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