND C3D  O3D       O3D  HO3N      C4D  H4D       C1D  N1N       N1N  C2N
+BOND C3N  C4N       C5N  C6N
+BOND C2N  H2N       C3N  C7N       C7N  O7N       C7N  N7N       N7N  H71N
+BOND N7N  H72N      C4N  H41N      C5N  H5N       C6N  HN6
+DOUBLE C2N  C3N       C4N  C5N       C6N  N1N
+! adenine impropers
+IMPR N6A  C6A  H61A H62A     C6A   N1A   C5A  N6A       
+! amide impropers
+IMPR C7N   N7N   C3N  O7N    C7N   C3N   N7N   O7N 
+IMPR N7N   C7N   H71N H72N   N7N   C7N   H72N  H71N
+! ring hydrogen impropers
+IMPR C6N   N1N   C5N  HN6    C5N   C6N   C4N   H5N
+IMPR C4N   C5N   C3N  H41N   C2N   C3N   N1N   H2N
+DONO H61A N6A
+DONO H62A N6A
+DONO HO2A O2B 
+DONO HO3A O3B 
+ACCE N1A
+ACCE N3A
+ACCE N7A
+ACCE O4B 
+ACCE O2B 
+ACCE O3B 
+ACCE O5B 
+ACCE O1A  PA
+ACCE O2A  PA
+ACCE O3
+ACCE O1N  PN
+ACCE O2N  PN
+ACCE O5D 
+ACCE O4D 
+ACCE O3D 
+ACCE O2D 
+ACCE O7N
+DONO HO2N O2D 
+DONO HO3N O3D 
+DONO H71N N7N
+DONO H72N N7N
+
+IC O4B   C4B   C5B   O5B    1.4602  109.06  141.71  112.09   1.4439
+IC O4B   C5B   *C4B  C3B    1.4602  109.06 -116.95  116.13   1.5393
+IC C3B   C5B   *C4B  H4B    1.5393  116.13 -123.66  110.37   1.1118
+IC C5B   C4B   O4B   C1B    1.5373  109.06 -136.33  109.65   1.4148
+IC C4B   O4B   C1B   N9A    1.4602  109.65 -135.81  111.11   1.4598
+IC N9A   O4B   *C1B  C2B    1.4598  111.11  122.68  107.19   1.5091
+IC N9A   O4B   *C1B  H1B    1.4598  111.11 -120.43  106.09   1.1157
+IC O4B   C1B   N9A   C4A    1.4148  111.11 -132.21  126.91   1.3718
+IC C4A   C1B   *N9A  C8A    1.3718  126.91 -179.77  127.02   1.3735
+IC C1B   N9A   C4A   C5A    1.4598  126.91 -179.47  105.60   1.3834
+IC C5A   N9A   *C4A  N3A    1.3834  105.60 -179.98  127.70   1.3425
+IC N9A   C4A   C5A   C6A    1.3718  105.60  179.90  116.93   1.4100
+IC C6A   C4A   *C5A  N7A    1.4100  116.93 -179.96  110.88   1.3888
+IC N7A   N9A   *C8A  H8A    1.3106  113.69  179.35  121.11   1.0928
+IC C4A   C5A   C6A   N1A    1.3834  116.93   -0.07  117.90   1.3546
+IC N1A   C5A   *C6A  N6A    1.3546  117.90  179.83  123.29   1.3450
+IC C5A   C6A   N1A   C2A    1.4100  117.90    0.12  118.20   1.3359
+IC N3A   N1A   *C2A  H2A    1.3354  129.50  179.91  115.36   1.0937
+IC C5A   C6A   N6A   H61A   1.4100  123.29 -178.42  117.49   0.9946
+IC H61A  C6A   *N6A  H62A   0.9946  117.49  176.18  120.81   0.9965
+IC C3B   C1B   *C2B  O2B    1.5071  101.20  117.08  111.89   1.4144
+IC C3B   C1B   *C2B  H2B    1.5071  101.20 -117.38  111.86   1.1141
+IC C1B   C2B   O2B   HO2A   1.5091  111.89  178.91  108.27   0.9632
+IC C2B   C4B   *C3B  O3B    1.5071  102.42  118.21  111.98   1.4364
+IC C2B   C4B   *C3B  H3B    1.5071  102.42 -117.88  107.58   1.1121
+IC C4B   C3B   O3B   HO3A   1.5393  111.98   53.77  108.82   0.9987
+IC C3B   C4B   C5B   O5B    1.5393  116.13   24.76  112.09   1.4439
+IC O5B   C4B   *C5B  H52A   1.4439  112.09 -118.16  109.00   1.1133
+IC H52A  C4B   *C5B  H51A   1.1133  109.00 -114.98  109.51   1.1161
+IC C4B   C5B   O5B   PA     1.5373  112.09   94.39  121.28   1.5826
+IC C5B   O5B   PA    O3     1.4439  121.28  148.70   94.54   1.4969
+IC O3    O5B   *PA   O1A    1.4969   94.54 -121.80  106.23   1.4772
+IC O1A   O5B   *PA   O2A    1.4772  106.23 -125.48  100.49   1.4822
+IC O5B   PA    O3    PN     1.5826   94.54 -171.26  103.25   1.5079
+IC PA    O3    PN    O5D    1.4969  103.25 -156.08   92.59   1.5791
+IC O5D   O3    *PN   O1N    1.5791   92.59 -108.10  112.08   1.4709
+IC O1N   O3    *PN   O2N    1.4709  112.08 -147.35  119.96   1.4872
+IC O3    PN    O5D   C5D    1.5079   92.59  169.85  121.25   1.4424
+IC PN    O5D   C5D   C4D    1.5791  121.25 -120.85  113.63   1.5461
+IC C4D   O5D   *C5D  H51N   1.5461  113.63 -118.98  107.36   1.1130
+IC H51N  O5D   *C5D  H52N   1.1130  107.36 -116.76  113.02   1.1173
+IC O5D   C5D   C4D   O4D    1.4424  113.63  -49.73  112.77   1.4709
+IC O4D   C5D   *C4D  C3D    1.4709  112.77  124.54  119.31   1.5563
+IC O4D   C5D   *C4D  H4D    1.4709  112.77 -115.70  107.56   1.1116
+IC C5D   C4D   C3D   C2D    1.5461  119.31 -156.53   99.76   1.5184
+IC C2D   C4D   *C3D  O3D    1.5184   99.76  119.65  119.67   1.4380
+IC C2D   C4D   *C3D  H3D    1.5184   99.76 -115.32  107.95   1.1119
+IC C4D   C3D   C2D   C1D    1.5563   99.76   43.53  100.45   1.5351
+IC C1D   C3D   *C2D  O2D    1.5351  100.45  123.80  111.51   1.4145
+IC C1D   C3D   *C2D  H2D    1.5351  100.45 -114.84  109.59   1.1136
+IC C3D   C2D   O2D   HO2N   1.5184  111.51  -13.38  103.51   0.9747
+IC C4D   C3D   O3D   HO3N   1.5563  119.67   42.59  111.67   0.9972
+IC O4D   C2D   *C1D  N1N    1.4197  103.46  122.07  115.99   1.5110
+IC O4D   C2D   *C1D  H1D    1.4197  103.46 -113.32  108.74   1.1122
+IC C2D   C1D   N1N   C2N    1.5351  115.99   48.31  121.57   1.3422
+IC C2N   C1D   *N1N  C6N    1.3422  121.57 -175.31  121.05   1.3474
+IC C1D   N1N   C6N   C5N    1.5110  121.05  177.97  122.74   1.3691
+IC C5N   N1N   *C6N  HN6    1.3691  122.74 -171.45  116.89   1.0961
+IC N1N   C6N   C5N   C4N    1.3474  122.74   -3.94  119.48   1.3753
+IC C4N   C6N   *C5N  H5N    1.3753  119.48 -170.98  120.63   1.0956
+IC C6N   C5N   C4N   C3N    1.3691  119.48    1.56  118.55   1.3864
+IC C3N   C5N   *C4N  H41N   1.3864  118.55 -175.37  120.26   1.0910
+IC C3N   N1N   *C2N  H2N    1.3745  123.21  178.08  117.05   1.0911
+IC C2N   C4N   *C3N  C7N    1.3745  118.63 -178.85  118.88   1.5091
+IC C4N   C3N   C7N   N7N    1.3864  118.88   23.83  117.95   1.3519
+IC N7N   C3N   *C7N  O7N    1.3519  117.95  175.54  118.43   1.2254
+IC C3N   C7N   N7N   H71N   1.5091  117.95  160.64  114.22   0.9962
+IC H71N  C7N   *N7N  H72N   0.9962  114.22 -140.75  118.52   1.0129
+PATCH FIRST NONE LAST NONE   
+
+RESI NAI         -2.00  ! reduced nicotinamide adenine dinucleotide, NADH, jjp1/adm jr.
+                        ! some PDB files use NAD for NADH
+                        ! atom names correspond to pdb nomenclature
+                        ! checked for consistency with new NA params, adm jr., 9/98
+                        ! note that differences with respect to published results exist
+                        ! due to new NA params
+                        !
+GROUP                   !
+ATOM C4B  CN7     0.16  !                H61A  H62A
+ATOM H4B  HN7     0.09  !                   \  /
+ATOM O4B  ON6B   -0.50  !                   N6A
+ATOM C1B  CN7B    0.16  !                    |
+ATOM H1B  HN7     0.09  !                   C6A
+GROUP                   !                  //  \
+ATOM C5A  CN5     0.28  !                 N1A  C5A--N7A\\
+ATOM N7A  NN4    -0.71  !                  |    ||     C8A-H8A
+ATOM C8A  CN4     0.34  !                 C2A  C4A--N9A/
+ATOM H8A  HN3     0.12  !                 / \\ /     \
+ATOM N9A  NN2    -0.05  !              H2A  N3A       \
+                        !                              \
+ATOM N1A  NN3A   -0.74  !                               \
+ATOM C2A  CN4     0.50  !                                \
+ATOM H2A  HN3     0.13  !    O1N     O1A    H52AH4B  O4B  \
+ATOM N3A  NN3A   -0.75  !     |       |      |    \ /   \  \
+ATOM C4A  CN5     0.43  ! O5D PN-O3--PA-O5B -C5B -C4B    C1B 
+ATOM C6A  CN2     0.46  ! \   |       |      |     \     / \
+                        !  \ O2N     O2A    H51A C3B -C2B  H1B 
+ATOM N6A  NN1    -0.77  !   \                     / \   / \
+ATOM H61A HN1     0.38  !    \                O3B  H3B O2B H2B 
+ATOM H62A HN1     0.38  !     \                 |       |
+GROUP                   !      \              HO3A     HO2A
+ATOM C2B  CN7B    0.14  !       \                        H71N
+ATOM H2B  HN7     0.09  !        \                          \
+ATOM O2B  ON5    -0.66  !         \                    H72N-N7N  H41NH42N
+ATOM HO2A HN5     0.43  !          \                          \    \ /
+GROUP                   !           \                         C7N  C4N
+ATOM C3B  CN7     0.14  !            \                        / \  /  \
+ATOM H3B  HN7     0.09  !             \                    O7N  C3N  C5N-H5N
+ATOM O3B  ON5    -0.66  !              \                          |    |
+ATOM HO3A HN5     0.43  !               \ H51N H4D O4D       H2N-C2N C6N-HN6
+GROUP                   !                \ |    \ /   \            \  /
+ATOM C5B  CN8B   -0.08  !                 C5D --C4D    C1D ---------N1N
+ATOM H51A HN8     0.09  !                  |     \     / \
+ATOM H52A HN8     0.09  !                 H52N   C3D -C2D H1D 
+ATOM PA   P       1.50  !                       / \   / \
+ATOM O1A  ON3    -0.82  !                   O3D  H3D O2D H2D 
+ATOM O2A  ON3    -0.82  !                    |       |
+ATOM O5B  ON2    -0.62  !                   HO3N    HO2N
+ATOM O3   ON2    -0.68
+ATOM PN   P       1.50
+ATOM O1N  ON3    -0.82
+ATOM O2N  ON3    -0.82
+ATOM O5D  ON2    -0.62
+ATOM C5D  CN8B   -0.08
+ATOM H51N HN8     0.09
+ATOM H52N HN8     0.09
+GROUP
+ATOM C2D  CN7B    0.14
+ATOM H2D  HN7     0.09
+ATOM O2D  ON5    -0.66
+ATOM HO2N HN5     0.43
+GROUP
+ATOM C3D  CN7     0.14
+ATOM H3D  HN7     0.09
+ATOM O3D  ON5    -0.66
+ATOM HO3N HN5     0.43
+GROUP
+ATOM C1D  CN7B    0.16
+ATOM H1D  HN7     0.09
+ATOM C4D  CN7     0.16
+ATOM H4D  HN7     0.09
+ATOM O4D  ON6B   -0.50
+GROUP
+ATOM N1N  NN2    -0.27 !N2
+ATOM C6N  CN3C   -0.06 !C3
+ATOM HN6  HN6     0.17 !H4
+ATOM C5N  CN3    -0.18 !C5
+ATOM H5N  HN6     0.14 !H6
+ATOM C4N  CN8    -0.28 !C7
+ATOM H41N HN8     0.09 !H8
+ATOM H42N HN8     0.09 !H17
+ATOM C3N  CN3     0.36 !C9
+ATOM C2N  CN3C   -0.10 !C10
+ATOM H2N  HN6     0.14 !H11
+ATOM C7N  CN1A    0.55 !C12
+ATOM O7N  ON1    -0.51 !O13
+ATOM N7N  NN1    -0.72 !N14
+ATOM H71N HN1     0.26 !H15  ! trans to amide O
+ATOM H72N HN1     0.32 !H16  ! cis to amide O
+
+BOND N1A  C2A       N3A  C4A       C5A  C6A
+BOND C6A  N6A       C5A  N7A       C8A  N9A
+BOND N9A  C4A       C2A  H2A       N6A  H61A      N6A  H62A      C8A  H8A
+DOUBLE  C6A  N1A      C2A  N3A      C4A  C5A      N7A  C8A
+BOND N9A  C1B       C1B  C2B       C2B  C3B       C3B  C4B       C4B  O4B 
+BOND O4B  C1B       C1B  H1B       C2B  O2B       O2B  HO2A      C2B  H2B 
+BOND C3B  H3B       C3B  O3B       O3B  HO3A      C4B  H4B       C4B  C5B 
+BOND C5B  H52A      C5B  H51A      C5B  O5B       O5B  PA        PA   O1A
+BOND PA   O2A       PA   O3        O3   PN        PN   O1N       PN   O2N
+BOND PN   O5D       O5D  C5D       C5D  H51N      C5D  H52N      C5D  C4D 
+BOND C4D  O4D       O4D  C1D       C1D  C2D       C2D  C3D       C3D  C4D 
+BOND C1D  H1D       C2D  H2D       C2D  O2D       O2D  HO2N      C3D  H3D 
+BOND C3D  O3D       O3D  HO3N      C4D  H4D       C1D  N1N       N1N  C2N
+BOND C3N  C4N       C4N  C5N       C6N  N1N
+BOND C2N  H2N       C3N  C7N       C7N  O7N       C7N  N7N       N7N  H71N
+BOND N7N  H72N      C4N  H41N      C4N  H42N      C5N  H5N       C6N  HN6
+DOUBLE  C2N  C3N      C5N  C6N
+! adenine impropers
+IMPR N6A  C6A  H61A H62A     C6A  N1A  C5A  N6A       
+! amide impropers
+IMPR C7N   N7N   C3N  O7N    C7N   C3N   N7N   O7N
+IMPR N7N   C7N   H71N H72N   N7N   C7N   H72N  H71N
+! ring hydrogen impropers
+IMPR C6N   N1N   C5N  HN6    C5N   C6N   C4N   H5N
+IMPR C4N   C5N   C3N  H41N   C2N   C3N   N1N   H2N
+DONO H61A N6A
+DONO H62A N6A
+DONO HO2A O2B 
+DONO HO3A O3B 
+ACCE N1A
+ACCE N3A
+ACCE N7A
+ACCE O4B 
+ACCE O2B 
+ACCE O3B 
+ACCE O5B 
+ACCE O1A  PA
+ACCE O2A  PA
+ACCE O3
+ACCE O1N  PN
+ACCE O2N  PN
+ACCE O5D 
+ACCE O4D 
+ACCE O3D 
+ACCE O2D 
+ACCE O7N
+DONO HO2N O2D 
+DONO HO3N O3D 
+DONO H71N N7N
+DONO H72N N7N
+
+IC O4B   C4B   C5B   O5B    1.4592  109.88  127.15  112.06   1.4436
+IC O4B   C5B   *C4B  C3B    1.4592  109.88 -119.04  118.31   1.5383
+IC C3B   C5B   *C4B  H4B    1.5383  118.31 -123.09  109.39   1.1113
+IC C5B   C4B   O4B   C1B    1.5404  109.88 -146.22  109.49   1.4139
+IC C4B   O4B   C1B   N9A    1.4592  109.49 -127.93  110.13   1.4603
+IC N9A   O4B   *C1B  C2B    1.4603  110.13  122.48  107.68   1.5154
+IC N9A   O4B   *C1B  H1B    1.4603  110.13 -120.39  106.05   1.1153
+IC O4B   C1B   N9A   C4A    1.4139  110.13 -117.96  127.68   1.3725
+IC C4A   C1B   *N9A  C8A    1.3725  127.68  177.86  126.28   1.3734
+IC C1B   N9A   C4A   C5A    1.4603  127.68  178.99  105.54   1.3840
+IC C5A   N9A   *C4A  N3A    1.3840  105.54  179.70  127.97   1.3431
+IC N9A   C4A   C5A   C6A    1.3725  105.54 -179.81  117.00   1.4096
+IC C6A   C4A   *C5A  N7A    1.4096  117.00  179.47  111.00   1.3884
+IC N7A   N9A   *C8A  H8A    1.3113  113.83  179.81  121.02   1.0926
+IC C4A   C5A   C6A   N1A    1.3840  117.00   -0.40  118.02   1.3545
+IC N1A   C5A   *C6A  N6A    1.3545  118.02  179.70  123.12   1.3454
+IC C5A   C6A   N1A   C2A    1.4096  118.02    0.07  118.03   1.3365
+IC N3A   N1A   *C2A  H2A    1.3345  129.58  179.79  115.39   1.0936
+IC C5A   C6A   N6A   H61A   1.4096  123.12 -178.46  117.57   0.9939
+IC H61A  C6A   *N6A  H62A   0.9939  117.57  176.57  120.42   0.9965
+IC C3B   C1B   *C2B  O2B    1.5103  102.02  117.99  111.67   1.4134
+IC C3B   C1B   *C2B  H2B    1.5103  102.02 -117.32  112.17   1.1132
+IC C1B   C2B   O2B   HO2A   1.5154  111.67 -163.97  107.58   0.9678
+IC C2B   C4B   *C3B  O3B    1.5103  101.80  116.77  110.83   1.4344
+IC C2B   C4B   *C3B  H3B    1.5103  101.80 -119.13  108.74   1.1128
+IC C4B   C3B   O3B   HO3A   1.5383  110.83   54.91  107.95   0.9983
+IC C3B   C4B   C5B   O5B    1.5383  118.31    8.12  112.06   1.4436
+IC O5B   C4B   *C5B  H52A   1.4436  112.06 -118.83  109.45   1.1125
+IC H52A  C4B   *C5B  H51A   1.1125  109.45 -115.45  109.09   1.1167
+IC C4B   C5B   O5B   PA     1.5404  112.06  103.36  120.31   1.5832
+IC C5B   O5B   PA    O3     1.4436  120.31  176.42   94.39   1.5047
+IC O3    O5B   *PA   O1A    1.5047   94.39 -120.03  104.05   1.4804
+IC O1A   O5B   *PA   O2A    1.4804  104.05 -123.95  100.78   1.4839
+IC O5B   PA    O3    PN     1.5832   94.39 -178.56  100.47   1.5104
+IC PA    O3    PN    O5D    1.5047  100.47 -170.27   94.47   1.5770
+IC O5D   O3    *PN   O1N    1.5770   94.47 -107.91  114.74   1.4790
+IC O1N   O3    *PN   O2N    1.4790  114.74 -147.43  117.97   1.4863
+IC O3    PN    O5D   C5D    1.5104   94.47 -177.92  120.58   1.4431
+IC PN    O5D   C5D   C4D    1.5770  120.58 -122.07  113.80   1.5459
+IC C4D   O5D   *C5D  H51N   1.5459  113.80 -119.75  107.60   1.1121
+IC H51N  O5D   *C5D  H52N   1.1121  107.60 -117.14  112.75   1.1171
+IC O5D   C5D   C4D   O4D    1.4431  113.80  -64.50  112.96   1.4660
+IC O4D   C5D   *C4D  C3D    1.4660  112.96  127.07  120.95   1.5529
+IC O4D   C5D   *C4D  H4D    1.4660  112.96 -113.76  106.56   1.1112
+IC C5D   C4D   C3D   C2D    1.5459  120.95 -160.75   99.47   1.5206
+IC C2D   C4D   *C3D  O3D    1.5206   99.47  121.69  119.59   1.4385
+IC C2D   C4D   *C3D  H3D    1.5206   99.47 -114.49  107.55   1.1109
+IC C4D   C3D   C2D   C1D    1.5529   99.47   42.83  101.15   1.5416
+IC C1D   C3D   *C2D  O2D    1.5416  101.15  126.12  112.03   1.4127
+IC C1D   C3D   *C2D  H2D    1.5416  101.15 -113.62  108.86   1.1129
+IC C3D   C2D   O2D   HO2N   1.5206  112.03  -33.33  102.61   0.9714
+IC C4D   C3D   O3D   HO3N   1.5529  119.59   46.10  109.78   0.9937
+IC O4D   C2D   *C1D  N1N    1.4246  103.98  123.05  117.48   1.5125
+IC O4D   C2D   *C1D  H1D    1.4246  103.98 -113.06  108.45   1.1101
+IC C2D   C1D   N1N   C2N    1.5416  117.48   21.65  124.87   1.3754
+IC C2N   C1D   *N1N  C6N    1.3754  124.87 -167.67  121.17   1.3759
+IC C1D   N1N   C6N   C5N    1.5125  121.17  126.10  120.49   1.3282
+IC C5N   N1N   *C6N  HN6    1.3282  120.49 -173.51  119.76   1.0882
+IC N1N   C6N   C5N   C4N    1.3759  120.49   26.68  121.42   1.5170
+IC C4N   C6N   *C5N  H5N    1.5170  121.42 -140.43  114.25   1.0930
+IC C6N   C5N   C4N   C3N    1.3282  121.42   -4.55  109.89   1.5374
+IC C3N   C5N   *C4N  H41N   1.5374  109.89  127.11  113.12   1.1052
+IC C3N   C5N   *C4N  H42N   1.5374  109.89 -116.77  106.76   1.1126
+IC C3N   N1N   *C2N  H2N    1.3514  121.98 -179.23  117.66   1.0902
+IC C2N   C4N   *C3N  C7N    1.3514  119.70  156.64  121.99   1.5300
+IC C4N   C3N   C7N   N7N    1.5374  121.99   23.57  115.90   1.3567
+IC N7N   C3N   *C7N  O7N    1.3567  115.90  178.78  122.04   1.2305
+IC C3N   C7N   N7N   H71N   1.5300  115.90  162.43  114.68   0.9962
+IC H71N  C7N   *N7N  H72N   0.9962  114.68 -141.25  117.82   1.0104
+PATCH FIRST NONE LAST NONE
+
+RESI NAP         -2.00  ! oxidized nicotinamide adenine dinucleotide, NADP+, adm jr.
