* CHARMM27 Custom Parameter File
* Heme for Cytochrome c
* Felix Autenrieth, Emad Tajkhorshid, Jerome Baudry, Zan Luthey-Schulten; last update 12/19/2005
* Classical force field parameters for the heme prosthetic group of cytochrome c. 
* Journal of Computational Chemistry, 25, 1613-1622 (2004)
* Journal of Physical Chemistry B, 108, 20376-20387 (2004)

BONDS
!
!V(bond) = Kb(b - b0)**2
!
!Kb: kcal/mole/A**2
!b0: A
!
!atom type Kb          b0
!
! added for cyt c HEME 
! Felix Autenrieth, Emad Tajkhorshid, Jerome Baudry, Zan Luthey-Schulten

S    FE    300.000     2.4500 ! ALLOW   ALI SUL ION
                ! from DFT calculation
S    CT1   240.000     1.8100 ! ALLOW   ALI SUL ION
                ! fitted to C-S s   9/26/92 (FL)
NR2  FE     65.000     2.0000 ! ALLOW HEM
                ! Heme (6-liganded): His ligand (KK 11/12/03)
                ! Vibration comparison with RAI 2003
NPH  FE    270.200     2.000 ! ALLOW HEM
                ! Heme (6-liganded): porphyrin macrocycle (KK 11/12/03)
CPB  CT1   450.000     1.3800 ! Copied from "CPB C", 
                ! Heme (6-liganded): substituents (KK 05/13/91)

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
!
! added for cyt c HEME 
! Felix Autenrieth, Emad Tajkhorshid, Jerome Baudry, Zan Luthey-Schulten

CT1   S     CT2     34.000    95.00    
                ! expt. MeEtS,    3/26/92 (FL) 
CPB   CT1   S       58.000   114.50   !
                ! expt. MeEtS,    3/26/92 (FL)
CT3   CT1   S       58.000   114.50   !
                ! expt. MeEtS,     3/26/92 (FL)
S     CT1   HA      65.000   126.74 ! copied from "S C HA". 
                ! expt. MeEtS,    3/26/92 (FL)
CPA  CPB  CT1      70.000   126.7400 ! copied from "CPA  CPB  C ".  
                ! Heme (6-liganded): substituents (KK 05/13/91)
CPB  CT1    CT3      70.000   121.5000 ! copied from "CPB  C    C". 
                ! Heme (6-liganded): substituents (KK 05/13/91)
CPB  CPB  CT1      70.000   126.7500 ! copied from "CPB CPB C". 
                ! Heme (6-liganded): substituents (KK 05/13/91)
HA   CT1  CPB    50.000   120.0000 ! copied from "HA   C    CPB". 
                ! Heme (6-liganded): substituents (KK 05/13/91)
CT2   S     CT2     34.000    95.00   ! ALLOW   ALI SUL ION
                ! expt. MeEtS,    3/26/92 (FL)
CT2   S     FE      34.000    90.00   ! ALLOW HEM
                ! Heme (6-liganded): ligand links (KK 05/13/91)
CT3   S     FE      34.000    90.00   ! ALLOW HEM
                ! Heme (6-liganded): ligand links (KK 05/13/91)
NR2   FE    S       50.000   177.00   ! 
S     FE    NPH     50.000    89.00   ! 


DIHEDRALS
!
!V(dihedral) = Kchi(1 + cos(n(chi) - delta))
!
!Kchi: kcal/mole
!n: multiplicity
!delta: degrees
!
!atom types             Kchi    n   delta
!
! added for cyt c HEME 
! Felix Autenrieth, Emad Tajkhorshid, Jerome Baudry, Zan Luthey-Schulten

NPH     FE   NR2   CPH2        0.047    4     0.00 ! FROM DFT dihedral drive 
NPH     FE   NR2   CPH1        0.047    4     0.00 ! FROM DFT dihedral drive

NPH     FE   S     CT3        0.04     4     0.00 ! FROM DFT dihedral drive 
                ! Heme (6-liganded): 
NPH     FE   S     CT2        0.04     4     0.00 ! FROM DFT dihedral drive 
                ! Heme (6-liganded): 
!! -----------------------------------------------------------------
!! We are going to remove the following 0-barrier, and change the atom types
!! and  introduce a new term for the dihedral angle here. 
! -----------------------------------------------------------
!CT2  S  C  CPB     0.0000     2   180.00 ! ALLOW AR
!                ! Force constant set to zero 
!CT2  S  C  CPB    0.0000     2   180.00 ! ALLOW AR
!                ! Force constant set to zero 
!CT3  S  C  CPB     0.0000     2   180.00 ! ALLOW AR
!                ! Force constant set to zero 
!CT3  S  C  CPB    0.0000     2   180.00 ! ALLOW AR
!                ! Force constant set to zero 
! -----------------------------------------------------------
CT1  S  CT2 CT1   0.24 1 180 ! adopted from "C C S C" bonds in charmm
CT1  S  CT2 CT1   0.37 3   0 ! adopted from "C C S C" bonds in charmm
CT2  S  CT1 CPB   0.24 1 180 ! adopted from "C C S C" bonds in charmm
CT2  S  CT1 CPB   0.37 3   0 ! adopted from "C C S C" bonds in charmm
CT3  S  CT1 CPB   0.24 1 180 ! adopted from "C C S C" bonds in charmm
CT3  S  CT1 CPB   0.37 3   0 ! adopted from "C C S C" bonds in charmm
CT2  S  CT1 CT3   0.24 1 180 ! adopted from "C C S C" bonds in charmm
CT2  S  CT1 CT3   0.37 3   0 ! adopted from "C C S C" bonds in charmm
CT2  S  CT1 HA    0.28 3   0 ! adopted from "C S C H" bonds in charmm
CT1  S  CT2 HA    0.28 3   0 ! adopted from "C S C H" bonds in charmm
! -----------------------------------------------------------
! -----------------------------------------------------------

X    CPB  CT1    X        3.0000  2   180.00 ! copied from "X    CPB  C    X". 
                ! Heme (6-liganded): substituents (KK 05/13/91)


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
!
! added for cyt c HEME 
! Felix Autenrieth, Emad Tajkhorshid, Jerome Baudry, Zan Luthey-Schulten

NR2 CPH1 CPH2 FE      29.4000         0      0.0000

CPB  X    X    CT1      90.0000         0      0.0000 !copied from "CPB  X    X    C". 
                ! Heme (6-liganded): substituents (KK 05/13/91)