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par_heme_b.inp
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* 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)
S CE1 240.000 1.8100 ! ALLOW ALI SUL ION !
! copied from S CT1 above (JPB 2/5/09)
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)
CPB CE1 450.000 1.3800 ! Copied from "CPB C",
! Heme (6-liganded): duplicated (JPB 09/19/08)
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
CE1 S CT2 34.000 95.00
! jpb
CE2 CE1 S 58.000 114.50 !
! jpb
CPB CE1 S 58.000 114.50 !
! 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)
S CE1 HE1 65.000 126.74 ! copied from "S C HA".
! jpb
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 CE1 CE2 70.000 121.5000 ! copied from "CPB C C".
! Heme (6-liganded): substituents (JPB 09/19/08)
CPB CPB CT1 70.000 126.7500 ! copied from "CPB CPB C".
! Heme (6-liganded): substituents (KK 05/13/91)
CPB CPB CE1 70.000 126.7500 ! copied from "CPB CPB C".
! Heme (6-liganded): substituents (JPB 9/19/08)
HA CT1 CPB 50.000 120.0000 ! copied from "HA C CPB".
! Heme (6-liganded): substituents (KK 05/13/91)
HE1 CE1 CPB 50.000 120.0000 ! copied from "HA C CPB".
! Heme (6-liganded): substituents (JPB 9/19/08)
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
! -----------------------------------------------------------
CE1 S CT2 CT1 0.24 1 180 ! adopted from "C C S C" bonds in charmm
CE1 S CT2 CT1 0.37 3 0 ! adopted from "C C S C" bonds in charmm
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
CE2 S CT1 CPB 0.24 1 180 ! adopted from "C C S C" bonds in charmm
CE2 S CT1 CPB 0.37 3 0 ! adopted from "C C S C" bonds in charmm
CT2 S CE1 CE2 0.24 1 180 ! adopted from "C C S C" bonds in charmm
CT2 S CE1 CE2 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
CT2 S CE1 CPB 0.24 1 180 ! adopted from "C C S C" bonds in charmm
CT2 S CE1 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
CT2 S CE1 HE1 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
CE1 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)
X CPB CE1 X 3.0000 2 180.00 ! copied from "X CPB C X".
! Heme (6-liganded): substituents (JPB 9/19/08)
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)
CPB X X CE1 90.0000 0 0.0000 !copied from "CPB X X C".
! Heme (6-liganded): substituents (JPB 9/19/08)