+                        ! atom names correspond to pdb nomenclature
+                        ! checked for consistency with new NA params, adm jr., 9/98
+                        ! note that differences with respect to published results exist
+                        ! due to new NA params
+                        !
+GROUP                   !
+ATOM C4B  CN7     0.16  !                H61A  H62A
+ATOM H4B  HN7     0.09  !                   \  /
+ATOM O4B  ON6B   -0.50  !                   N6A
+ATOM C1B  CN7B    0.16  !                    |
+ATOM H1B  HN7     0.09  !                   C6A
+GROUP                   !                  //  \
+ATOM C5A  CN5     0.28  !                 N1A  C5A--N7A\\
+ATOM N7A  NN4    -0.71  !                  |    ||     C8A-H8A
+ATOM C8A  CN4     0.34  !                 C2A  C4A--N9A/
+ATOM H8A  HN3     0.12  !                 / \\ /     \
+ATOM N9A  NN2    -0.05  !              H2A  N3A       \
+                        !                              \
+ATOM N1A  NN3A   -0.74  !                               \
+ATOM C2A  CN4     0.50  !                                \
+ATOM H2A  HN3     0.13  !    O1N     O1A    H52AH4B  O4B  \
+ATOM N3A  NN3A   -0.75  !     |       |      |    \ /   \  \
+ATOM C4A  CN5     0.43  !O5D PN-O3--PA-O5B -C5B -C4B    C1B
+ATOM C6A  CN2     0.46  ! \   |       |      |     \     / \
+                        !  \ O2N     O2A    H51A C3B -C2B  H1B
+ATOM N6A  NN1    -0.77  !   \                     / \   / \
+ATOM H61A HN1     0.38  !    \                O3B  H3B O2B H2B
+ATOM H62A HN1     0.38  !     \                |        |
+GROUP                   !      \             HO3A O1X =P2B==O2X  (-)
+ATOM C2B  CN7B    0.01  !       \                       |    H71N
+ATOM H2B  HN7     0.09  !        \                HO2A-O3X    /
+ATOM O2B  ON2    -0.62  !         \                    H72N-N7N    H41N
+ATOM P2B  P       1.50  !          \                          \     |
+ATOM O1X  ON3    -0.82  !           \                         C7N  C4N
+ATOM O2X  ON3    -0.82  !            \                        / \  /  \
+ATOM O3X  ON4    -0.68  !             \                    O7N  C3N  C5N-H5N
+ATOM HO2A HN4     0.34  !              \                          |    |
+GROUP                   !               \                         |    |
+ATOM C3B  CN7     0.14  !                \ H51N H4D O4D       H2N-C2N C6N-HN6
+ATOM H3B  HN7     0.09  !                 \ |    \ /   \           \   /
+ATOM O3B  ON5    -0.66  !                  C5D --C4D    C1D --------N1N
+ATOM HO3A HN5     0.43  !                   |     \     / \
+GROUP                   !                 H52N   C3D--C2D H1D 
+ATOM C5B  CN8B   -0.08  !                        / \   / \  
+ATOM H51A HN8     0.09  !                    O3D  H3D O2D H2D   
+ATOM H52A HN8     0.09  !                     |       |
+ATOM PA   P       1.50  !                    HO3N    HO2N   
+ATOM O1A  ON3    -0.82  !
+ATOM O2A  ON3    -0.82  !
+ATOM O5B  ON2    -0.62  !
+ATOM O3   ON2    -0.68
+ATOM PN   P       1.50
+ATOM O1N  ON3    -0.82
+ATOM O2N  ON3    -0.82
+ATOM O5D  ON2    -0.62
+ATOM C5D  CN8B   -0.08
+ATOM H51N HN8     0.09
+ATOM H52N HN8     0.09 
+GROUP                  
+ATOM C2D  CN7B    0.14 
+ATOM H2D  HN7     0.09 
+ATOM O2D  ON5    -0.66
+ATOM HO2N HN5     0.43
+GROUP
+ATOM C3D  CN7     0.14
+ATOM H3D  HN7     0.09
+ATOM O3D  ON5    -0.66
+ATOM HO3N HN5     0.43
+GROUP
+ATOM C1D  CN7B    0.16
+ATOM H1D  HN7     0.09
+ATOM C4D  CN7     0.16
+ATOM H4D  HN7     0.09
+ATOM O4D  ON6B   -0.50
+GROUP                  
+ATOM N1N  NN2    -0.07
+ATOM C6N  CN3B    0.16
+ATOM HN6  HN3B    0.19
+ATOM C5N  CN3    -0.10
+ATOM H5N  HN3B    0.16
+ATOM C4N  CN3A   -0.05
+ATOM H41N HN3B    0.16 !H4N in official nomenclature
+ATOM C3N  CN3     0.05 
+ATOM C2N  CN3B    0.18
+ATOM H2N  HN3B    0.16
+ATOM C7N  CN1A    0.68 
+ATOM O7N  ON1    -0.40 
+ATOM N7N  NN1    -0.82
+ATOM H71N HN1     0.34  ! trans to amide O
+ATOM H72N HN1     0.36  ! cis to amide O
+
+BOND N1A  C2A       N3A  C4A       C5A  C6A
+BOND C6A  N6A       C5A  N7A       C8A  N9A
+BOND N9A  C4A       C2A  H2A       N6A  H61A      N6A  H62A      C8A  H8A
+DOUBLE C6A  N1A       C2A  N3A       C4A  C5A      N7A  C8A
+BOND N9A  C1B       C1B  C2B       C2B  C3B       C3B  C4B       C4B  O4B 
+BOND O4B  C1B       C1B  H1B       C2B  O2B       O2B  P2B      C2B  H2B 
+BOND C3B  H3B       C3B  O3B       O3B  HO3A      C4B  H4B       C4B  C5B 
+BOND C5B  H52A      C5B  H51A      C5B  O5B       O5B  PA        PA   O1A
+BOND PA   O2A       PA   O3        O3   PN        PN   O1N       PN   O2N
+BOND PN   O5D       O5D  C5D       C5D  H51N      C5D  H52N      C5D  C4D 
+BOND C4D  O4D       O4D  C1D       C1D  C2D       C2D  C3D       C3D  C4D 
+BOND C1D  H1D       C2D  H2D       C2D  O2D       O2D  HO2N      C3D  H3D 
+BOND C3D  O3D       O3D  HO3N      C4D  H4D       C1D  N1N       N1N  C2N
+BOND C3N  C4N       C5N  C6N
+BOND C2N  H2N       C3N  C7N       C7N  O7N       C7N  N7N       N7N  H71N
+BOND N7N  H72N      C4N  H41N      C5N  H5N       C6N  HN6
+BOND P2B  O1X       P2B  O2X       P2B  O3X       O3X  HO2A
+DOUBLE C2N  C3N       C4N  C5N       C6N  N1N
+! adenine impropers
+IMPR N6A  C6A  H61A H62A     C6A  N1A  C5A  N6A
+! amide impropers
+IMPR C7N   N7N   C3N  O7N    C7N   C3N   N7N   O7N 
+IMPR N7N   C7N   H71N H72N   N7N   C7N   H72N  H71N
+! ring hydrogen impropers
+IMPR C6N   N1N   C5N  HN6    C5N   C6N   C4N   H5N
+IMPR C4N   C5N   C3N  H41N   C2N   C3N   N1N   H2N
+DONO H61A N6A
+DONO H62A N6A
+DONO HO2A O2B 
+DONO HO3A O3B 
+ACCE N1A
+ACCE N3A
+ACCE N7A
+ACCE O4B 
+ACCE O2B 
+ACCE O3B 
+ACCE O5B 
+ACCE O1A  PA
+ACCE O2A  PA
+ACCE O3
+ACCE O1N  PN
+ACCE O2N  PN
+ACCE O5D 
+ACCE O4D 
+ACCE O3D 
+ACCE O2D 
+ACCE O7N
+DONO HO2N O2D 
+DONO HO3N O3D 
+DONO H71N N7N
+DONO H72N N7N
+DONO HO2A O3X 
+ACCE O3X 
+ACCE O1X 
+ACCE O2X 
+ACCE O2B 
+
+IC O4B   C4B   C5B   O5B    1.4585  109.71  159.30  112.46   1.4473
+IC O4B   C5B   *C4B  C3B    1.4585  109.71 -116.16  111.85   1.5464
+IC C3B   C5B   *C4B  H4B    1.5464  111.85 -123.40  110.92   1.1115
+IC C5B   C4B   O4B   C1B    1.5376  109.71 -108.48  108.78   1.4075
+IC C4B   O4B   C1B   N9A    1.4585  108.78 -152.38  111.04   1.4568
+IC N9A   O4B   *C1B  C2B    1.4568  111.04  121.73  107.16   1.5067
+IC N9A   O4B   *C1B  H1B    1.4568  111.04 -121.01  106.15   1.1159
+IC O4B   C1B   N9A   C4A    1.4075  111.04 -116.40  127.62   1.3704
+IC C4A   C1B   *N9A  C8A    1.3704  127.62 -179.20  126.23   1.3719
+IC C1B   N9A   C4A   C5A    1.4568  127.62 -179.21  105.46   1.3840
+IC C5A   N9A   *C4A  N3A    1.3840  105.46 -179.98  128.09   1.3448
+IC N9A   C4A   C5A   C6A    1.3704  105.46  179.01  116.94   1.4094
+IC C6A   C4A   *C5A  N7A    1.4094  116.94 -179.45  111.14   1.3881
+IC N7A   N9A   *C8A  H8A    1.3133  113.83  179.37  120.83   1.0924
+IC C4A   C5A   C6A   N1A    1.3840  116.94   -0.02  118.16   1.3545
+IC N1A   C5A   *C6A  N6A    1.3545  118.16 -179.37  122.98   1.3453
+IC C5A   C6A   N1A   C2A    1.4094  118.16   -0.02  117.86   1.3367
+IC N3A   N1A   *C2A  H2A    1.3332  129.71  178.74  115.38   1.0931
+IC C5A   C6A   N6A   H61A   1.4094  122.98  174.65  117.36   0.9937
+IC H61A  C6A   *N6A  H62A   0.9937  117.36 -169.69  119.66   0.9963
+IC C3B   C1B   *C2B  O2B    1.5188  101.16  119.53  108.66   1.4398
+IC C3B   C1B   *C2B  H2B    1.5188  101.16 -116.17  111.47   1.1163
+IC C1B   C2B   O2B   P2B    1.5067  108.66  164.95  121.64   1.5624
+IC C2B   O2B   P2B   O3X    1.4398  121.64 -145.91  106.75   1.5575
+IC O3X   O2B   *P2B  O1X    1.5575  106.75  112.52  112.63   1.4723
+IC O1X   O2B   *P2B  O2X    1.4723  112.63  135.09  111.70   1.4730
+IC O2B   P2B   O3X   HO2A   1.5624  106.75  179.79  107.64   0.9606
+IC C1B   C2B   O2B   HO2A   1.5067  108.66  140.65  141.83   3.3318
+IC C2B   C4B   *C3B  O3B    1.5188  105.43  121.35  109.34   1.4348
+IC C2B   C4B   *C3B  H3B    1.5188  105.43 -117.32  108.06   1.1126
+IC C4B   C3B   O3B   HO3A   1.5464  109.34   51.56  106.53   0.9936
+IC C3B   C4B   C5B   O5B    1.5464  111.85   43.14  112.46   1.4473
+IC O5B   C4B   *C5B  H52A   1.4473  112.46 -119.04  108.58   1.1125
+IC H52A  C4B   *C5B  H51A   1.1125  108.58 -116.00  109.43   1.1155
+IC C4B   C5B   O5B   PA     1.5376  112.46   78.42  120.97   1.5816
+IC C5B   O5B   PA    O3     1.4473  120.97  163.89   94.51   1.5036
+IC O3    O5B   *PA   O1A    1.5036   94.51 -121.21  105.58   1.4802
+IC O1A   O5B   *PA   O2A    1.4802  105.58 -126.12  102.35   1.4824
+IC O5B   PA    O3    PN     1.5816   94.51 -169.65  103.13   1.5074
+IC PA    O3    PN    O5D    1.5036  103.13 -158.88   92.67   1.5783
+IC O5D   O3    *PN   O1N    1.5783   92.67 -107.59  112.84   1.4735
+IC O1N   O3    *PN   O2N    1.4735  112.84 -147.96  119.72   1.4863
+IC O3    PN    O5D   C5D    1.5074   92.67  167.85  121.64   1.4408
+IC PN    O5D   C5D   C4D    1.5783  121.64 -119.99  113.59   1.5457
+IC C4D   O5D   *C5D  H51N   1.5457  113.59 -118.85  107.20   1.1125
+IC H51N  O5D   *C5D  H52N   1.1125  107.20 -116.81  112.97   1.1169
+IC O5D   C5D   C4D   O4D    1.4408  113.59  -47.57  113.01   1.4697
+IC O4D   C5D   *C4D  C3D    1.4697  113.01  124.91  119.42   1.5538
+IC O4D   C5D   *C4D  H4D    1.4697  113.01 -115.69  107.46   1.1114
+IC C5D   C4D   C3D   C2D    1.5457  119.42 -158.23   99.73   1.5185
+IC C2D   C4D   *C3D  O3D    1.5185   99.73  119.79  119.52   1.4371
+IC C2D   C4D   *C3D  H3D    1.5185   99.73 -115.26  108.09   1.1115
+IC C4D   C3D   C2D   C1D    1.5538   99.73   43.62  100.48   1.5339
+IC C1D   C3D   *C2D  O2D    1.5339  100.48  123.65  111.48   1.4144
+IC C1D   C3D   *C2D  H2D    1.5339  100.48 -114.85  109.66   1.1132
+IC C3D   C2D   O2D   HO2N   1.5185  111.48  -19.41  103.55   0.9759
+IC C4D   C3D   O3D   HO3N   1.5538  119.52   41.07  112.08   0.9969
+IC O4D   C2D   *C1D  N1N    1.4209  103.89  122.79  115.51   1.5069
+IC O4D   C2D   *C1D  H1D    1.4209  103.89 -113.36  108.85   1.1120
+IC C2D   C1D   N1N   C2N    1.5339  115.51   54.88  121.01   1.3424
+IC C2N   C1D   *N1N  C6N    1.3424  121.01 -177.68  121.58   1.3487
+IC C1D   N1N   C6N   C5N    1.5069  121.58 -178.88  122.67   1.3689
+IC C5N   N1N   *C6N  HN6    1.3689  122.67 -174.63  117.18   1.0940
+IC N1N   C6N   C5N   C4N    1.3487  122.67   -2.95  119.09   1.3746
+IC C4N   C6N   *C5N  H5N    1.3746  119.09 -173.56  121.44   1.0955
+IC C6N   C5N   C4N   C3N    1.3689  119.09   -1.00  119.02   1.3830
+IC C3N   C5N   *C4N  H41N   1.3830  119.02 -178.05  120.48   1.0937
+IC C3N   N1N   *C2N  H2N    1.3696  123.10  177.36  117.15   1.0905
+IC C2N   C4N   *C3N  C7N    1.3696  118.55 -179.48  116.96   1.5065
+IC C4N   C3N   C7N   N7N    1.3830  116.96   49.86  116.48   1.3522
+IC N7N   C3N   *C7N  O7N    1.3522  116.48  169.66  118.17   1.2276
+IC C3N   C7N   N7N   H71N   1.5065  116.48 -148.55  113.04   1.0028
+IC H71N  C7N   *N7N  H72N   1.0028  113.04  127.16  116.64   1.0104
+PATCH FIRST NONE LAST NONE   
+
+RESI NDP         -3.00  ! reduced nicotinamide adenine dinucleotide, NADPH, VARNAI/adm jr.
