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toppar_water_ions.str
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toppar_water_ions.str
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* 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
!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
!
CAL OCL -0.12 3.232 ! Rong Shen and Benoit Roux, personal communication
CAL OC -0.12 3.232 ! Rong Shen and Benoit Roux, personal communication
CAL OC2D2 -0.12 3.232 ! Rong Shen and Benoit Roux, personal communication
CAL OG2D2 -0.12 3.232 ! Rong Shen and Benoit Roux, personal communication
END
BOMLEV @bom @PARA
WRNLEV @wrn @PARA
return