* 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 shift vatom vdistance vswitch - 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 SOD OC -0.075020 3.190 ! For prot carboxylate groups !SOD OCL -0.075020 3.190 ! For lipid carboxylate groups !SOD OC2D2 -0.075020 3.190 ! For carb carboxylate groups !SOD OG2D2 -0.075020 3.190 ! For CGenFF carboxylate groups END