diff --git a/auto_namd_python/__init__.py b/auto_namd_python/__init__.py deleted file mode 100644 index e69de29..0000000 diff --git a/auto_namd_python/functions.py b/auto_namd_python/functions.py deleted file mode 100644 index 26e6194..0000000 --- a/auto_namd_python/functions.py +++ /dev/null @@ -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 diff --git a/auto_namd_python/job.py b/auto_namd_python/job.py deleted file mode 100644 index ca75d86..0000000 --- a/auto_namd_python/job.py +++ /dev/null @@ -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 diff --git a/auto_namd_python/simulate.py b/auto_namd_python/simulate.py deleted file mode 100644 index 5e236f7..0000000 --- a/auto_namd_python/simulate.py +++ /dev/null @@ -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 diff --git a/run.py b/run.py deleted file mode 100755 index 3f82d0c..0000000 --- a/run.py +++ /dev/null @@ -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) diff --git a/run_analysis.py b/run_analysis.py new file mode 100644 index 0000000..909a0a8 --- /dev/null +++ b/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() diff --git a/run_simulation.py b/run_simulation.py new file mode 100755 index 0000000..f5f9551 --- /dev/null +++ b/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) diff --git a/tests/0-forcefields/par_all36_lipid.prm b/tests/0-forcefields/par_all36_lipid.prm new file mode 100644 index 0000000..411e764 --- /dev/null +++ b/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 diff --git a/tests/0-forcefields/par_all36_na.prm b/tests/0-forcefields/par_all36_na.prm new file mode 100644 index 0000000..6f25eb4 --- /dev/null +++ b/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 diff --git a/tests/0-forcefields/par_all36m_prot.prm b/tests/0-forcefields/par_all36m_prot.prm new file mode 100644 index 0000000..f1359b6 --- /dev/null +++ b/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 diff --git a/tests/0-forcefields/toppar_all36_na_nad_ppi.str b/tests/0-forcefields/toppar_all36_na_nad_ppi.str new file mode 100644 index 0000000..6abeee3 --- /dev/null +++ b/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 + + diff --git a/tests/0-forcefields/toppar_water_ions_namd.str b/tests/0-forcefields/toppar_water_ions_namd.str new file mode 100644 index 0000000..5b73432 --- /dev/null +++ b/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 +