+                        ! from NADH and 3PHO
+                        ! checked for consistency with new NA params, adm jr., 9/98
+                        ! note that differences with respect to published results exist
+                        ! due to new NA params
+                        !
+GROUP                   !
+ATOM C4B  CN7     0.16  !                H61A  H62A
+ATOM H4B  HN7     0.09  !                   \  /
+ATOM O4B  ON6B   -0.50  !                   N6A
+ATOM C1B  CN7B    0.16  !                    |
+ATOM H1B  HN7     0.09  !                   C6A
+GROUP                   !                  //  \
+ATOM C5A  CN5     0.28  !                 N1A  C5A--N7A\\
+ATOM N7A  NN4    -0.71  !                  |    ||     C8A-H8A
+ATOM C8A  CN4     0.34  !                 C2A  C4A--N9A/
+ATOM H8A  HN3     0.12  !                 / \\ /     \
+ATOM N9A  NN2    -0.05  !              H2A  N3A       \
+                        !                              \
+ATOM N1A  NN3A   -0.74  !                               \
+ATOM C2A  CN4     0.50  !                                \
+ATOM H2A  HN3     0.13  !    O1N     O1A    H52AH4B  O4B  \
+ATOM N3A  NN3A   -0.75  !     |       |      |    \ /   \  \
+ATOM C4A  CN5     0.43  ! O5D PN-O3--PA-O5B -C5B -C4B    C1B 
+ATOM C6A  CN2     0.46  ! \   |       |      |     \     / \
+                        !  \ O2N     O2A    H51A C3B -C2B  H1B 
+ATOM N6A  NN1    -0.77  !   \                     / \   / \
+ATOM H61A HN1     0.38  !    \                O3B  H3B O2B H2B 
+ATOM H62A HN1     0.38  !     \                |        |
+GROUP                   !      \             HO3A O1X =P2B==O2X  (-)
+ATOM C2B  CN7B    0.01  !       \                       |    H71N
+ATOM H2B  HN7     0.09  !        \                HO2A-O3X    /
+ATOM O2B  ON2    -0.62  !         \                    H72N-N7N  H41NH42N
+ATOM P2B  P       1.50  !          \                          \    \ /
+ATOM O1X  ON3    -0.82  !           \                         C7N  C4N
+ATOM O2X  ON3    -0.82  !            \                        / \  /  \
+ATOM O3X  ON4    -0.68  !             \                    O7N  C3N  C5N-H5N
+ATOM HO2A HN4     0.34  !              \                          |    |
+GROUP                   !               \                         |    |
+ATOM C3B  CN7     0.14  !                \ H51N H4D O4D       H2N-C2N C6N-HN6
+ATOM H3B  HN7     0.09  !                 \ |    \ /   \           \   /
+ATOM O3B  ON5    -0.66  !                  C5D --C4D    C1D --------N1N
+ATOM HO3A HN5     0.43  !                   |     \     / \
+GROUP                   !                 H52N   C3D -C2D  H1D 
+ATOM C5B  CN8B   -0.08  !                        / \   / \  
+ATOM H51A HN8     0.09  !                    O3D  H3D O2D H2D   
+ATOM H52A HN8     0.09  !                     |       |
+ATOM PA   P       1.50  !                    HO3N    HO2N   
+ATOM O1A  ON3    -0.82  !                   
+ATOM O2A  ON3    -0.82  !                    
+ATOM O5B  ON2    -0.62  !                   
+ATOM O3   ON2    -0.68
+ATOM PN   P       1.50
+ATOM O1N  ON3    -0.82
+ATOM O2N  ON3    -0.82
+ATOM O5D  ON2    -0.62
+ATOM C5D  CN8B   -0.08
+ATOM H51N HN8     0.09
+ATOM H52N HN8     0.09
+GROUP
+ATOM C2D  CN7B    0.14
+ATOM H2D  HN7     0.09
+ATOM O2D  ON5    -0.66
+ATOM HO2N HN5     0.43
+GROUP
+ATOM C3D  CN7     0.14
+ATOM H3D  HN7     0.09
+ATOM O3D  ON5    -0.66
+ATOM HO3N HN5     0.43
+GROUP
+ATOM C1D  CN7B    0.16
+ATOM H1D  HN7     0.09
+ATOM C4D  CN7     0.16
+ATOM H4D  HN7     0.09
+ATOM O4D  ON6B   -0.50
+GROUP
+ATOM N1N  NN2    -0.27 !N2
+ATOM C6N  CN3C   -0.06 !C3
+ATOM HN6  HN6     0.17 !H4
+ATOM C5N  CN3    -0.18 !C5
+ATOM H5N  HN6     0.14 !H6
+ATOM C4N  CN8    -0.28 !C7
+ATOM H41N HN8     0.09 !H8
+ATOM H42N HN8     0.09 !H17
+ATOM C3N  CN3     0.36 !C9
+ATOM C2N  CN3C   -0.10 !C10
+ATOM H2N  HN6     0.14 !H11
+ATOM C7N  CN1A    0.55 !C12
+ATOM O7N  ON1    -0.51 !O13
+ATOM N7N  NN1    -0.72 !N14
+ATOM H71N HN1     0.26 !H15  ! trans to amide O
+ATOM H72N HN1     0.32 !H16  ! cis to amide O
+BOND N1A  C2A       N3A  C4A       C5A  C6A
+BOND C6A  N6A       C5A  N7A       C8A  N9A
+BOND N9A  C4A       C2A  H2A       N6A  H61A      N6A  H62A      C8A  H8A
+DOUBLE C6A  N1A       C2A  N3A       C4A  C5A      N7A  C8A
+BOND N9A  C1B       C1B  C2B       C2B  C3B       C3B  C4B       C4B  O4B 
+BOND O4B  C1B       C1B  H1B       C2B  O2B       O2B  P2B       C2B  H2B 
+BOND C3B  H3B       C3B  O3B       O3B  HO3A      C4B  H4B       C4B  C5B 
+BOND C5B  H52A      C5B  H51A      C5B  O5B       O5B  PA        PA   O1A
+BOND PA   O2A       PA   O3        O3   PN        PN   O1N       PN   O1N
+BOND PN   O5D       O5D  C5D       C5D  H51N      C5D  H52N      C5D  C4D 
+BOND C4D  O4D       O4D  C1D       C1D  C2D       C2D  C3D       C3D  C4D 
+BOND C1D  H1D       C2D  H2D       C2D  O2D       O2D  HO2N      C3D  H3D 
+BOND C3D  O3D       O3D  HO3N      C4D  H4D       C1D  N1N       N1N  C2N
+BOND C3N  C4N       C5N  C6N       
+BOND C2N  H2N       C3N  C7N       C7N  O7N       C7N  N7N       N7N  H71N
+BOND N7N  H72N      C4N  H41N      C4N  H42N      C5N  H5N       C6N  HN6
+BOND P2B  O1X       P2B  O2X       P2B  O3X       O3X  HO2A
+DOUBLE C2N  C3N       C4N  C5N       C6N  N1N
+! adenine impropers
+IMPR N6A  C6A    H61A H62A   C6A   N1A   C5A   N6A
+! amide impropers
+IMPR C7N   N7N   C3N  O7N    C7N   C3N   N7N   O7N
+IMPR N7N   C7N   H71N H72N   N7N   C7N   H72N  H71N
+! ring hydrogen impropers
+IMPR C6N   N1N   C5N  HN6    C5N   C6N   C4N   H5N
+IMPR C4N   C5N   C3N  H41N   C2N   C3N   N1N   H2N
+DONO H61A N6A
+DONO H62A N6A
+DONO HO3A O3B 
+ACCE N1A
+ACCE N3A
+ACCE N7A
+ACCE O4B 
+ACCE O3B 
+ACCE O5B 
+ACCE O1A  PA
+ACCE O2A  PA
+ACCE O3
+ACCE O1N  PN
+ACCE O2N  PN
+ACCE O5D 
+ACCE O4D 
+ACCE O3D 
+ACCE O2D 
+ACCE O7N
+DONO HO2N O2D 
+DONO HO3N O3D 
+DONO H71N N7N
+DONO H72N N7N
+DONO HO2A O3X 
+ACCE O3X 
+ACCE O1X 
+ACCE O2X 
+ACCE O2B  
+
+IC O4B   C4B   C5B   O5B    1.4582  108.69  147.29  113.38   1.4416
+IC O4B   C5B   *C4B  C3B    1.4582  108.69 -118.37  116.42   1.5453
+IC C3B   C5B   *C4B  H4B    1.5453  116.42 -123.26  110.26   1.1108
+IC C5B   C4B   O4B   C1B    1.5423  108.69 -124.93  109.48   1.4122
+IC C4B   O4B   C1B   N9A    1.4582  109.48 -147.01  110.04   1.4652
+IC N9A   O4B   *C1B  C2B    1.4652  110.04  124.33  107.34   1.5182
+IC N9A   O4B   *C1B  H1B    1.4652  110.04 -119.42  105.83   1.1152
+IC O4B   C1B   N9A   C4A    1.4122  110.04  -86.61  125.65   1.3733
+IC C4A   C1B   *N9A  C8A    1.3733  125.65  178.34  128.52   1.3773
+IC C1B   N9A   C4A   C5A    1.4652  125.65  178.57  105.62   1.3829
+IC C5A   N9A   *C4A  N3A    1.3829  105.62  179.51  128.22   1.3485
+IC N9A   C4A   C5A   C6A    1.3733  105.62  178.87  117.03   1.4089
+IC C6A   C4A   *C5A  N7A    1.4089  117.03 -179.61  111.33   1.3844
+IC N7A   N9A   *C8A  H8A    1.3165  113.76 -178.62  121.49   1.0929
+IC C4A   C5A   C6A   N1A    1.3829  117.03    0.17  118.37   1.3553
+IC N1A   C5A   *C6A  N6A    1.3553  118.37 -179.13  122.76   1.3455
+IC C5A   C6A   N1A   C2A    1.4089  118.37   -0.08  117.58   1.3367
+IC N3A   N1A   *C2A  H2A    1.3316  129.88  179.50  115.45   1.0928
+IC C5A   C6A   N6A   H61A   1.4089  122.76  172.71  117.17   0.9924
+IC H61A  C6A   *N6A  H62A   0.9924  117.17 -165.83  118.92   0.9969
+IC C3B   C1B   *C2B  O2B    1.5172  100.70  117.95  111.52   1.4469
+IC C3B   C1B   *C2B  H2B    1.5172  100.70 -114.49  112.15   1.1158
+IC C1B   C2B   O2B   P2B    1.5182  111.52   88.87  120.26   1.5695
+IC C2B   O2B   P2B   O3X    1.4469  120.26  -89.09  105.16   1.5592
+IC O3X   O2B   *P2B  O1X    1.5592  105.16  112.49  112.19   1.4735
+IC O1X   O2B   *P2B  O2X    1.4735  112.19  138.98  113.24   1.4714
+IC O2B   P2B   O3X   HO2A   1.5695  105.16 -143.03  105.24   0.9629
+IC C1B   C2B   O2B   HO2A   1.5182  111.52   52.38  125.15   3.2167
+IC C2B   C4B   *C3B  O3B    1.5172  104.21  119.99  110.36   1.4348
+IC C2B   C4B   *C3B  H3B    1.5172  104.21 -117.77  107.81   1.1123
+IC C4B   C3B   O3B   HO3A   1.5453  110.36   61.04  107.59   0.9899
+IC C3B   C4B   C5B   O5B    1.5453  116.42   28.91  113.38   1.4416
+IC O5B   C4B   *C5B  H52A   1.4416  113.38 -118.10  108.23   1.1129
+IC H52A  C4B   *C5B  H51A   1.1129  108.23 -115.04  109.34   1.1144
+IC C4B   C5B   O5B   PA     1.5423  113.38   90.70  124.02   1.5733
+IC C5B   O5B   PA    O3     1.4416  124.02  151.99   89.67   1.5604
+IC O3    O5B   *PA   O1A    1.5604   89.67 -118.40  102.31   1.4957
+IC O1A   O5B   *PA   O2A    1.4957  102.31 -121.55   98.60   1.4978
+IC O5B   PA    O3    PN     1.5733   89.67  175.92   82.07   1.5171
+IC PA    O3    PN    O5D    1.5604   82.07 -130.29  100.52   1.5806
+IC O5D   O3    *PN   O1N    1.5806  100.52 -112.12  108.73   1.4864
+IC O1N   O3    *PN   O2N    1.4864  108.73  147.44  159.68   5.2397
+IC O3    PN    O5D   C5D    1.5171  100.52 -156.02  122.16   1.4407
+IC PN    O5D   C5D   C4D    1.5806  122.16 -155.55  113.98   1.5556
+IC C4D   O5D   *C5D  H51N   1.5556  113.98 -119.58  108.24   1.1127
+IC H51N  O5D   *C5D  H52N   1.1127  108.24 -117.86  112.23   1.1172
+IC O5D   C5D   C4D   O4D    1.4407  113.98  -39.97  113.27   1.4728
+IC O4D   C5D   *C4D  C3D    1.4728  113.27  123.24  116.41   1.5466
+IC O4D   C5D   *C4D  H4D    1.4728  113.27 -117.97  108.11   1.1097
+IC C5D   C4D   C3D   C2D    1.5556  116.41 -137.48  104.59   1.5300
+IC C2D   C4D   *C3D  O3D    1.5300  104.59  128.04  115.55   1.4371
+IC C2D   C4D   *C3D  H3D    1.5300  104.59 -114.00  106.10   1.1131
+IC C4D   C3D   C2D   C1D    1.5466  104.59   26.25  103.50   1.5376
+IC C1D   C3D   *C2D  O2D    1.5376  103.50  127.18  111.43   1.4128
+IC C1D   C3D   *C2D  H2D    1.5376  103.50 -113.70  107.89   1.1128
+IC C3D   C2D   O2D   HO2N   1.5300  111.43  -33.45  103.13   0.9733
+IC C4D   C3D   O3D   HO3N   1.5466  115.55   84.57  105.43   0.9941
+IC O4D   C2D   *C1D  N1N    1.4276  105.00  128.25  117.48   1.5144
+IC O4D   C2D   *C1D  H1D    1.4276  105.00 -111.04  107.28   1.1120
+IC C2D   C1D   N1N   C2N    1.5376  117.48   57.37  120.71   1.3843
+IC C2N   C1D   *N1N  C6N    1.3843  120.71  160.76  120.55   1.3815
+IC C1D   N1N   C6N   C5N    1.5144  120.55 -170.31  124.26   1.3287
+IC C5N   N1N   *C6N  HN6    1.3287  124.26 -178.43  118.52   1.0918
+IC N1N   C6N   C5N   C4N    1.3815  124.26    9.43  123.21   1.5077
+IC C4N   C6N   *C5N  H5N    1.5077  123.21 -145.56  114.70   1.0925
+IC C6N   C5N   C4N   C3N    1.3287  123.21   -9.51  109.08   1.5286
+IC C3N   C5N   *C4N  H41N   1.5286  109.08  123.86  111.86   1.1053
+IC C3N   C5N   *C4N  H42N   1.5286  109.08 -119.79  109.00   1.1069
+IC C3N   N1N   *C2N  H2N    1.3470  124.38 -176.93  117.74   1.0900
+IC C2N   C4N   *C3N  C7N    1.3470  121.40 -164.55  123.17   1.5301
+IC C4N   C3N   C7N   N7N    1.5286  123.17   17.57  116.23   1.3547
+IC N7N   C3N   *C7N  O7N    1.3547  116.23 -179.04  120.83   1.2310
+IC C3N   C7N   N7N   H71N   1.5301  116.23  173.93  118.74   0.9953
+IC H71N  C7N   *N7N  H72N   0.9953  118.74 -160.46  121.30   1.0065
+
+PATCH FIRST NONE LAST NONE
+
+!old NAD/NADP nomenclature for both residue and atom names.  maintained
+!for back compatibility.  residue names differ from current nomenclature
+
+!following was NAD in old nomenclature; change to NAD1 to avoid conflict with
+!new nomenclature
+!
+RESI NAD1        -1.00  ! oxidized nicotinamide adenine dinucleotide, jjp1/adm jr.
+                        ! atom names correspond to pdb nomenclature
+                        ! checked for consistency with new NA params, adm jr., 9/98
+                        ! note that differences with respect to published results exist
+                        ! due to new NA params
+GROUP                   !
