*>>>>> CHARMM22 All-Hydrogen Parameter File for Proteins <<<<<<<<
*>>>>> Includes phi, psi cross term map (CMAP) correction <<<<<<<
*>>>>>>>>>>>>>>>>>>>>>> December, 2003 <<<<<<<<<<<<<<<<<<<<<<<<<<
* All comments to ADM jr. via the CHARMM web site: www.charmm.org
*               parameter set discussion forum
*

! references
!
!PROTEINS
!
!MacKerell, A.D., Jr,. Feig, M., Brooks, C.L., III, Extending the
!treatment of backbone energetics in protein force fields: limitations
!of gas-phase quantum mechanics in reproducing protein conformational
!distributions in molecular dynamics simulations, Journal of
!Computational Chemistry, 25: 1400-1415, 2004.
!
!MacKerell, Jr., A. D.; Bashford, D.; Bellott, M.; Dunbrack Jr., R.L.;
!Evanseck, J.D.; Field, M.J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.;
!Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F.T.K.; Mattos,
!C.; Michnick, S.; Ngo, T.; Nguyen, D.T.; Prodhom, B.; Reiher, III,
!W.E.; Roux, B.; Schlenkrich, M.; Smith, J.C.; Stote, R.; Straub, J.;
!Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M.  All-atom
!empirical potential for molecular modeling and dynamics Studies of
!proteins.  Journal of Physical Chemistry B, 1998, 102, 3586-3616.
!
!IONS (see lipid and nucleic acid topology and parameter files for
!additional ions
!
!ZINC
!
!Roland H. Stote and Martin Karplus, Zinc Binding in Proteins and
!Solution: A Simple but Accurate Nonbonded Representation, PROTEINS:
!Structure, Function, and Genetics 23:12-31 (1995)
!

BONDS
!
!V(bond) = Kb(b - b0)**2
!
!Kb: kcal/mole/A**2
!b0: A
!
!atom type Kb          b0
!
HT   HT      0.000     1.5139 ! ALLOW WAT
                ! FROM TIPS3P GEOMETRY (FOR SHAKE/W PARAM)
OT   HT    450.000     0.9572 ! ALLOW   WAT
                ! FROM TIPS3P GEOM
!AMBER parameters for methyl chloride
!CL   CCL   279.000     1.786       ! from AMBER
CL   CCL     0.000     0.000       ! zeroed, use Morse instead
CCL  HCL   340.400     1.090       ! from AMBER

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     55.000   104.5200 ! ALLOW WAT
                ! TIP3P GEOMETRY, ADM JR.
!AMBER parameters for methyl chloride
CL   CCL  HCL    40.200   105.50000    !from AMBER 
HCL  CCL  HCL    39.300   109.44000    !from AMBER
CL   CCL  CL      0.000     0.0    !for cp2k not to complain

DIHEDRALS
!
!V(dihedral) = Kchi(1 + cos(n(chi) - delta))
!
!Kchi: kcal/mole
!n: multiplicity
!delta: degrees
!
!atom types             Kchi    n   delta
!
X    NPH  CPA  X        0.0000  2     0.00 ! ALLOW HEM
                ! Heme (6-liganded): dummy for "auto dihe" (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
!
CPB  CPA  NPH  CPA    20.8000         0      0.0000 ! ALLOW HEM
                ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)


NONBONDED nbxmod  5 atom cdiel shift vatom vdistance vswitch -
cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 
                !adm jr., 5/08/91, suggested cutoff scheme
!
!V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6]
!
!epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j)
!Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j
!
!atom  ignored    epsilon      Rmin/2   ignored   eps,1-4       Rmin/2,1-4
!
HT     0.000000  -0.046000     0.224500 ! ALLOW WAT
                !TIP3P HYDROGEN PARAMETERS, adm jr., NBFIX obsolete
OT     0.000000  -0.152100     1.768200 ! ALLOW   WAT
                !TIP3P OXYGEN PARAMETERS, adm jr., NBFIX obsolete
!AMBER GAFF parameters for methyl chloride
CCL    0.000000  -0.109400     1.908000
HCL    0.000000  -0.015700     1.387000 
!averaged AMBER parameters for the chlorine and chloride
CL     0.000000  -0.265000     1.948000
CLA    0.000000  -0.265000     1.948000

HBOND CUTHB 0.5  ! If you want to do hbond analysis (only), then use
                 ! READ PARAM APPEND CARD
                 ! to append hbond parameters from the file: par_hbond.inp

END
