* 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 -1 HX 1.00800 H ! hydroxide hydrogen MASS -1 OT 15.99940 O ! TIPS3P WATER OXYGEN MASS -1 OX 15.99940 O ! hydroxide oxygen MASS -1 HPER 1.00800 H ! H of H2O2 MASS -1 OPER 15.99900 O ! O of H2O2 MASS -1 LIT 6.94100 LI ! Lithium ion MASS -1 SOD 22.98977 NA ! Sodium Ion MASS -1 MG 24.30500 MG ! Magnesium Ion MASS -1 POT 39.09830 K ! Potassium Ion MASS -1 CAL 40.08000 CA ! Calcium Ion MASS -1 RUB 85.46780 RB ! Rubidium Ion MASS -1 CES 132.90545 CS ! Cesium Ion MASS -1 BAR 137.32700 BA ! Barium Ion MASS -1 ZN 65.37000 ZN ! zinc (II) cation MASS -1 CAD 112.41100 CD ! cadmium (II) cation MASS -1 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 RESI H2O2 0.000 ! hydrogen peroxide ! Orabi and English, JCTC. 2018, 14, 2808-2821 ! ! HP2 ! \ ! OP2--OP1 ! \ ! HP1 ! GROUP ATOM HP1 HPER 0.41 ATOM OP1 OPER -0.41 ATOM OP2 OPER -0.41 ATOM HP2 HPER 0.41 BOND HP1 OP1 OP1 OP2 OP2 HP2 DONOR HP1 OP1 DONOR HP2 OP2 ACCEPTOR OP1 ACCEPTOR OP2 IC HP1 OP1 OP2 HP2 0.963 99.92 111.71 99.92 0.963 PATCH FIRST NONE LAST NONE ! 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 -1 HX 1.00800 ! hydroxide hydrogen MASS -1 OT 15.99940 ! TIPS3P WATER OXYGEN MASS -1 OX 15.99940 ! hydroxide oxygen MASS -1 HPER 1.00800 ! H of H2O2 MASS -1 OPER 15.99900 ! O of H2O2 MASS -1 LIT 6.94100 ! Lithium ion MASS -1 SOD 22.98977 ! Sodium Ion MASS -1 MG 24.30500 ! Magnesium Ion MASS -1 POT 39.09830 ! Potassium Ion MASS -1 CAL 40.08000 ! Calcium Ion MASS -1 RUB 85.46780 ! Rubidium Ion MASS -1 CES 132.90545 ! Cesium Ion MASS -1 BAR 137.32700 ! Barium Ion MASS -1 ZN 65.37000 ! zinc (II) cation MASS -1 CAD 112.41100 ! cadmium (II) cation MASS -1 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 HPER OPER 521.0 0.963 ! H2O2 OPER OPER 285.5 1.442 ! H2O2 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 HPER OPER OPER 60.4 99.92 ! H2O2 DIHEDRALS ! !V(dihedral) = Kchi(1 + cos(n(chi) - delta)) ! !Kchi: kcal/mole !n: multiplicity !delta: degrees ! !atom types Kchi n delta ! HPER OPER OPER HPER 2.02 2 0.0 ! H2O2 ! 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 !for hydrogen peroxide HPER 0.0 -0.046 0.2245 OPER 0.0 -0.20384 1.67423 !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 ! ! prot SOD OC -0.07502 3.23 ! osmotic P; carboxylate =O SOD OS -0.07502 3.13 ! POPC optim.; ester =O !! NA !SOD ON3 -0.07502 3.16 ! POPC optim.; phosphate =O UNVALIDATED LIT ON3 -0.0167 3.1775 ! Savelyev and MacKerell, JPCB 2015 !! lipid 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 !! carb SOD OC2D2 -0.07502 3.23 ! osmotic P; carboxylate =O SOD OC2DP -0.07502 3.16 ! POPC optim.; phosphate =O !! CGenFF SOD OG2D2 -0.07502 3.23 ! osmotic P; carboxylate =O ! OG2D1 in CGenFF shared between esters, amides, aldehydes,... !SOD OG2D1 -0.07502 3.13 ! POPC optim.; ester =O SOD OG2P1 -0.07502 3.16 ! POPC optim.; phosphate =O ! Chloride CLA LIT -0.0187 3.6875 ! Savelyev and MacKerell, JPCB 2015 CLA SOD -0.0839 3.7310 ! Savelyev and MacKerell, JPCB 2015 CLA POT -0.1142 4.0810 ! Savelyev and MacKerell, JPCB 2015 !Potassium NBFixes !carboxylate O POT OC -0.1022 3.524 ! PNAS, 111: E5354-E5362 (2014) POT OCL -0.1022 3.524 ! PNAS, 111: E5354-E5362 (2014) POT OC2D2 -0.1022 3.524 ! PNAS, 111: E5354-E5362 (2014) POT OG2D2 -0.1022 3.524 ! PNAS, 111: E5354-E5362 (2014) !Calcium NBFixes: 2019-8 CAL CLA -0.134164 3.727 ! from J. Phys. Chem. B 2018, 122, 1484−1494 CAL O2L -0.12 3.256 ! from J. Phys. Chem. B 2018, 122, 1484−1494 CAL OC2DP -0.12 3.256 ! from J. Phys. Chem. B 2018, 122, 1484−1494 CAL OG2P1 -0.12 3.256 ! from J. Phys. Chem. B 2018, 122, 1484−1494 !carboxylate O CAL OCL -0.12 3.232 ! Rong Shen and Benoit Roux, personal communication CAL OC -0.12 3.232 ! Nature Structural & Molecular Biology 23: 590 (2016) CAL OC2D2 -0.12 3.232 ! CAL OG2D2 -0.12 3.232 ! END BOMLEV @bom @PARA WRNLEV @wrn @PARA return