+ATOM AC4' CN7     0.16  !                AH61  AH62
+ATOM AH4' HN7     0.09  !                   \  /
+ATOM AO4' ON6B   -0.50  !                   AN6
+ATOM AC1' CN7B    0.16  !                    |
+ATOM AH1' HN7     0.09  !                   AC6
+GROUP                   !                  //  \
+ATOM AC5  CN5     0.28  !                 AN1  AC5--AN7\\
+ATOM AN7  NN4    -0.71  !                  |    ||     AC8-AH8
+ATOM AC8  CN4     0.34  !                 AC2  AC4--AN9/
+ATOM AH8  HN3     0.12  !                 / \\ /     \
+ATOM AN9  NN2    -0.05  !              AH2  AN3       \
+                        !                              \
+ATOM AN1  NN3A   -0.74  !                               \
+ATOM AC2  CN4     0.50  !                                \
+ATOM AH2  HN3     0.13  !    NO1     AO1    AH5sAH4' AO4' \
+ATOM AN3  NN3A   -0.75  !     |       |      |    \ /   \  \
+ATOM AC4  CN5     0.43  ! NO5'NP-O3--AP-AO5'-AC5'-AC4'   AC1'
+ATOM AC6  CN2     0.46  ! \   |       |      |     \     / \
+                        !  \ NO2     AO2    AH5' AC3'-AC2' AH1'
+ATOM AN6  NN1    -0.77  !   \                     / \   / \
+ATOM AH61 HN1     0.38  !    \                AO3' AH3'AO2'AH2'
+ATOM AH62 HN1     0.38  !     \                 |       |
+GROUP                   !      \              AH3T     AH2T
+ATOM AC2' CN7B    0.14  !       \                        NH71
+ATOM AH2' HN7     0.09  !        \                          \ 
+ATOM AO2' ON5    -0.66  !         \                    NH72-NN7    NH4
+ATOM AH2T HN5     0.43  !          \                          \     |
+GROUP                   !           \                         NC7  NC4
+ATOM AC3' CN7     0.14  !            \                        / \  /  \
+ATOM AH3' HN7     0.09  !             \                    NO7  NC3  NC5-NH5
+ATOM AO3' ON5    -0.66  !              \                          |    |
+ATOM AH3T HN5     0.43  !               \ NH5s NH4'NO4'      NH2-NC2 NC6-NH6
+GROUP                   !                \ |    \ /   \            \+ /   
+ATOM AC5' CN8B   -0.08  !                 NC5'--NC4'   NC1'---------NN1
+ATOM AH5' HN8     0.09  !                  |     \     / \
+ATOM AH5s HN8     0.09  !                 NH5'   NC3'-NC2'NH1'
+ATOM AP   P       1.50  !                       / \   / \
+ATOM AO1  ON3    -0.82  !                   NO3' NH3'NO2'NH2'
+ATOM AO2  ON3    -0.82  !                    |       |
+ATOM AO5' ON2    -0.62  !                   NH3T    NH2T
+ATOM O3   ON2    -0.68
+ATOM NP   P       1.50
+ATOM NO1  ON3    -0.82
+ATOM NO2  ON3    -0.82
+ATOM NO5' ON2    -0.62
+ATOM NC5' CN8B   -0.08
+ATOM NH5s HN8     0.09
+ATOM NH5' HN8     0.09 
+GROUP                  
+ATOM NC2' CN7B    0.14 
+ATOM NH2' HN7     0.09 
+ATOM NO2' ON5    -0.66
+ATOM NH2T HN5     0.43
+GROUP
+ATOM NC3' CN7     0.14
+ATOM NH3' HN7     0.09
+ATOM NO3' ON5    -0.66
+ATOM NH3T HN5     0.43
+GROUP
+ATOM NC1' CN7B    0.16
+ATOM NH1' HN7     0.09
+ATOM NC4' CN7     0.16
+ATOM NH4' HN7     0.09
+ATOM NO4' ON6B   -0.50
+GROUP                  
+ATOM NN1  NN2    -0.07
+ATOM NC6  CN3B    0.16
+ATOM NH6  HN3B    0.19
+ATOM NC5  CN3    -0.10
+ATOM NH5  HN3B    0.16
+ATOM NC4  CN3A   -0.05
+ATOM NH4  HN3B    0.16
+ATOM NC3  CN3     0.05 
+ATOM NC2  CN3B    0.18
+ATOM NH2  HN3B    0.16
+ATOM NC7  CN1A    0.68 
+ATOM NO7  ON1    -0.40 
+ATOM NN7  NN1    -0.82
+ATOM NH71 HN1     0.34  ! trans to amide O
+ATOM NH72 HN1     0.36  ! cis to amide O
+
+BOND AN1  AC2       AN3  AC4       AC5  AC6
+BOND AC6  AN6       AC5  AN7       AC8  AN9
+BOND AN9  AC4       AC2  AH2       AN6  AH61      AN6  AH62      AC8  AH8
+DOUBLE AC6  AN1       AC2  AN3       AC4  AC5      AN7  AC8
+BOND AN9  AC1'      AC1' AC2'      AC2' AC3'      AC3' AC4'      AC4' AO4'
+BOND AO4' AC1'      AC1' AH1'      AC2' AO2'      AO2' AH2T      AC2' AH2'
+BOND AC3' AH3'      AC3' AO3'      AO3' AH3T      AC4' AH4'      AC4' AC5'
+BOND AC5' AH5s      AC5' AH5'      AC5' AO5'      AO5' AP        AP   AO1
+BOND AP   AO2       AP   O3        O3   NP        NP   NO1       NP   NO2
+BOND NP   NO5'      NO5' NC5'      NC5' NH5s      NC5' NH5'      NC5' NC4'
+BOND NC4' NO4'      NO4' NC1'      NC1' NC2'      NC2' NC3'      NC3' NC4'
+BOND NC1' NH1'      NC2' NH2'      NC2' NO2'      NO2' NH2T      NC3' NH3'
+BOND NC3' NO3'      NO3' NH3T      NC4' NH4'      NC1' NN1       NN1  NC2
+BOND NC3  NC4       NC5  NC6
+BOND NC2  NH2       NC3  NC7       NC7  NO7       NC7  NN7       NN7  NH71
+BOND NN7  NH72      NC4  NH4       NC5  NH5       NC6  NH6
+DOUBLE NC2  NC3       NC4  NC5       NC6  NN1
+! adenine impropers
+IMPR AN6  AC6  AH61 AH62     AC6   AN1   AC5  AN6       
+! amide impropers
+IMPR NC7   NN7   NC3  NO7    NC7   NC3   NN7   NO7 
+IMPR NN7   NC7   NH71 NH72   NN7   NC7   NH72  NH71
+! ring hydrogen impropers
+IMPR NC6   NN1   NC5  NH6    NC5   NC6   NC4   NH5
+IMPR NC4   NC5   NC3  NH4    NC2   NC3   NN1   NH2
+DONO AH61 AN6
+DONO AH62 AN6
+DONO AH2T AO2'
+DONO AH3T AO3'
+ACCE AN1
+ACCE AN3
+ACCE AN7
+ACCE AO4'
+ACCE AO2'
+ACCE AO3'
+ACCE AO5'
+ACCE AO1  AP
+ACCE AO2  AP
+ACCE O3
+ACCE NO1  NP
+ACCE NO2  NP
+ACCE NO5'
+ACCE NO4'
+ACCE NO3'
+ACCE NO2'
+ACCE NO7
+DONO NH2T NO2'
+DONO NH3T NO3'
+DONO NH71 NN7
+DONO NH72 NN7
+IC AP     O3     NP     NO5'   1.4863   65.28 -169.00   98.59   1.5977
+IC AC5'   AO5'   AP     O3     1.4232  127.31 -165.10  103.27   1.4863
+IC AC5'   AO5'   AP     AO2    1.4232  127.31   73.33  111.48   1.4836
+IC AH5S   AC5'   AC4'   AC3'   0.9935  120.00  -58.20  111.58   1.6942
+IC AP     O3     NP     NO1    1.4863   65.28   78.51  108.97   1.4756
+IC AP     O3     NP     NO2    1.4863   65.28  -54.29  112.88   1.4636
+IC AP     AO5'   AC5'   AC4'   1.5901  127.31  121.29  111.63   1.5491
+IC AO1    AP     AO5'   AC5'   1.5901  127.31  121.29  127.31   1.4232
+IC AO5'   AC5'   AC4'   AC3'   1.4232  111.63  -58.20  111.58   1.6942
+IC AC5'   AC4'   AC3'   AO3'   1.5491  111.58  128.42  114.19   1.4337
+IC AH3T   AO3'   AC3'   AC4'   0.9671   98.77  147.40  114.19   1.6942
+IC AO4'   AC3'   *AC4   AC5'   1.8868  112.95 -118.10  111.58   1.5491
+IC AC2'   AC4'   *AC3'  AO3'   1.5097   93.22 -117.72  114.19   1.4337
+IC AC4'   AC3'   AC2'   AC1'   1.6942   93.22  -12.93  117.82   1.5415
+IC AC3'   AC2'   AC1'   AN9    1.5097  117.82  135.56  115.01   1.4847
+IC AO4'   AC1'   AN9    AC4    1.3646   95.44  -90.72  125.96   1.4013
+IC AC1'   AC4    *AN9   AC8    1.4847  125.96 -176.52  105.34   1.3777
+IC AC4    AN9    AC8    AN7    1.4013  105.34   -0.07  114.01   1.3282
+IC AC8    AN9    AC4    AC5    1.3777  105.34    0.11  105.06   1.3782
+IC AC8    AN7    AC5    AC6    1.3282  103.21 -179.92  130.78   1.4146
+IC AN7    AC5    AC6    AN1    1.3814  130.78 -179.94  117.85   1.3482
+IC AC5    AC6    AN1    AC2    1.4146  117.85   -0.14  118.87   1.3300
+IC AN9    AC5    *AC4   AN3    1.4013  105.06 -179.67  126.14   1.3648
+IC AC5    AN1    *AC6   AN6    1.4146  117.85  179.89  119.69   1.3419
+IC AN1    AC6    AN6    AH61   1.3482  119.69   -0.39  116.60   0.9912
+IC AH61   AC6    *AN6   AH62   0.9912  116.60 -179.02  116.94   0.9978
+IC AC5    AN1    *AC6   AN6    1.4146  117.85  179.89  119.69   1.3419
+IC AN1    AC6    AN6    AH61   1.3482  119.69   -0.39  116.60   0.9912
+IC AH61   AC6    *AN6   AH62   0.9912  116.60 -179.02  116.94   0.9978
+IC AN9    AN7    *AC8   AH8    1.3777  114.01 -179.37  126.34   1.0962
+IC AN1    AN3    *AC2   AH2    1.3300  129.42  179.97  114.82   1.0928
+IC AC1'   AC3'   *AC2   AO2'   1.5415  117.82 -145.06  114.13   1.4294
+IC AH2'   AO2'   AC2'   AC3'   2.0386   31.12  -93.63  114.13   1.5097
+IC AH2T   AO2'   AC2'   AC3'   0.9953   99.36  -93.63  114.13   1.5097
+IC AO4'   AC2'   *AC1'  AH1'   1.3646  120.77 -114.99  109.65   1.1105
+IC AC1'   AC3'   *AC2   AH2'   1.5415  117.82  108.23   86.44   1.0999
+IC AC2'   AC4'   *AC3'  AH3'   1.5097   93.22  117.28  111.94   1.1110
+IC AC3'   AO4'   *AC4   AH4'   1.6942  112.95 -140.26   57.99   1.0000
+IC AC4'   AO5'   *AC5   AH5'   1.5491  111.63 -123.75  111.23   1.1111
+IC AC4'   AO5'   *AC5   AH5'   1.5491  111.63 -123.75  111.23   1.1111
+IC NC5'   NO5'   NP     NO2    1.4451  128.40  -49.72  108.83   1.4636
+IC NH5S   NC5'   NO5'   NP     1.1110  109.50  115.00  128.40   1.5977
+IC NH5'   NC5'   NO5'   NP     1.1110  109.50 -115.00  128.40   1.5977
+IC NP     NO5'   NC5'   NC4'   1.5977  128.40    0.00  110.10   1.5160
+IC NO5'   NC5'   NC4'   NC3'   1.4451  110.10    0.00  108.50   1.5160
+IC NC5'   NC4'   NC3'   NC2'   1.5160  108.50    0.00  111.00   1.5160
+IC NC4'   NC3'   NC2'   NC1'   1.5160  111.00    0.00  105.50   1.5270
+IC NC3'   NC2'   NC1'   NO4'   1.5160  105.50    0.00  105.00   1.4100
+IC NC2'   NC1'   NO4'   NC4'   1.5270  105.00    0.00  117.86   1.4712
+IC NO2'   NC2'   NC1'   NO4'   1.4200  110.10  180.00  105.00   1.4100
+IC NH2T   NO2'   NC2'   NC1'   0.9600  106.00  180.00  110.10   1.5270
+IC NO4'   NC2'   *NC1'  NH1'   1.4100  105.00 -115.00  110.10   1.1110
+IC NC1'   NC3'   *NC2   NH2'   1.5270  105.50  115.00  110.10   1.1110
+IC NC2'   NC4'   *NC3   NH3'   1.5160  111.00  115.00  110.10   1.1110
+IC NC3'   NO4'   *NC4   NH4'   1.5160  100.64 -115.00  107.24   1.1110
+IC NC4'   NO5'   *NC5   NH5'   1.5160  110.10 -115.00  109.50   1.1110
+IC NC4'   NO5'   *NC5   NH5S   1.5160  110.10  115.00  109.50   1.1110
+IC NC3'   NC2'   NC1'   NN1    1.5160  105.50    0.00  113.70   1.4800
+IC NO3'   NC3'   NC2'   NC1'   1.4200  110.10  180.00  105.50   1.5270
+IC NH3T   NO3'   NC3'   NC2'   0.9600  106.00  180.00  110.10   1.5160
+IC NC2'   NC1'   NN1    NC2    1.5270  113.70    0.00  121.70   1.3150
+IC NC1'   NN1    NC2    NC3    1.4800  121.70    0.00  122.00   1.3500
+IC NN1    NC2    NC3    NC4    1.3150  122.00    0.00  118.00   1.3600
+IC NC2    NC3    NC4    NC5    1.3500  118.00    0.00  118.00   1.3600
+IC NC3    NC4    NC5    NC6    1.3600  118.00    0.00  118.00   1.3500
+IC NC4    NC5    NC6    NN1    1.3600  118.00    0.00  124.51   1.2199
+IC NC5    NC6    NN1    NC2    1.3500  124.51    0.00  119.49   1.3150
+IC NN1    NC2    NC3    NC7    1.3150  122.00    0.00  131.80   1.4800
+IC NC2    NC3    NC7    NO7    1.3500  131.80    0.00  118.50   1.2300
+IC NC2    NC3    NC7    NN7    1.3500  131.80    0.00  113.00   1.3600
+IC NO7    NC7    NN7    NH71   1.2300    0.00  180.00  120.00   1.0000
+IC NO7    NC7    NN7    NH72   1.2300    0.00    0.00  120.00   1.0000
+IC NC2    NC3    NC4    NH4    1.3500  118.00    0.00  121.00   1.0900
+IC NC3    NC4    NC5    NH5    1.3600  118.00    0.00  119.00   1.0900
+IC NC4    NC5    NC6    NH6    1.3600  118.00    0.00  120.50   1.0900
+IC NC6    NN1    NC2    NH2    1.2199  119.49    0.00  117.50   1.0900
+PATCH FIRST NONE LAST NONE   
+
+RESI NADH        -2.00  ! reduced nicotinamide adenine dinucleotide, jjp1/adm jr.
+                        ! atom names correspond to pdb nomenclature
+                        ! checked for consistency with new NA params, adm jr., 9/98
+                        ! note that differences with respect to published results exist
+                        ! due to new NA params
+                        !
+GROUP                   !
