* Toplogy and parameter information for water and ions. * !Testcase !test_water_ions.inp ! IMPORTANT NOTE: this file contains NBFixes between carboxylates and sodium, ! which will only apply if the main files containing carboxylate atom types ! have been read in first! !references ! !TIP3P water model ! !W.L. Jorgensen; J.Chandrasekhar; J.D. Madura; R.W. Impey; !M.L. Klein; "Comparison of simple potential functions for !simulating liquid water", J. Chem. Phys. 79 926-935 (1983). ! !IONS ! !Ions from Roux and coworkers ! !Beglov, D. and Roux, B., Finite Representation of an Infinite !Bulk System: Solvent Boundary Potential for Computer Simulations, !Journal of Chemical Physics, 1994, 100: 9050-9063 ! !ZINC ! !Stote, R.H. and Karplus, M. Zinc Binding in Proteins and !Solution: A Simple but Accurate Nonbonded Representation, PROTEINS: !Structure, Function, and Genetics 23:12-31 (1995) !test "append" to determine if previous toppar files have been read and !add append to "read rtf card" if true set nat ?NATC set app !We're exploiting what is arguably a bug in the parser. On the left hand side, !the quotes have priority, so NAT is correctly substituted. On the right hand !side, the ? has priority and NATC" (sic) is not a valid substitution... if "@NAT" ne "?NATC" if @nat ne 0 set app append read rtf card @app * 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 @app * 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 END ! The following section contains NBFixes for sodium interacting with ! carboxylate oxygens of various CHARMM force fields. It will generate ! level -1 warnings whenever any of these force fields have not been ! read prior to the current stream file. Since we don't want to force ! the user to always read all the force fields, we're suppressing the ! warnings. The only side effect is that you will have "most severe ! warning was at level 0" at the end of your output. Also note that ! the user is responsible for reading the current file last if they ! want the NBFixes to apply. A more elegant solution would require new ! features to be added to CHARMM. ! parallel fix, to avoid duplicated messages in the log set para if ?NUMNODE gt 1 set para node 0 set wrn ?WRNLEV ! Some versions of CHARMM don't seem to initialize wrnlev... if "@WRN" eq "?WRNLEV" set wrn 5 set bom ?bomlev WRNLEV -1 @PARA BOMLEV -1 @PARA read para card flex append * NBFix between carboxylate and sodium * ! These NBFixes will only apply if the main files have been read in first!!! NBFIX !new SOD NBFIX values ! Simulations of Anionic Lipid Membranes: Development of Interaction-Specific ! Ion Parameters and Validation using NMR Data. ! Venable, R.M.; Luo, Y,; Gawrisch, K.; Roux, B.; Pastor, R.W. ! J. Phys. Chem. B 2013, 117 (35), pp 10183–10192. DOI: 10.1021/jp401512z ! SOD OCL -0.07502 3.23 ! osmotic P; carboxylate =O SOD OBL -0.07502 3.13 ! POPC optim.; ester =O SOD O2L -0.07502 3.16 ! POPC optim.; phosphate =O ! SOD OC -0.07502 3.23 ! For prot carboxylate groups SOD OC2D2 -0.07502 3.23 ! For carb carboxylate groups SOD OG2D2 -0.07502 3.23 ! For CGenFF carboxylate groups END BOMLEV @bom @PARA WRNLEV @wrn @PARA return