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auto_namd_python/tests/0-forcefields/toppar_water_ions_namd.str

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* 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
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