+ATOM AC4' CN7     0.16  !                AH61  AH62
+ATOM AH4' HN7     0.09  !                   \  /
+ATOM AO4' ON6B   -0.50  !                   AN6
+ATOM AC1' CN7B    0.16  !                    |
+ATOM AH1' HN7     0.09  !                   AC6
+GROUP                   !                  //  \
+ATOM AC5  CN5     0.28  !                 AN1  AC5--AN7\\
+ATOM AN7  NN4    -0.71  !                  |    ||     AC8-AH8
+ATOM AC8  CN4     0.34  !                 AC2  AC4--AN9/
+ATOM AH8  HN3     0.12  !                 / \\ /     \
+ATOM AN9  NN2    -0.05  !              AH2  AN3       \
+                        !                              \
+ATOM AN1  NN3A   -0.74  !                               \
+ATOM AC2  CN4     0.50  !                                \
+ATOM AH2  HN3     0.13  !    NO1     AO1    AH5sAH4' AO4' \
+ATOM AN3  NN3A   -0.75  !     |       |      |    \ /   \  \
+ATOM AC4  CN5     0.43  ! NO5'NP-O3--AP-AO5'-AC5'-AC4'   AC1'
+ATOM AC6  CN2     0.46  ! \   |       |      |     \     / \
+                        !  \ NO2     AO2    AH5' AC3'-AC2' AH1'
+ATOM AN6  NN1    -0.77  !   \                     / \   / \
+ATOM AH61 HN1     0.38  !    \                AO3' AH3'AO2'AH2'
+ATOM AH62 HN1     0.38  !     \                 |       |
+GROUP                   !      \              AH3T     AH2T
+ATOM AC2' CN7B    0.14  !       \                        NH71
+ATOM AH2' HN7     0.09  !        \                          \
+ATOM AO2' ON5    -0.66  !         \                    NH72-NN7  NH4 NH42
+ATOM AH2T HN5     0.43  !          \                          \    \ /
+GROUP                   !           \                         NC7  NC4
+ATOM AC3' CN7     0.14  !            \                        / \  /  \
+ATOM AH3' HN7     0.09  !             \                    NO7  NC3  NC5-NH5
+ATOM AO3' ON5    -0.66  !              \                          |    |
+ATOM AH3T HN5     0.43  !               \ NH5s NH4'NO4'      NH2-NC2 NC6-NH6
+GROUP                   !                \ |    \ /   \            \  /
+ATOM AC5' CN8B   -0.08  !                 NC5'--NC4'   NC1'---------NN1
+ATOM AH5' HN8     0.09  !                  |     \     / \
+ATOM AH5s HN8     0.09  !                 NH5'   NC3'-NC2'NH1'
+ATOM AP   P       1.50  !                       / \   / \
+ATOM AO1  ON3    -0.82  !                   NO3' NH3'NO2'NH2'
+ATOM AO2  ON3    -0.82  !                    |       |
+ATOM AO5' ON2    -0.62  !                   NH3T    NH2T
+ATOM O3   ON2    -0.68
+ATOM NP   P       1.50
+ATOM NO1  ON3    -0.82
+ATOM NO2  ON3    -0.82
+ATOM NO5' ON2    -0.62
+ATOM NC5' CN8B   -0.08
+ATOM NH5s HN8     0.09
+ATOM NH5' HN8     0.09
+GROUP
+ATOM NC2' CN7B    0.14
+ATOM NH2' HN7     0.09
+ATOM NO2' ON5    -0.66
+ATOM NH2T HN5     0.43
+GROUP
+ATOM NC3' CN7     0.14
+ATOM NH3' HN7     0.09
+ATOM NO3' ON5    -0.66
+ATOM NH3T HN5     0.43
+GROUP
+ATOM NC1' CN7B    0.16
+ATOM NH1' HN7     0.09
+ATOM NC4' CN7     0.16
+ATOM NH4' HN7     0.09
+ATOM NO4' ON6B   -0.50
+GROUP
+ATOM NN1  NN2    -0.27 !N2
+ATOM NC6  CN3C   -0.06 !C3
+ATOM NH6  HN6     0.17 !H4
+ATOM NC5  CN3    -0.18 !C5
+ATOM NH5  HN6     0.14 !H6
+ATOM NC4  CN8    -0.28 !C7
+ATOM NH4  HN8     0.09 !H8
+ATOM NH42 HN8     0.09 !H17
+ATOM NC3  CN3     0.36 !C9
+ATOM NC2  CN3C   -0.10 !C10
+ATOM NH2  HN6     0.14 !H11
+ATOM NC7  CN1A    0.55 !C12
+ATOM NO7  ON1    -0.51 !O13
+ATOM NN7  NN1    -0.72 !N14
+ATOM NH71 HN1     0.26 !H15  ! trans to amide O
+ATOM NH72 HN1     0.32 !H16  ! cis to amide O
+
+BOND AN1  AC2       AN3  AC4       AC5  AC6
+BOND AC6  AN6       AC5  AN7       AC8  AN9
+BOND AN9  AC4       AC2  AH2       AN6  AH61      AN6  AH62      AC8  AH8
+DOUBLE  AC6  AN1      AC2  AN3      AC4  AC5      AN7  AC8
+BOND AN9  AC1'      AC1' AC2'      AC2' AC3'      AC3' AC4'      AC4' AO4'
+BOND AO4' AC1'      AC1' AH1'      AC2' AO2'      AO2' AH2T      AC2' AH2'
+BOND AC3' AH3'      AC3' AO3'      AO3' AH3T      AC4' AH4'      AC4' AC5'
+BOND AC5' AH5s      AC5' AH5'      AC5' AO5'      AO5' AP        AP   AO1
+BOND AP   AO2       AP   O3        O3   NP        NP   NO1       NP   NO2
+BOND NP   NO5'      NO5' NC5'      NC5' NH5s      NC5' NH5'      NC5' NC4'
+BOND NC4' NO4'      NO4' NC1'      NC1' NC2'      NC2' NC3'      NC3' NC4'
+BOND NC1' NH1'      NC2' NH2'      NC2' NO2'      NO2' NH2T      NC3' NH3'
+BOND NC3' NO3'      NO3' NH3T      NC4' NH4'      NC1' NN1       NN1  NC2
+BOND NC3  NC4       NC4  NC5       NC6  NN1
+BOND NC2  NH2       NC3  NC7       NC7  NO7       NC7  NN7       NN7  NH71
+BOND NN7  NH72      NC4  NH4       NC4  NH42      NC5  NH5       NC6  NH6
+DOUBLE  NC2  NC3      NC5  NC6
+! adenine impropers
+IMPR AN6  AC6  AH61 AH62     AC6  AN1  AC5  AN6       
+! amide impropers
+IMPR NC7   NN7   NC3  NO7    NC7   NC3   NN7   NO7
+IMPR NN7   NC7   NH71 NH72   NN7   NC7   NH72  NH71
+! ring hydrogen impropers
+IMPR NC6   NN1   NC5  NH6    NC5   NC6   NC4   NH5
+IMPR NC4   NC5   NC3  NH4    NC2   NC3   NN1   NH2
+DONO AH61 AN6
+DONO AH62 AN6
+DONO AH2T AO2'
+DONO AH3T AO3'
+ACCE AN1
+ACCE AN3
+ACCE AN7
+ACCE AO4'
+ACCE AO2'
+ACCE AO3'
+ACCE AO5'
+ACCE AO1  AP
+ACCE AO2  AP
+ACCE O3
+ACCE NO1  NP
+ACCE NO2  NP
+ACCE NO5'
+ACCE NO4'
+ACCE NO3'
+ACCE NO2'
+ACCE NO7
+DONO NH2T NO2'
+DONO NH3T NO3'
+DONO NH71 NN7
+DONO NH72 NN7
+IC AP     O3     NP     NO5'   1.5477  110.11  175.47   98.59   1.5945
+IC AC5'   AO5'   AP     O3     1.4379  124.23 -120.69   96.29   1.5477
+IC AC5'   AO5'   AP     AO2    1.4379  124.23   -4.20  104.25   1.4838
+IC AH5S   AC5'   AC4'   AC3'   1.1127  107.45 -172.00  111.64   1.5309
+IC AP     O3     NP     NO1    1.5477  110.11   63.14  114.14   1.4739
+IC AP     O3     NP     NO2    1.5477  110.11  -73.96  111.08   1.4835
+IC AP     AO5'   AC5'   AC4'   1.5968  124.23  104.17  111.45   1.5366
+IC AO1    AP     AO5'   AC5'   1.4736  106.06  122.59  124.23   1.4379
+IC AO5'   AC5'   AC4'   AC3'   1.4379  111.45  -54.02  111.64   1.5309
+IC AC5'   AC4'   AC3'   AO3'   1.5366  111.64  117.91  108.23   1.4176
+IC AH3T   AO3'   AC3'   AC4'   0.9780  101.86  -77.83  108.23   1.5309
+IC AO4'   AC3'   *AC4   AC5'   3.7210   30.68   12.44   22.46   6.0953
+IC AC2'   AC4'   *AC3'  AO3'   1.5171  107.22 -123.00  108.23   1.4176
+IC AC4'   AC3'   AC2'   AC1'   1.5309  107.22  -27.93   98.01   1.5397
+IC AC3'   AC2'   AC1'   AN9    1.5171   98.01  168.03  114.25   1.4756
+IC AO4'   AC1'   AN9    AC4    1.4308  112.85 -160.05  123.87   1.3958
+IC AC1'   AC4    *AN9   AC8    1.4756  123.87  160.62  105.30   1.3614
+IC AC4    AN9    AC8    AN7    1.3958  105.30    2.73  114.72   1.3222
+IC AC8    AN9    AC4    AC5    1.3614  105.30   -0.85  105.33   1.3777
+IC AC8    AN7    AC5    AC6    1.3222  102.89 -175.73  131.43   1.4163
+IC AN7    AC5    AC6    AN1    1.3877  131.43  177.76  117.35   1.3499
+IC AC5    AC6    AN1    AC2    1.4163  117.35    0.19  119.36   1.3330
+IC AN9    AC5    *AC4   AN3    1.3958  105.33 -177.76  126.56   1.3567
+IC AC5    AN1    *AC6   AN6    1.4163  117.35  178.91  119.82   1.3439
+IC AN1    AC6    AN6    AH61   1.3499  119.82   -2.82  115.89   0.9932
+IC AH61   AC6    *AN6   AH62   0.9932  115.89 -173.48  118.52   0.9961
+IC AC5    AN1    *AC6   AN6    1.4163  117.35  178.91  119.82   1.3439
+IC AN1    AC6    AN6    AH61   1.3499  119.82   -2.82  115.89   0.9932
+IC AH61   AC6    *AN6   AH62   0.9932  115.89 -173.48  118.52   0.9961
+IC AN9    AN7    *AC8   AH8    1.3614  114.72  173.63  127.58   1.0942
+IC AN1    AN3    *AC2   AH2    1.3330  128.86  179.26  114.95   1.0940
+IC AC1'   AC3'   *AC2   AO2'   4.3577   16.73   79.16   23.49   5.5426
+IC AH2'   AO2'   AC2'   AC3'   2.0992   29.77  125.89  110.79   1.5171
+IC AH2T   AO2'   AC2'   AC3'   0.9759  105.90    7.59  110.79   1.5171
+IC AO4'   AC2'   *AC1'  AH1'   1.4308  104.32 -114.05  107.95   1.1153
+IC AC1'   AC3'   *AC2   AH2'   4.3577   16.73  138.52   14.56   4.3331
+IC AC2'   AC4'   *AC3'  AH3'   1.5171  107.22  118.77  114.33   1.1023
+IC AC3'   AO4'   *AC4   AH4'   4.6236   30.68   55.38   18.92   5.2267
+IC AC4'   AO5'   *AC5   AH5'   5.8410    8.40  125.34   12.50   6.6777
+IC AC4'   AO5'   *AC5   AH5'   5.8410    8.40  125.34   12.50   6.6777
+IC NC5'   NO5'   NP     NO2    1.4351  125.31   34.31  105.69   1.4835
+IC NH5S   NC5'   NO5'   NP     1.1087  111.20   -6.79  125.31   1.5945
+IC NH5'   NC5'   NO5'   NP     1.1115  107.95  108.24  125.31   1.5945
+IC NP     NO5'   NC5'   NC4'   1.5945  125.31 -133.06  113.61   1.5644
+IC NO5'   NC5'   NC4'   NC3'   1.4351  113.61   37.01  114.92   1.5111
+IC NC5'   NC4'   NC3'   NC2'   1.5644  114.92   71.49   99.06   1.5369
+IC NC4'   NC3'   NC2'   NC1'   1.5111   99.06   54.76   97.08   1.5500
+IC NC3'   NC2'   NC1'   NO4'   1.5369   97.08  -39.12  103.14   1.4628
+IC NC2'   NC1'   NO4'   NC4'   1.5500  103.14    9.47  109.09   1.4960
+IC NO2'   NC2'   NC1'   NO4'   1.4207  114.02 -166.39  103.14   1.4628
+IC NH2T   NO2'   NC2'   NC1'   0.9638  100.52  -89.37  114.02   1.5500
+IC NO4'   NC2'   *NC1'  NH1'   1.4628  103.14 -111.22  105.40   1.1096
+IC NC1'   NC3'   *NC2   NH2'   2.4663   46.96  -41.97   34.01   3.9460
+IC NC2'   NC4'   *NC3   NH3'   3.9136   23.54 -115.76   16.12   3.6674
+IC NC3'   NO4'   *NC4   NH4'   5.4003   24.61  -39.21   14.97   6.7904
+IC NC4'   NO5'   *NC5   NH5'   5.9665   13.65  -41.47   15.17   7.7670
+IC NC4'   NO5'   *NC5   NH5S   5.9665   13.65  -87.41   13.92   6.7251
+IC NC3'   NC2'   NC1'   NN1    1.5369   97.08   88.64  116.58   1.5502
+IC NO3'   NC3'   NC2'   NC1'   1.4176  119.76 -172.52   97.08   1.5500
+IC NH3T   NO3'   NC3'   NC2'   0.9717  103.61   17.81  119.76   1.5369
+IC NC2'   NC1'   NN1    NC2    1.5500  116.58  -19.65  116.34   1.3499
+IC NC1'   NN1    NC2    NC3    1.5502  116.34  134.66  130.57   1.3607
+IC NN1    NC2    NC3    NC4    1.3499  130.57    5.82  111.74   1.5356
+IC NC2    NC3    NC4    NC5    1.3607  111.74   -1.05  119.26   1.5319
+IC NC3    NC4    NC5    NC6    1.5356  119.26   -1.26  113.69   1.3745
+IC NC4    NC5    NC6    NN1    1.5319  113.69   -0.29  128.15   1.3388
+IC NC5    NC6    NN1    NC2    1.3745  128.15    4.14  116.26   1.3499
+IC NN1    NC2    NC3    NC7    1.3499  130.57 -147.46  122.72   1.5282
+IC NC2    NC3    NC7    NO7    1.3607  122.72 -140.47  119.41   1.2169
+IC NC2    NC3    NC7    NN7    1.3607  122.72   46.61  116.68   1.3621
+IC NO7    NC7    NN7    NH71   1.2169  123.49 -177.07  120.21   1.0093
+IC NO7    NC7    NN7    NH72   1.2169  123.49   -4.94  119.16   1.0014
+IC NC2    NC3    NC4    NH4    1.3607  111.74 -135.39  112.16   1.1099
+IC NC2    NC3    NC4    NH42   1.3607  111.74  114.48  103.52   1.1129
+IC NC3    NC4    NC5    NH5    1.5356  119.26 -171.18  122.65   1.0912
+IC NC4    NC5    NC6    NH6    1.5319  113.69  179.92  118.00   1.0878
+IC NC6    NN1    NC2    NH2    1.3388  116.26  162.03  117.47   1.0731
+PATCH FIRST NONE LAST NONE
+
+RESI NADP        -2.00  ! oxidized nicotinamide adenine dinucleotide,
+                        ! NADP+, adm jr.
+                        ! atom names correspond to pdb nomenclature
+                        ! checked for consistency with new NA params, adm jr., 9/98
+                        ! note that differences with respect to published results exist
+                        ! due to new NA params
+                        !
+GROUP                   !
+ATOM AC4' CN7     0.16  !                AH61  AH62
+ATOM AH4' HN7     0.09  !                   \  /
+ATOM AO4' ON6B   -0.50  !                   AN6
+ATOM AC1' CN7B    0.16  !                    |
+ATOM AH1' HN7     0.09  !                   AC6
+GROUP                   !                  //  \
+ATOM AC5  CN5     0.28  !                 AN1  AC5--AN7\\
+ATOM AN7  NN4    -0.71  !                  |    ||     AC8-AH8
+ATOM AC8  CN4     0.34  !                 AC2  AC4--AN9/
+ATOM AH8  HN3     0.12  !                 / \\ /     \
+ATOM AN9  NN2    -0.05  !              AH2  AN3       \
+                        !                              \
+ATOM AN1  NN3A   -0.74  !                               \
+ATOM AC2  CN4     0.50  !                                \
+ATOM AH2  HN3     0.13  !    NO1     AO1    AH5sAH4' AO4' \
+ATOM AN3  NN3A   -0.75  !     |       |      |    \ /   \  \
+ATOM AC4  CN5     0.43  ! NO5'NP-O3--AP-AO5'-AC5'-AC4'   AC1'
+ATOM AC6  CN2     0.46  ! \   |       |      |     \     / \
+                        !  \ NO2     AO2    AH5' AC3'-AC2' AH1'
+ATOM AN6  NN1    -0.77  !   \                     / \   / \
+ATOM AH61 HN1     0.38  !    \                AO3' AH3'AO2'AH2'
+ATOM AH62 HN1     0.38  !     \                |        |
+GROUP                   !      \             AH3T AO1P=AP2==AO2P (-)
+ATOM AC2' CN7B    0.01  !       \                       |    NH71
+ATOM AH2' HN7     0.09  !        \                AH2T-AO2T   /
+ATOM AO2' ON2    -0.62  !         \                    NH72-NN7  NH4 NH42
+ATOM AP2  P       1.50  !          \                          \    \ /
+ATOM AO1P ON3    -0.82  !           \                         NC7  NC4
+ATOM AO2P ON3    -0.82  !            \                        / \  /  \
+ATOM AO2T ON4    -0.68  !             \                    NO7  NC3  NC5-NH5
+ATOM AH2T HN4     0.34  !              \                          |    |
+GROUP                   !               \                         |    |
+ATOM AC3' CN7     0.14  !                \ NH5s NH4'NO4'      NH2-NC2 NC6-NH6
+ATOM AH3' HN7     0.09  !                 \ |    \ /   \           \   /
+ATOM AO3' ON5    -0.66  !                  NC5'--NC4'   NC1'--------NN1
+ATOM AH3T HN5     0.43  !                   |     \     / \
+GROUP                   !                 NH5'   NC3'-NC2'NH1'
+ATOM AC5' CN8B   -0.08  !                        / \   / \  
+ATOM AH5' HN8     0.09  !                    NO3' NH3'NO2'NH2'  
+ATOM AH5s HN8     0.09  !                     |       |
+ATOM AP   P       1.50  !                    NH3T    NH2T   
+ATOM AO1  ON3    -0.82  !
+ATOM AO2  ON3    -0.82  !
+ATOM AO5' ON2    -0.62  !
