* 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