+ATOM O3   ON2    -0.68
+ATOM NP   P       1.50
+ATOM NO1  ON3    -0.82
+ATOM NO2  ON3    -0.82
+ATOM NO5' ON2    -0.62
+ATOM NC5' CN8B   -0.08
+ATOM NH5s HN8     0.09
+ATOM NH5' HN8     0.09 
+GROUP                  
+ATOM NC2' CN7B    0.14 
+ATOM NH2' HN7     0.09 
+ATOM NO2' ON5    -0.66
+ATOM NH2T HN5     0.43
+GROUP
+ATOM NC3' CN7     0.14
+ATOM NH3' HN7     0.09
+ATOM NO3' ON5    -0.66
+ATOM NH3T HN5     0.43
+GROUP
+ATOM NC1' CN7B    0.16
+ATOM NH1' HN7     0.09
+ATOM NC4' CN7     0.16
+ATOM NH4' HN7     0.09
+ATOM NO4' ON6B   -0.50
+GROUP                  
+ATOM NN1  NN2    -0.07
+ATOM NC6  CN3B    0.16
+ATOM NH6  HN3B    0.19
+ATOM NC5  CN3    -0.10
+ATOM NH5  HN3B    0.16
+ATOM NC4  CN3A   -0.05
+ATOM NH4  HN3B    0.16
+ATOM NC3  CN3     0.05 
+ATOM NC2  CN3B    0.18
+ATOM NH2  HN3B    0.16
+ATOM NC7  CN1A    0.68 
+ATOM NO7  ON1    -0.40 
+ATOM NN7  NN1    -0.82
+ATOM NH71 HN1     0.34  ! trans to amide O
+ATOM NH72 HN1     0.36  ! cis to amide O
+
+BOND AN1  AC2       AN3  AC4       AC5  AC6
+BOND AC6  AN6       AC5  AN7       AC8  AN9
+BOND AN9  AC4       AC2  AH2       AN6  AH61      AN6  AH62      AC8  AH8
+DOUBLE AC6  AN1       AC2  AN3       AC4  AC5      AN7  AC8
+BOND AN9  AC1'      AC1' AC2'      AC2' AC3'      AC3' AC4'      AC4' AO4'
+BOND AO4' AC1'      AC1' AH1'      AC2' AO2'      AO2' AP2      AC2' AH2'
+BOND AC3' AH3'      AC3' AO3'      AO3' AH3T      AC4' AH4'      AC4' AC5'
+BOND AC5' AH5s      AC5' AH5'      AC5' AO5'      AO5' AP        AP   AO1
+BOND AP   AO2       AP   O3        O3   NP        NP   NO1       NP   NO2
+BOND NP   NO5'      NO5' NC5'      NC5' NH5s      NC5' NH5'      NC5' NC4'
+BOND NC4' NO4'      NO4' NC1'      NC1' NC2'      NC2' NC3'      NC3' NC4'
+BOND NC1' NH1'      NC2' NH2'      NC2' NO2'      NO2' NH2T      NC3' NH3'
+BOND NC3' NO3'      NO3' NH3T      NC4' NH4'      NC1' NN1       NN1  NC2
+BOND NC3  NC4       NC5  NC6
+BOND NC2  NH2       NC3  NC7       NC7  NO7       NC7  NN7       NN7  NH71
+BOND NN7  NH72      NC4  NH4       NC5  NH5       NC6  NH6
+BOND AP2  AO1P      AP2  AO2P      AP2  AO2T      AO2T AH2T
+DOUBLE NC2  NC3       NC4  NC5       NC6  NN1
+! adenine impropers
+IMPR AN6  AC6  AH61 AH62     AC6  AN1  AC5  AN6
+! amide impropers
+IMPR NC7   NN7   NC3  NO7    NC7   NC3   NN7   NO7 
+IMPR NN7   NC7   NH71 NH72   NN7   NC7   NH72  NH71
+! ring hydrogen impropers
+IMPR NC6   NN1   NC5  NH6    NC5   NC6   NC4   NH5
+IMPR NC4   NC5   NC3  NH4    NC2   NC3   NN1   NH2
+DONO AH61 AN6
+DONO AH62 AN6
+DONO AH2T AO2'
+DONO AH3T AO3'
+ACCE AN1
+ACCE AN3
+ACCE AN7
+ACCE AO4'
+ACCE AO2'
+ACCE AO3'
+ACCE AO5'
+ACCE AO1  AP
+ACCE AO2  AP
+ACCE O3
+ACCE NO1  NP
+ACCE NO2  NP
+ACCE NO5'
+ACCE NO4'
+ACCE NO3'
+ACCE NO2'
+ACCE NO7
+DONO NH2T NO2'
+DONO NH3T NO3'
+DONO NH71 NN7
+DONO NH72 NN7
+DONO AH2T AO2T
+ACCE AO2T
+ACCE AO1P
+ACCE AO2P
+ACCE AO2'
+IC AP     O3     NP     NO5'   1.4863   65.28 -169.00   98.59   1.5977
+IC AC5'   AO5'   AP     O3     1.4232  127.31 -165.10  103.27   1.4863
+IC AC5'   AO5'   AP     AO2    1.4232  127.31   73.33  111.48   1.4836
+IC AH5S   AC5'   AC4'   AC3'   0.9935  120.00  -58.20  111.58   1.6942
+IC AP     O3     NP     NO1    1.4863   65.28   78.51  108.97   1.4756
+IC AP     O3     NP     NO2    1.4863   65.28  -54.29  112.88   1.4636
+IC AP     AO5'   AC5'   AC4'   1.5901  127.31  121.29  111.63   1.5491
+IC AO1    AP     AO5'   AC5'   1.5901  127.31  121.29  127.31   1.4232
+IC AO5'   AC5'   AC4'   AC3'   1.4232  111.63  -58.20  111.58   1.6942
+IC AC5'   AC4'   AC3'   AO3'   1.5491  111.58  128.42  114.19   1.4337
+IC AH3T   AO3'   AC3'   AC4'   0.9671   98.77  147.40  114.19   1.6942
+IC AO4'   AC3'   *AC4   AC5'   1.8868  112.95 -118.10  111.58   1.5491
+IC AC2'   AC4'   *AC3'  AO3'   1.5097   93.22 -117.72  114.19   1.4337
+IC AC4'   AC3'   AC2'   AC1'   1.6942   93.22  -12.93  117.82   1.5415
+IC AC3'   AC2'   AC1'   AN9    1.5097  117.82  135.56  115.01   1.4847
+IC AO4'   AC1'   AN9    AC4    1.3646   95.44  -90.72  125.96   1.4013
+IC AC1'   AC4    *AN9   AC8    1.4847  125.96 -176.52  105.34   1.3777
+IC AC4    AN9    AC8    AN7    1.4013  105.34   -0.07  114.01   1.3282
+IC AC8    AN9    AC4    AC5    1.3777  105.34    0.11  105.06   1.3782
+IC AC8    AN7    AC5    AC6    1.3282  103.21 -179.92  130.78   1.4146
+IC AN7    AC5    AC6    AN1    1.3814  130.78 -179.94  117.85   1.3482
+IC AC5    AC6    AN1    AC2    1.4146  117.85   -0.14  118.87   1.3300
+IC AN9    AC5    *AC4   AN3    1.4013  105.06 -179.67  126.14   1.3648
+IC AC5    AN1    *AC6   AN6    1.4146  117.85  179.89  119.69   1.3419
+IC AN1    AC6    AN6    AH61   1.3482  119.69   -0.39  116.60   0.9912
+IC AH61   AC6    *AN6   AH62   0.9912  116.60 -179.02  116.94   0.9978
+IC AC5    AN1    *AC6   AN6    1.4146  117.85  179.89  119.69   1.3419
+IC AN1    AC6    AN6    AH61   1.3482  119.69   -0.39  116.60   0.9912
+IC AH61   AC6    *AN6   AH62   0.9912  116.60 -179.02  116.94   0.9978
+IC AN9    AN7    *AC8   AH8    1.3777  114.01 -179.37  126.34   1.0962
+IC AN1    AN3    *AC2   AH2    1.3300  129.42  179.97  114.82   1.0928
+IC AC1'   AC3'   *AC2   AO2'   1.5415  117.82 -145.06  114.13   1.4294
+IC AH2'   AO2'   AC2'   AC3'   2.0386   31.12  -93.63  114.13   1.5097
+IC AH2T   AO2'   AC2'   AC3'   0.9953   99.36  -93.63  114.13   1.5097
+IC AO4'   AC2'   *AC1'  AH1'   1.3646  120.77 -114.99  109.65   1.1105
+IC AC1'   AC3'   *AC2   AH2'   1.5415  117.82  108.23   86.44   1.0999
+IC AC2'   AC4'   *AC3'  AH3'   1.5097   93.22  117.28  111.94   1.1110
+IC AC3'   AO4'   *AC4   AH4'   1.6942  112.95 -140.26   57.99   1.0000
+IC AC4'   AO5'   *AC5   AH5'   1.5491  111.63 -123.75  111.23   1.1111
+IC AC4'   AO5'   *AC5   AH5'   1.5491  111.63 -123.75  111.23   1.1111
+IC NC5'   NO5'   NP     NO2    1.4451  128.40  -49.72  108.83   1.4636
+IC NH5S   NC5'   NO5'   NP     1.1110  109.50  115.00  128.40   1.5977
+IC NH5'   NC5'   NO5'   NP     1.1110  109.50 -115.00  128.40   1.5977
+IC NP     NO5'   NC5'   NC4'   1.5977  128.40    0.00  110.10   1.5160
+IC NO5'   NC5'   NC4'   NC3'   1.4451  110.10    0.00  108.50   1.5160
+IC NC5'   NC4'   NC3'   NC2'   1.5160  108.50    0.00  111.00   1.5160
+IC NC4'   NC3'   NC2'   NC1'   1.5160  111.00    0.00  105.50   1.5270
+IC NC3'   NC2'   NC1'   NO4'   1.5160  105.50    0.00  105.00   1.4100
+IC NC2'   NC1'   NO4'   NC4'   1.5270  105.00    0.00  117.86   1.4712
+IC NO2'   NC2'   NC1'   NO4'   1.4200  110.10  180.00  105.00   1.4100
+IC NH2T   NO2'   NC2'   NC1'   0.9600  106.00  180.00  110.10   1.5270
+IC NO4'   NC2'   *NC1'  NH1'   1.4100  105.00 -115.00  110.10   1.1110
+IC NC1'   NC3'   *NC2   NH2'   1.5270  105.50  115.00  110.10   1.1110
+IC NC2'   NC4'   *NC3   NH3'   1.5160  111.00  115.00  110.10   1.1110
+IC NC3'   NO4'   *NC4   NH4'   1.5160  100.64 -115.00  107.24   1.1110
+IC NC4'   NO5'   *NC5   NH5'   1.5160  110.10 -115.00  109.50   1.1110
+IC NC4'   NO5'   *NC5   NH5S   1.5160  110.10  115.00  109.50   1.1110
+IC NC3'   NC2'   NC1'   NN1    1.5160  105.50    0.00  113.70   1.4800
+IC NO3'   NC3'   NC2'   NC1'   1.4200  110.10  180.00  105.50   1.5270
+IC NH3T   NO3'   NC3'   NC2'   0.9600  106.00  180.00  110.10   1.5160
+IC NC2'   NC1'   NN1    NC2    1.5270  113.70    0.00  121.70   1.3150
+IC NC1'   NN1    NC2    NC3    1.4800  121.70    0.00  122.00   1.3500
+IC NN1    NC2    NC3    NC4    1.3150  122.00    0.00  118.00   1.3600
+IC NC2    NC3    NC4    NC5    1.3500  118.00    0.00  118.00   1.3600
+IC NC3    NC4    NC5    NC6    1.3600  118.00    0.00  118.00   1.3500
+IC NC4    NC5    NC6    NN1    1.3600  118.00    0.00  124.51   1.2199
+IC NC5    NC6    NN1    NC2    1.3500  124.51    0.00  119.49   1.3150
+IC NN1    NC2    NC3    NC7    1.3150  122.00    0.00  131.80   1.4800
+IC NC2    NC3    NC7    NO7    1.3500  131.80    0.00  118.50   1.2300
+IC NC2    NC3    NC7    NN7    1.3500  131.80    0.00  113.00   1.3600
+IC NO7    NC7    NN7    NH71   1.2300    0.00  180.00  120.00   1.0000
+IC NO7    NC7    NN7    NH72   1.2300    0.00    0.00  120.00   1.0000
+IC NC2    NC3    NC4    NH4    1.3500  118.00    0.00  121.00   1.0900
+IC NC3    NC4    NC5    NH5    1.3600  118.00    0.00  119.00   1.0900
+IC NC4    NC5    NC6    NH6    1.3600  118.00    0.00  120.50   1.0900
+IC NC6    NN1    NC2    NH2    1.2199  119.49    0.00  117.50   1.0900
+IC AC3'   AC2'   AO2'   AP2    0.0000  000.00  180.00  000.00   0.0000
+IC AC2'   AO2'   AP2    AO2T   0.0000  000.00  -39.52  000.00   0.0000
+IC AO2T   AO2'   *AP2   AO1P   0.0000  000.00 -115.82  000.00   0.0000
+IC AO2T   AO2'   *AP2   AO2P   0.0000  000.00  115.90  000.00   0.0000
+IC AH2T   AO2T   AP2    AO2'   0.0000  000.00  180.00  000.00   0.0000
+PATCH FIRST NONE LAST NONE   
+
+RESI NDPH        -3.00  ! reduced nicotinamide adenine dinucleotide
+                        ! NADPH, VARNAI/adm jr.
+                        ! from NADH and 3PHO
+                        ! checked for consistency with new NA params, adm jr., 9/98
+                        ! note that differences with respect to published results exist
+                        ! due to new NA params
+                        !
+GROUP                   !
+ATOM AC4' CN7     0.16  !                AH61  AH62
+ATOM AH4' HN7     0.09  !                   \  /
+ATOM AO4' ON6B   -0.50  !                   AN6
+ATOM AC1' CN7B    0.16  !                    |
+ATOM AH1' HN7     0.09  !                   AC6
+GROUP                   !                  //  \
+ATOM AC5  CN5     0.28  !                 AN1  AC5--AN7\\
+ATOM AN7  NN4    -0.71  !                  |    ||     AC8-AH8
+ATOM AC8  CN4     0.34  !                 AC2  AC4--AN9/
+ATOM AH8  HN3     0.12  !                 / \\ /     \
+ATOM AN9  NN2    -0.05  !              AH2  AN3       \
+                        !                              \
+ATOM AN1  NN3A   -0.74  !                               \
+ATOM AC2  CN4     0.50  !                                \
+ATOM AH2  HN3     0.13  !    NO1     AO1    AH5sAH4' AO4' \
+ATOM AN3  NN3A   -0.75  !     |       |      |    \ /   \  \
+ATOM AC4  CN5     0.43  ! NO5'NP-O3--AP-AO5'-AC5'-AC4'   AC1'
+ATOM AC6  CN2     0.46  ! \   |       |      |     \     / \
+                        !  \ NO2     AO2    AH5' AC3'-AC2' AH1'
+ATOM AN6  NN1    -0.77  !   \                     / \   / \
+ATOM AH61 HN1     0.38  !    \                AO3' AH3'AO2'AH2'
+ATOM AH62 HN1     0.38  !     \                |        |
+GROUP                   !      \             AH3T AO1P=AP2==AO2P (-)
+ATOM AC2' CN7B    0.01  !       \                       |    NH71
+ATOM AH2' HN7     0.09  !        \                AH2T-AO2T   /
+ATOM AO2' ON2    -0.62  !         \                    NH72-NN7  NH4 NH42
+ATOM AP2  P       1.50  !          \                          \    \ /
+ATOM AO1P ON3    -0.82  !           \                         NC7  NC4
+ATOM AO2P ON3    -0.82  !            \                        / \  /  \
+ATOM AO2T ON4    -0.68  !             \                    NO7  NC3  NC5-NH5
+ATOM AH2T HN4     0.34  !              \                          |    |
+GROUP                   !               \                         |    |
+ATOM AC3' CN7     0.14  !                \ NH5s NH4'NO4'      NH2-NC2 NC6-NH6
+ATOM AH3' HN7     0.09  !                 \ |    \ /   \           \   /
+ATOM AO3' ON5    -0.66  !                  NC5'--NC4'   NC1'--------NN1
+ATOM AH3T HN5     0.43  !                   |     \     / \
+GROUP                   !                 NH5'   NC3'-NC2'NH1'
+ATOM AC5' CN8B   -0.08  !                        / \   / \  
+ATOM AH5' HN8     0.09  !                    NO3' NH3'NO2'NH2'  
+ATOM AH5s HN8     0.09  !                     |       |
+ATOM AP   P       1.50  !                    NH3T    NH2T   
+ATOM AO1  ON3    -0.82  !                   
+ATOM AO2  ON3    -0.82  !                    
+ATOM AO5' ON2    -0.62  !                   
+ATOM O3   ON2    -0.68
+ATOM NP   P       1.50
+ATOM NO1  ON3    -0.82
+ATOM NO2  ON3    -0.82
+ATOM NO5' ON2    -0.62
+ATOM NC5' CN8B   -0.08
+ATOM NH5s HN8     0.09
+ATOM NH5' HN8     0.09
+GROUP
+ATOM NC2' CN7B    0.14
+ATOM NH2' HN7     0.09
+ATOM NO2' ON5    -0.66
+ATOM NH2T HN5     0.43
+GROUP
+ATOM NC3' CN7     0.14
+ATOM NH3' HN7     0.09
+ATOM NO3' ON5    -0.66
+ATOM NH3T HN5     0.43
+GROUP
+ATOM NC1' CN7B    0.16
+ATOM NH1' HN7     0.09
+ATOM NC4' CN7     0.16
+ATOM NH4' HN7     0.09
+ATOM NO4' ON6B   -0.50
+GROUP
+ATOM NN1  NN2    -0.27 !N2
+ATOM NC6  CN3C   -0.06 !C3
+ATOM NH6  HN6     0.17 !H4
+ATOM NC5  CN3    -0.18 !C5
+ATOM NH5  HN6     0.14 !H6
+ATOM NC4  CN8    -0.28 !C7
+ATOM NH4  HN8     0.09 !H8
+ATOM NH42 HN8     0.09 !H17
+ATOM NC3  CN3     0.36 !C9
+ATOM NC2  CN3C   -0.10 !C10
+ATOM NH2  HN6     0.14 !H11
+ATOM NC7  CN1A    0.55 !C12
+ATOM NO7  ON1    -0.51 !O13
+ATOM NN7  NN1    -0.72 !N14
+ATOM NH71 HN1     0.26 !H15  ! trans to amide O
+ATOM NH72 HN1     0.32 !H16  ! cis to amide O
+BOND AN1  AC2       AN3  AC4       AC5  AC6
+BOND AC6  AN6       AC5  AN7       AC8  AN9
+BOND AN9  AC4       AC2  AH2       AN6  AH61      AN6  AH62      AC8  AH8
+DOUBLE AC6  AN1       AC2  AN3       AC4  AC5      AN7  AC8
+BOND AN9  AC1'      AC1' AC2'      AC2' AC3'      AC3' AC4'      AC4' AO4'
+BOND AO4' AC1'      AC1' AH1'      AC2' AO2'      AO2' AP2       AC2' AH2'
+BOND AC3' AH3'      AC3' AO3'      AO3' AH3T      AC4' AH4'      AC4' AC5'
+BOND AC5' AH5s      AC5' AH5'      AC5' AO5'      AO5' AP        AP   AO1
+BOND AP   AO2       AP   O3        O3   NP        NP   NO1       NP   NO2
+BOND NP   NO5'      NO5' NC5'      NC5' NH5s      NC5' NH5'      NC5' NC4'
+BOND NC4' NO4'      NO4' NC1'      NC1' NC2'      NC2' NC3'      NC3' NC4'
+BOND NC1' NH1'      NC2' NH2'      NC2' NO2'      NO2' NH2T      NC3' NH3'
+BOND NC3' NO3'      NO3' NH3T      NC4' NH4'      NC1' NN1       NN1  NC2
+BOND NC3  NC4       NC5  NC6       
+BOND NC2  NH2       NC3  NC7       NC7  NO7       NC7  NN7       NN7  NH71
+BOND NN7  NH72      NC4  NH4       NC4  NH42      NC5  NH5       NC6  NH6
+BOND AP2  AO1P      AP2  AO2P      AP2  AO2T      AO2T AH2T
+DOUBLE NC2  NC3       NC4  NC5       NC6  NN1
+! adenine impropers
+IMPR AN6  AC6    AH61 AH62   AC6   AN1   AC5   AN6
+! amide impropers
+IMPR NC7   NN7   NC3  NO7    NC7   NC3   NN7   NO7
+IMPR NN7   NC7   NH71 NH72   NN7   NC7   NH72  NH71
+! ring hydrogen impropers
+IMPR NC6   NN1   NC5  NH6    NC5   NC6   NC4   NH5
+IMPR NC4   NC5   NC3  NH4    NC2   NC3   NN1   NH2
+DONO AH61 AN6
+DONO AH62 AN6
+DONO AH3T AO3'
+ACCE AN1
+ACCE AN3
+ACCE AN7
+ACCE AO4'
+ACCE AO3'
+ACCE AO5'
+ACCE AO1  AP
+ACCE AO2  AP
+ACCE O3
+ACCE NO1  NP
+ACCE NO2  NP
+ACCE NO5'
+ACCE NO4'
+ACCE NO3'
+ACCE NO2'
+ACCE NO7
+DONO NH2T NO2'
+DONO NH3T NO3'
+DONO NH71 NN7
+DONO NH72 NN7
+DONO AH2T AO2T
+ACCE AO2T
+ACCE AO1P
+ACCE AO2P
+ACCE AO2' 
+! the following ICs will not totally IC BUILD NADPH
+IC AP     O3     NP     NO5'   1.5477  110.11  175.47   98.59   1.5945
+IC AC5'   AO5'   AP     O3     1.4379  124.23 -120.69   96.29   1.5477
+IC AC5'   AO5'   AP     AO2    1.4379  124.23   -4.20  104.25   1.4838
+IC AH5S   AC5'   AC4'   AC3'   1.1127  107.45 -172.00  111.64   1.5309
+IC AP     O3     NP     NO1    1.5477  110.11   63.14  114.14   1.4739
+IC AP     O3     NP     NO2    1.5477  110.11  -73.96  111.08   1.4835
+IC AP     AO5'   AC5'   AC4'   1.5968  124.23  104.17  111.45   1.5366
+IC AO1    AP     AO5'   AC5'   1.4736  106.06  122.59  124.23   1.4379
+IC AO5'   AC5'   AC4'   AC3'   1.4379  111.45  -54.02  111.64   1.5309
+IC AC5'   AC4'   AC3'   AO3'   1.5366  111.64  117.91  108.23   1.4176
+IC AH3T   AO3'   AC3'   AC4'   0.9780  101.86  -77.83  108.23   1.5309
+IC AO4'   AC3'   *AC4   AC5'   3.7210   30.68   12.44   22.46   6.0953
+IC AC2'   AC4'   *AC3'  AO3'   1.5171  107.22 -123.00  108.23   1.4176
+IC AC4'   AC3'   AC2'   AC1'   1.5309  107.22  -27.93   98.01   1.5397
+IC AC3'   AC2'   AC1'   AN9    1.5171   98.01  168.03  114.25   1.4756
+IC AO4'   AC1'   AN9    AC4    1.4308  112.85 -160.05  123.87   1.3958
+IC AC1'   AC4    *AN9   AC8    1.4756  123.87  160.62  105.30   1.3614
+IC AC4    AN9    AC8    AN7    1.3958  105.30    2.73  114.72   1.3222
+IC AC8    AN9    AC4    AC5    1.3614  105.30   -0.85  105.33   1.3777
+IC AC8    AN7    AC5    AC6    1.3222  102.89 -175.73  131.43   1.4163
+IC AN7    AC5    AC6    AN1    1.3877  131.43  177.76  117.35   1.3499
+IC AC5    AC6    AN1    AC2    1.4163  117.35    0.19  119.36   1.3330
+IC AN9    AC5    *AC4   AN3    1.3958  105.33 -177.76  126.56   1.3567
+IC AC5    AN1    *AC6   AN6    1.4163  117.35  178.91  119.82   1.3439
+IC AN1    AC6    AN6    AH61   1.3499  119.82   -2.82  115.89   0.9932
+IC AH61   AC6    *AN6   AH62   0.9932  115.89 -173.48  118.52   0.9961
+IC AC5    AN1    *AC6   AN6    1.4163  117.35  178.91  119.82   1.3439
+IC AN1    AC6    AN6    AH61   1.3499  119.82   -2.82  115.89   0.9932
+IC AH61   AC6    *AN6   AH62   0.9932  115.89 -173.48  118.52   0.9961
+IC AN9    AN7    *AC8   AH8    1.3614  114.72  173.63  127.58   1.0942
+IC AN1    AN3    *AC2   AH2    1.3330  128.86  179.26  114.95   1.0940
+IC AO4'   AC2'   *AC1'  AH1'   1.4308  104.32 -114.05  107.95   1.1153
+IC AC1'   AC3'   *AC2   AH2'   4.3577   16.73  138.52   14.56   4.3331
+IC AC2'   AC4'   *AC3'  AH3'   1.5171  107.22  118.77  114.33   1.1023
+IC AC3'   AO4'   *AC4   AH4'   4.6236   30.68   55.38   18.92   5.2267
+IC AC4'   AO5'   *AC5   AH5'   5.8410    8.40  125.34   12.50   6.6777
+IC AC4'   AO5'   *AC5   AH5'   5.8410    8.40  125.34   12.50   6.6777
+IC NC5'   NO5'   NP     NO2    1.4351  125.31   34.31  105.69   1.4835
+IC NH5S   NC5'   NO5'   NP     1.1087  111.20   -6.79  125.31   1.5945
+IC NH5'   NC5'   NO5'   NP     1.1115  107.95  108.24  125.31   1.5945
+IC NP     NO5'   NC5'   NC4'   1.5945  125.31 -133.06  113.61   1.5644
+IC NO5'   NC5'   NC4'   NC3'   1.4351  113.61   37.01  114.92   1.5111
+IC NC5'   NC4'   NC3'   NC2'   1.5644  114.92   71.49   99.06   1.5369
+IC NC4'   NC3'   NC2'   NC1'   1.5111   99.06   54.76   97.08   1.5500
+IC NC3'   NC2'   NC1'   NO4'   1.5369   97.08  -39.12  103.14   1.4628
+IC NC2'   NC1'   NO4'   NC4'   1.5500  103.14    9.47  109.09   1.4960
+IC NO2'   NC2'   NC1'   NO4'   1.4207  114.02 -166.39  103.14   1.4628
+IC NH2T   NO2'   NC2'   NC1'   0.9638  100.52  -89.37  114.02   1.5500
+IC NO4'   NC2'   *NC1'  NH1'   1.4628  103.14 -111.22  105.40   1.1096
+IC NC1'   NC3'   *NC2   NH2'   2.4663   46.96  -41.97   34.01   3.9460
+IC NC2'   NC4'   *NC3   NH3'   3.9136   23.54 -115.76   16.12   3.6674
+IC NC3'   NO4'   *NC4   NH4'   5.4003   24.61  -39.21   14.97   6.7904
+IC NC4'   NO5'   *NC5   NH5'   5.9665   13.65  -41.47   15.17   7.7670
+IC NC4'   NO5'   *NC5   NH5S   5.9665   13.65  -87.41   13.92   6.7251
+IC NC3'   NC2'   NC1'   NN1    1.5369   97.08   88.64  116.58   1.5502
+IC NO3'   NC3'   NC2'   NC1'   1.4176  119.76 -172.52   97.08   1.5500
+IC NH3T   NO3'   NC3'   NC2'   0.9717  103.61   17.81  119.76   1.5369
+IC NC2'   NC1'   NN1    NC2    1.5500  116.58  -19.65  116.34   1.3499
+IC NC1'   NN1    NC2    NC3    1.5502  116.34  134.66  130.57   1.3607
+IC NN1    NC2    NC3    NC4    1.3499  130.57    5.82  111.74   1.5356
+IC NC2    NC3    NC4    NC5    1.3607  111.74   -1.05  119.26   1.5319
+IC NC3    NC4    NC5    NC6    1.5356  119.26   -1.26  113.69   1.3745
+IC NC4    NC5    NC6    NN1    1.5319  113.69   -0.29  128.15   1.3388
+IC NC5    NC6    NN1    NC2    1.3745  128.15    4.14  116.26   1.3499
+IC NN1    NC2    NC3    NC7    1.3499  130.57 -147.46  122.72   1.5282
+IC NC2    NC3    NC7    NO7    1.3607  122.72 -140.47  119.41   1.2169
+IC NC2    NC3    NC7    NN7    1.3607  122.72   46.61  116.68   1.3621
+IC NO7    NC7    NN7    NH71   1.2169  123.49 -177.07  120.21   1.0093
+IC NO7    NC7    NN7    NH72   1.2169  123.49   -4.94  119.16   1.0014
+IC NC2    NC3    NC4    NH4    1.3607  111.74 -135.39  112.16   1.1099
+IC NC2    NC3    NC4    NH42   1.3607  111.74  114.48  103.52   1.1129
+IC NC3    NC4    NC5    NH5    1.5356  119.26 -171.18  122.65   1.0912
+IC NC4    NC5    NC6    NH6    1.5319  113.69  179.92  118.00   1.0878
+IC NC6    NN1    NC2    NH2    1.3388  116.26  162.03  117.47   1.0731
+IC AC3'   AC2'   AO2'   AP2    0.0000  000.00  180.00  000.00   0.0000
+IC AC2'   AO2'   AP2    AO2T   0.0000  000.00  -39.52  000.00   0.0000
+IC AO2T   AO2'   *AP2   AO1P   0.0000  000.00 -115.82  000.00   0.0000
+IC AO2T   AO2'   *AP2   AO2P   0.0000  000.00  115.90  000.00   0.0000
+IC AH2T   AO2T   AP2    AO2'   0.0000  000.00  180.00  000.00   0.0000
+PATCH FIRST NONE LAST NONE
+
+end
+
+read para card flex append
+* NAD, PPI parameters
+*
+
+ATOMS
+MASS  -1  HN3B       1.00800 ! NAD+ aromatic hydrogen
+MASS  -1  CN1A      12.01100 ! NAD+/NADH amide carbonyl carbon
+MASS  -1  CN3A      12.01100 ! NAD+ aromatic carbon
+MASS  -1  CN3B      12.01100 ! NAD+ aromatic carbon
+MASS  -1  CN3C      12.01100 ! NADH aromatic carbon
+MASS  -1  P3        30.97400 ! pyrophosphate phosphorus
+MASS  -1  P4        30.97400 ! protonated pyrophosphate phosphorus
+
+BONDS
+!
+!atom types  Kb          b0
+!
+!NICH parameters to maintain back compatibility following
+!atom type switch from HN3 to HN6
+CN3C HN6    374.0       1.09    !nadh/ppi, jjp1/adm jr. 7/95
+CN3  HN6    350.0       1.09    !nadh, adm jr., 8/98
+!
+CN1A CN3    302.0       1.480   !nad/ppi, jjp1/adm jr. 7/95
+CN1A NN1    560.0       1.360   !nad/ppi, jjp1/adm jr. 7/95
+CN1A ON1    860.0       1.230   !nad/ppi, jjp1/adm jr. 7/95
+CN3A CN3    450.0       1.360   !nad/ppi, jjp1/adm jr. 7/95
+CN3B CN3    420.0       1.350   !nad/ppi, jjp1/adm jr. 7/95
+CN3C CN3    420.0       1.320   !nadh/ppi, jjp1/adm jr. 7/95
+CN3  CN8    222.5       1.490   !nadh/ppi, jjp1/adm jr. 7/95
+CN3  HN3B   350.0       1.09    !nad/ppi, jjp1/adm jr. 7/95
+CN3A HN3B   350.0       1.09    !nad/ppi, jjp1/adm jr. 7/95
+CN3B HN3B   350.0       1.09    !nad/ppi, jjp1/adm jr. 7/95
+CN3C HN3    374.0       1.09    !nadh/ppi, jjp1/adm jr. 7/95
+CN3B NN2    420.0       1.315   !nad/ppi, jjp1/adm jr. 7/95
+CN3C NN2    420.0       1.355   !nadh/ppi, jjp1/adm jr. 7/95
+ON2  P3     300.0       1.68    !nad/ppi, jjp1/adm jr. 7/95
+ON3  P3     480.0       1.53    !nad/ppi, jjp1/adm jr. 7/95
+ON2  P4     300.0       1.68    !PPI2, from nad/ppi, adm jr. 7/01
+ON3  P4     480.0       1.53    !PPI2, from nad/ppi, adm jr. 7/01
+ON4  P4     237.0       1.58    !PPI2, from MP_1, ADM Jr.
+
+ANGLES
+!
+!atom types     Ktheta    Theta0   Kub     S0
+!
+!NICH parameters to maintain back compatibility following
+!atom type switch from HN3 to HN6
+CN3  CN1A NN1     85.0     113.0  80.0  2.46 !nad/ppi, jjp1/adm jr. 7/95
+CN3  CN1A ON1     85.0     118.5  20.0  2.43 !nad/ppi, jjp1/adm jr. 7/95
+NN1  CN1A ON1     85.0     128.5  20.0  2.17 !nad/ppi, jjp1/adm jr. 7/95
+NN2  CN3C HN6     42.0     119.0  !nad/ppi, jjp1/adm jr. 7/95
+HN6  CN3C CN3     42.0     119.0  !nadh/ppi, jjp1/adm jr. 7/95
+HN6  CN3  CN8     30.0     116.0  !nadh/ppi, jjp1/adm jr. 7/95
+CN3C CN3  HN6     42.0     119.0  !nadh/ppi, jjp1/adm jr. 7/95
+CN1A CN3  CN3C     5.0     107.8  !nad/ppi, jjp1/adm jr. 7/95
+CN1A CN3  CN8    125.0     124.2  !nadh/ppi, jjp1/adm jr. 7/95
+CN3A CN3  CN1A    40.0     110.2  !nad/ppi, jjp1/adm jr. 7/95
+CN3B CN3  CN1A    10.0     131.8  !nad/ppi, jjp1/adm jr. 7/95
+CN3  CN3A CN3     50.0     118.0  !nad/ppi, jjp1/adm jr. 7/95
+CN3A CN3  CN3B    40.0     118.0  !nad/ppi, jjp1/adm jr. 7/95
+CN3  CN3  CN8     53.5     108.5  !nadh/ppi, jjp1/adm jr. 7/95
+CN3B CN3  CN8     53.5     108.5  !nad/ppi, jjp1/adm jr. 7/95
+CN3C CN3  CN8     43.5     128.0  !nad/ppi, jjp1/adm jr. 7/95
+CN3B CN3  HN3B    30.0     122.0  !nad/ppi, jjp1/adm jr. 7/95
+CN3A CN3  HN3B    30.0     119.0  !nad/ppi, jjp1/adm jr. 7/95
+CN3  CN3C HN3     42.0     119.0  !nadh/ppi, jjp1/adm jr. 7/95
+CN3C CN3  HN3     42.0     116.0  !nad/ppi, jjp1/adm jr. 7/95
+CN3  CN3A HN3B    80.0     121.0  !nad/ppi, jjp1/adm jr. 7/95
+CN3  CN3B HN3B    80.0     120.5  !nad/ppi, jjp1/adm jr. 7/95
+CN3  CN3B NN2    120.0     122.0  !nad/ppi, jjp1/adm jr. 7/95
+CN3  CN3C NN2     60.0     122.0  !nadh/ppi, jjp1/adm jr. 7/95
+CN8  CN3  HN3     30.0     116.0  !nadh/ppi, jjp1/adm jr. 7/95
+HN3B CN3B NN2     80.0     117.5  !nad/ppi, jjp1/adm jr. 7/95
+HN3  CN3C NN2     42.0     119.0  !nad/ppi, jjp1/adm jr. 7/95
+CN3  CN8  CN3    125.0     108.0  !nadh/ppi, jjp1/adm jr. 7/95
+CN3  CN8  HN8     55.0     110.10 !nadh/ppi, jjp1/adm jr. 7/95
+CN1A NN1  HN1     35.0     120.0  !nad/ppi, jjp1/adm jr. 7/95
+CN3B NN2  CN3B    30.0     120.0  !nad/ppi, jjp1/adm jr. 7/95
+CN3C NN2  CN3C    20.0     114.0  !nadh/ppi, jjp1/adm jr. 7/95
+CN3B NN2  CN7B    70.0     121.7  !nad/ppi, jjp1/adm jr. 7/95
+CN3C NN2  CN7B    70.0     121.7  !nad/ppi, jjp1/adm jr. 7/95
+CN3B NN2  HN2     32.0     117.4  !nad/ppi, jjp1/adm jr. 7/95
+CN3C NN2  HN2     39.0     123.0  !nad/ppi, jjp1/adm jr. 7/95
+CN9  ON2  P3      20.0     120.0  35.   2.33 !nad/ppi, jjp1/adm jr. 7/95
+P    ON2  P       15.0     140.0 -40.0  2.80 !nad/ppi, jjp1/adm jr. 7/95
+P3   ON2  P       15.0     140.0 -40.0  2.80 !nad/ppi, jjp1/adm jr. 7/95
+P4   ON2  P       45.0     140.0  40.0  3.15 !PPI2, from nad/ppi, adm jr., 7/01
+P3   ON2  P3      15.0     140.0 -40.0  2.80 !nad/ppi, jjp1/adm jr. 7/95
+HN4  ON4  P4      30.0     120.0  40.0  2.35 !PPI2, from MP_1, adm jr., 7/01
+CN7  CN7B ON2     115.0    109.7  !NF, 11/97, C4'C3'O3' for NADPH
+ON2  P4   ON4     48.1     100.0  !PPI2, from MP_1, adm jr., 7/01
+ON3  P4   ON4     98.9     108.23 !PPI2, from MP_1, adm jr., 7/01
+ON2  P3   ON2     80.0     104.3  !nad/ppi, jjp1/adm jr. 7/95
+ON2  P3   ON3     88.9     111.6  !nad/ppi, jjp1/adm jr. 7/95
+ON2  P4   ON3     88.9     105.0  !PPI2, from nad/ppi, adm jr., 7/01
+ON3  P3   ON3    104.0     120.0  !nad/ppi, jjp1/adm jr. 7/95
+ON3  P4   ON3    104.0     120.0  !PPI2, from nad/ppi, adm jr., 7/01
+
+DIHEDRALS
+!
+!atom types             Kchi    n   delta
+!
+ON4  P    ON2  CN7B     0.95    2     0.0  !for NADPH
+ON4  P    ON2  CN7B     0.50    3     0.0  !for NADPH
+! nicotinamide adenine dinucleotide
+CN3  NN2  CN3B HN3B     7.0     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
+HN2  NN2  CN3B HN3B     3.0     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
+HN3B CN3  CN3A HN3B     2.0     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
+HN3B CN3  CN3B HN3B     1.0     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
+NN2  CN3B CN3  HN3B     7.0     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
+CN3  CN1A CN3  HN3B     7.0     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
+CN1A CN3  CN3B HN3B     1.0     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
+CN1A CN3  CN3A HN3B     5.0     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
+CN3  CN1A CN3  HN3      7.0     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
+CN1A CN3  CN3  HN3      1.0     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
+CN3A CN3  CN1A ON1      2.38    2   180.0  !nad/ppi, jjp1/adm jr. 7/95
+CN3B CN3  CN1A ON1      2.38    2   180.0  !nad/ppi, jjp1/adm jr. 7/95
+CN3A CN3  CN1A NN1      0.35    1   180.0  !nad/ppi, jjp1/adm jr. 7/95
+CN3A CN3  CN1A NN1      0.62    2     0.0  !nad/ppi, jjp1/adm jr. 7/95
+CN3B CN3  CN1A NN1      0.35    1     0.0  !nad/ppi, jjp1/adm jr. 7/95
+CN3B CN3  CN1A NN1      0.62    2     0.0  !nad/ppi, jjp1/adm jr. 7/95
+CN3  CN3A CN3  CN1A     3.0     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
+CN3  CN3A CN3  CN3B     6.0     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
+NN2  CN3B CN3  CN3A     7.0     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
+CN3B NN2  CN3B CN3      4.0     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
+X    CN3  CN3A X        1.0     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
+X    CN3  CN3B X        1.0     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
+X    CN3  CN8  X        1.0     3   180.0  !nad/ppi, jjp1/adm jr. 7/95
+X    NN1  CN1A X        2.5     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
+X    NN2  CN3B X        1.0     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
+! nicotinamide adenine dinucleotide hydride, nadh
+CN8  CN3  CN1A ON1      1.00    2   180.0  !nadh, jjp1,adm jr. 4/95
+CN8  CN3  CN1A ON1      1.00    3     0.0  !nadh, jjp1,adm jr. 4/95
+CN8  CN3  CN1A ON1      0.40    6     0.0  !nadh, jjp1,adm jr. 4/95
+CN8  CN3  CN1A NN1      0.50    2   180.0  !nadh, jjp1,adm jr. 4/95
+CN8  CN3  CN1A NN1      0.35    3   180.0  !nadh, jjp1,adm jr. 4/95
+CN8  CN3  CN1A NN1      0.40    6     0.0  !nadh, jjp1,adm jr. 4/95
+CN3C CN3  CN1A ON1      0.30    1     0.0  !nadh, jjp1,adm jr. 4/95
+CN3C CN3  CN1A ON1      1.95    2   180.0  !nadh, jjp1,adm jr. 4/95
+CN3C CN3  CN1A NN1      1.10    1   180.0  !nadh, jjp1,adm jr. 4/95
+CN3C CN3  CN1A NN1      1.95    2   180.0  !nadh, jjp1,adm jr. 4/95
+HN2  NN2  CN3C HN3      4.0     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
+CN3  NN2  CN3C HN3      7.0     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
+NN2  CN3C CN3  HN3      7.0     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
+CN8  CN3  CN3C NN2      0.1     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
+CN3C CN3  CN8  CN3      4.0     3   180.0  !nad/ppi, jjp1/adm jr. 7/95
+CN1A CN3  CN3C NN2      2.5     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
+X    CN3  CN3C X        0.1     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
+X    NN2  CN3C X        0.1     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
+CN3C NN2  CN3C CN3      0.1     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
+! pyrophosphate (ppi)
+P3   ON2  P    ON2      0.03    2     0.0  !nad/ppi, jjp1/adm jr. 7/95
+P3   ON2  P    ON2      0.03    3     0.0  !nad/ppi, jjp1/adm jr. 7/95
+P    ON2  P3   ON2      0.03    2     0.0  !nad/ppi, jjp1/adm jr. 7/95
+P    ON2  P3   ON2      0.03    3     0.0  !nad/ppi, jjp1/adm jr. 7/95
+P3   ON2  P3   ON2      0.03    2     0.0  !nad/ppi, jjp1/adm jr. 7/95
+P3   ON2  P3   ON2      0.03    3     0.0  !nad/ppi, jjp1/adm jr. 7/95
+P    ON2  P    ON2      0.03    2     0.0  !nad/ppi, jjp1/adm jr. 7/95
+P    ON2  P    ON2      0.03    3     0.0  !nad/ppi, jjp1/adm jr. 7/95
+P    ON2  P    ON3      0.10    2     0.0  !nad/ppi, jjp1/adm jr. 7/95
+P    ON2  P    ON3      0.03    3     0.0  !nad/ppi, jjp1/adm jr. 7/95
+P    ON2  P3   ON3      0.10    2     0.0  !nad/ppi, jjp1/adm jr. 7/95
+P    ON2  P3   ON3      0.03    3     0.0  !nad/ppi, jjp1/adm jr. 7/95
+P3   ON2  P    ON3      0.10    2     0.0  !nad/ppi, jjp1/adm jr. 7/95
+P3   ON2  P    ON3      0.03    3     0.0  !nad/ppi, jjp1/adm jr. 7/95
+P3   ON2  P3   ON3      0.10    2     0.0  !nad/ppi, jjp1/adm jr. 7/95
+P3   ON2  P3   ON3      0.03    3     0.0  !nad/ppi, jjp1/adm jr. 7/95
+! protonated pyrophosphate (ppi2)
+P    ON2  P4   ON2      0.03    2     0.0  !from P ON2 P2 ON2, adm jr. 7/01
+P    ON2  P4   ON2      0.03    3     0.0  !from P ON2 P2 ON2, adm jr. 7/01
+P4   ON2  P    ON2      0.03    2     0.0  !from P ON2 P2 ON2, adm jr. 7/01
+P4   ON2  P    ON2      0.03    3     0.0  !from P ON2 P2 ON2, adm jr. 7/01
+P    ON2  P4   ON3      0.10    2     0.0  !from P ON2 P2 ON3, adm jr. 7/01
+P    ON2  P4   ON3      0.03    3     0.0  !from P ON2 P2 ON3, adm jr. 7/01
+P4   ON2  P    ON3      0.10    2     0.0  !from P ON2 P2 ON3, adm jr. 7/01
+P4   ON2  P    ON3      0.03    3     0.0  !from P ON2 P2 ON3, adm jr. 7/01
+P    ON2  P4   ON4      0.10    2     0.0  !from P ON2 P2 ON4, adm jr. 7/01
+P    ON2  P4   ON4      0.03    3     0.0  !from P ON2 P2 ON4, adm jr. 7/01
+X    ON4  P4   X        0.30    3     0.0  !from MP_1, adm jr.
+!for nadp/nadph (?), adm jr.
+HN7  CN7  CN7  CN7       0.195   3         0.0
+HN7  CN7B NN2  CN3B      0.195   3         0.0
+HN7  CN7B NN2  CN3C      0.195   3         0.0
+HN7  CN7  CN7B ON6       0.195   3         0.0
+HN7  CN7  CN7B ON2       0.195   3         0.0
+HN7  CN7  CN7B NN2       0.195   3         0.0
+!
+ON6  CN7B CN7  ON5       3.4     1       180.0 !gam
+CN7  CN7B NN2  CN3B      0.0     3         0.0
+CN8  CN7B NN2  CN3B      0.0     3         0.0 ! 25P1
+CN7B CN7B NN2  CN3B      0.0     3         0.0 ! for NADPH
+ON6  CN7B NN2  CN3B      0.0     3         0.0 !
+ON6B CN7B NN2  CN3B      0.0     3         0.0 ! for NADPH
+CN7  CN7B NN2  CN3C      0.0     3         0.0
+CN7B CN7B NN2  CN3C      0.0     3         0.0 ! for NADPH
+ON6  CN7B NN2  CN3C      0.0     3         0.0 !
+ON6B CN7B NN2  CN3C      0.0     3         0.0 ! for NADPH
+CN7  CN7  CN7B NN2       0.0     3         0.0
+CN8  CN7  CN7B NN2       0.0     3         0.0 ! 25P1
+CN7  CN7B NN2  CN5       0.3     3         0.0 ! NF
+CN7  CN7B NN2  CN4       0.0     3       180.0 ! NF
+ON2  CN7  CN7B NN2       0.0     3         0.0
+ON5  CN7  CN7B NN2       0.0     3         0.0
+
+IMPROPER
+!
+!atom types           Kpsi                   psi0
+!
+! nicotinamide adenine dinucleotide                                             
+CN3  CN3C CN8  HN6     15.0     0     0.0  !nich, jjp1/adm jr.
+HN3B X    X    CN3     15.0     0     0.0  !nad/ppi, jjp1/adm jr.
+HN3B X    X    CN3A    13.0     0     0.0  !nad/ppi, jjp1/adm jr.
+HN3B X    X    CN3B    13.0     0     0.0  !nad/ppi, jjp1/adm jr.
+HN2  CN3  CN3B NN2     50.0     0     0.0  !nad/ppi, jjp1/adm jr.
+HN1  HN1  CN1A NN1     -5.0     0     0.0  !nad/ppi, jjp1/adm jr.
+ON1  X    X    CN1A    40.0     0     0.0  !nad/ppi, jjp1/adm jr.
+HN3  X    X    CN3C    53.0     0     0.0  !nad/ppi, jjp1/adm jr.
+HN6  X    X    CN3C    53.0     0     0.0  !nich, adm jr.
+HN8  CN3  CN3  CN8     18.0     0     0.0  !nad/ppi, jjp1/adm jr.
+
+NONBONDED  NBXMOD 5  ATOM CDIEL FSHIFT VATOM VDISTANCE VFSWITCH -
+     CUTNB 14.0  CTOFNB 12.0  CTONNB 10.0  EPS 1.0  E14FAC 1.0  WMIN 1.5
+!
+!atom  ignored    epsilon      Rmin/2   ignored   eps,1-4       Rmin/2,1-4
+!
+HN3B     0.0       -0.046     0.9000 !nad/ppi, jjp1/adm jr.
+CN1A     0.0       -0.07      2.0000 ! nad/ppi, jjp1/adm jr. (protein CC)
+CN3A     0.0       -0.18      1.8000 ! nad/ppi, jjp1/adm jr.
+CN3B     0.0       -0.18      1.8000 ! nad/ppi, jjp1/adm jr.
+CN3C     0.0       -0.18      1.8000 ! nad/ppi, jjp1/adm jr.
+P3       0.0       -0.585     2.15  ! nad/ppi, jjp1/adm jr.
+P4       0.0       -0.585     2.15  ! for PPI2, adm jr.
+
+end
+
+

tests/0-forcefields/toppar_water_ions_namd.str

@@ -0,0 +1,239 @@
+* Toplogy and parameter information for water and ions.
+read rtf card append
+* Topology for water and ions
+*
+31  1
+
+MASS  1   HT    1.00800 H  ! TIPS3P WATER HYDROGEN
+MASS  2   HX    1.00800 H  ! hydroxide hydrogen
+MASS  3   OT   15.99940 O  ! TIPS3P WATER OXYGEN
+MASS  4   OX   15.99940 O  ! hydroxide oxygen
+MASS  5   LIT  	6.94100 LI ! Lithium ion
+MASS  6   SOD  22.98977 NA ! Sodium Ion
+MASS  7   MG   24.30500 MG ! Magnesium Ion
+MASS  8   POT  39.09830 K  ! Potassium Ion
+MASS  9   CAL  40.08000 CA ! Calcium Ion
+MASS  10  RUB  85.46780 RB ! Rubidium Ion
+MASS  11  CES 132.90545 CS ! Cesium Ion
+MASS  12  BAR 137.32700 BA ! Barium Ion
+MASS  13  ZN   65.37000 ZN ! zinc (II) cation
+MASS  14  CAD 112.41100 CD ! cadmium (II) cation
+MASS  15  CLA  35.45000 CL ! Chloride Ion
+
+default first none last none
+
+RESI TIP3         0.000 ! tip3p water model, generate using noangle nodihedral
+GROUP
+ATOM OH2  OT     -0.834
+ATOM H1   HT      0.417
+ATOM H2   HT      0.417
+BOND OH2 H1 OH2 H2 H1 H2    ! the last bond is needed for shake
+ANGLE H1 OH2 H2             ! required
+DONOR H1 OH2
+DONOR H2 OH2
+ACCEPTOR OH2
+PATCHING FIRS NONE LAST NONE
+
+RESI TP3M         0.000 ! "mmff" water model, as an analog of tip3p
+GROUP
+ATOM OH2  OT     -0.834 ! these charges are replaced by the mmff setup
+ATOM H1   HT      0.417 ! these charges are replaced by the mmff setup
+ATOM H2   HT      0.417 ! these charges are replaced by the mmff setup
+BOND OH2 H1 OH2 H2      ! omits the H1-H2 bond, which is needed for shake with tip3p
+ANGLE H1 OH2 H2         ! required
+DONOR H1 OH2
+DONOR H2 OH2
+ACCEPTOR OH2
+PATCHING FIRS NONE LAST NONE
+
+RESI OH       -1.00 ! hydroxide ion by adm.jr.
+GROUP
+ATOM O1 OX    -1.32
+ATOM H1 HX     0.32
+BOND O1 H1
+DONOR H1 O1
+ACCEPTOR O1
+
+! Ion parameters from Benoit Roux and Coworkers
+! As of 8/10 new NBFIX terms required
+!
+RESI LIT       1.00 ! Lithium Ion
+GROUP
+ATOM LIT  LIT  1.00
+PATCHING FIRST NONE LAST NONE
+
+RESI SOD       1.00 ! Sodium Ion
+GROUP
+ATOM SOD  SOD  1.00
+PATCHING FIRST NONE LAST NONE
+
+RESI MG        2.00 ! Magnesium Ion
+GROUP
+ATOM MG   MG   2.00
+PATCHING FIRST NONE LAST NONE
+
+RESI POT       1.00 ! Potassium Ion
+GROUP
+ATOM POT   POT 1.00
+PATCHING FIRST NONE LAST NONE
+
+RESI CAL       2.00 ! Calcium Ion
+GROUP
+ATOM CAL  CAL  2.00
+PATCHING FIRST NONE LAST NONE
+
+RESI RUB       1.00 ! Rubidium Ion
+GROUP
+ATOM RUB  RUB  1.00
+PATCHING FIRST NONE LAST NONE
+
+RESI CES       1.00 ! Cesium Ion
+GROUP
+ATOM CES  CES  1.00
+PATCHING FIRST NONE LAST NONE
+
+RESI BAR       2.00 ! Barium Ion
+GROUP
+ATOM BAR  BAR  2.00
+PATCHING FIRST NONE LAST NONE
+
+RESI ZN2       2.00 ! Zinc (II) cation, Roland Stote
+GROUP
+ATOM ZN   ZN   2.00
+PATCHING FIRST NONE LAST NONE
+
+RESI CD2       2.00 ! Cadmium (II) cation
+GROUP
+ATOM CD   CAD  2.00
+PATCHING FIRST NONE LAST NONE
+
+RESI CLA      -1.00 ! Chloride Ion
+GROUP
+ATOM CLA  CLA -1.00
+PATCHING FIRST NONE LAST NONE
+
+END
+
+read para card flex append
+* Parameters for water and ions
+*
+
+ATOMS
+MASS  1   HT    1.00800 ! TIPS3P WATER HYDROGEN
+MASS  2   HX    1.00800 ! hydroxide hydrogen
+MASS  3   OT   15.99940 ! TIPS3P WATER OXYGEN
+MASS  4   OX   15.99940 ! hydroxide oxygen
+MASS  5   LIT  	6.94100 ! Lithium ion
+MASS  6   SOD  22.98977 ! Sodium Ion
+MASS  7   MG   24.30500 ! Magnesium Ion
+MASS  8   POT  39.09830 ! Potassium Ion
+MASS  9   CAL  40.08000 ! Calcium Ion
+MASS  10  RUB  85.46780 ! Rubidium Ion
+MASS  11  CES 132.90545 ! Cesium Ion
+MASS  12  BAR 137.32700 ! Barium Ion
+MASS  13  ZN   65.37000 ! zinc (II) cation
+MASS  14  CAD 112.41100 ! cadmium (II) cation
+MASS  15  CLA  35.45000 ! Chloride Ion
+
+BONDS
+!
+!V(bond) = Kb(b - b0)**2
+!
+!Kb: kcal/mole/A**2
+!b0: A
+!
+!atom type Kb          b0
+!
+HT    HT      0.0       1.5139  ! from TIPS3P geometry (for SHAKE w/PARAM)
+HT    OT    450.0       0.9572  ! from TIPS3P geometry
+OX    HX    545.0       0.9700  ! hydroxide ion
+
+ANGLES
+!
+!V(angle) = Ktheta(Theta - Theta0)**2
+!
+!V(Urey-Bradley) = Kub(S - S0)**2
+!
+!Ktheta: kcal/mole/rad**2
+!Theta0: degrees
+!Kub: kcal/mole/A**2 (Urey-Bradley)
+!S0: A
+!
+!atom types     Ktheta    Theta0   Kub     S0
+!
+HT   OT   HT     55.0      104.52   ! FROM TIPS3P GEOMETRY
+
+DIHEDRALS
+!
+!V(dihedral) = Kchi(1 + cos(n(chi) - delta))
+!
+!Kchi: kcal/mole
+!n: multiplicity
+!delta: degrees
+!
+!atom types             Kchi    n   delta
+!
+
+
+!
+IMPROPER
+!
+!V(improper) = Kpsi(psi - psi0)**2
+!
+!Kpsi: kcal/mole/rad**2
+!psi0: degrees
+!note that the second column of numbers (0) is ignored
+!
+!atom types           Kpsi                   psi0
+!
+
+NONBONDED nbxmod  5 atom cdiel fshift vatom vdistance vfswitch -
+cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5
+
+!TIP3P LJ parameters
+HT       0.0       -0.046     0.2245
+OT       0.0       -0.1521    1.7682
+
+!for hydroxide
+OX     0.000000  -0.120000     1.700000 ! ALLOW   POL ION
+                ! JG 8/27/89
+HX     0.000000  -0.046000     0.224500 ! ALLOW PEP POL SUL ARO ALC
+                ! same as TIP3P hydrogen, adm jr., 7/20/89
+
+!ions
+LIT      0.0      -0.00233       1.2975  ! Lithium
+                   ! From S Noskov, target ddG(Li-Na) was 23-26.0 kcal/mol (see JPC B, Lamoureux&Roux,2006)
+SOD      0.0       -0.0469    1.41075  ! new CHARMM Sodium 
+                   ! ddG of -18.6 kcal/mol with K+ from S. Noskov
+MG       0.0       -0.0150    1.18500   ! Magnesium
+                   ! B. Roux dA = -441.65
+POT      0.0       -0.0870    1.76375   ! Potassium
+                   ! D. Beglovd and B. Roux, dA=-82.36+2.8 = -79.56 kca/mol
+CAL      0.0       -0.120      1.367    ! Calcium
+                   ! S. Marchand and B. Roux, dA = -384.8 kcal/mol
+RUB      0.0000    -0.15      1.90      ! Rubidium
+                   ! delta A with respect to POT is +6.0 kcal/mol in bulk water
+CES      0.0       -0.1900    2.100     ! Cesium
+                   ! delta A with respect to POT is +12.0 kcal/mol
+BAR      0.0       -0.150     1.890     ! Barium
+                   ! B. Roux, dA = dA[calcium] + 64.2 kcal/mol
+ZN     0.000000  -0.250000     1.090000 ! Zinc
+                   ! RHS March 18, 1990
+CAD    0.000000  -0.120000     1.357000 ! Cadmium
+                   ! S. Marchand and B. Roux, from delta delta G
+CLA      0.0       -0.150      2.27     ! Chloride
+                   ! D. Beglovd and B. Roux, dA=-83.87+4.46 = -79.40 kcal/mol
+
+NBFIX
+!              Emin         Rmin
+!            (kcal/mol)     (A)
+SOD    CLA      -0.083875   3.731 !  From osmotic pressure calibration, J. Phys.Chem.Lett. 1:183-189
+POT    CLA      -0.114236   4.081 !  From osmotic pressure calibration, J. Phys.Chem.Lett. 1:183-189
+
+!new SOD NBFIX values
+SOD    OC       -0.07502    3.23  ! osmotic P; carboxylate =O
+SOD    OS       -0.07502    3.13  ! POPC optim.; ester =O
+
+
+END
+