$FFDATA group  (optional, relevant if QuanPol is used)
$FFDATB group  (optional, relevant if QuanPol is used)
 
The input is given in subsections with a keyword at the
start of the subsection, and STOP at its end.
 
It is free format, but each line shall not exceed 79
characters, including space.
 
COORDINATES
NAME, NUC, X, Y, Z
         NAME    = The name of the atom.
         NUC     = nuclear charge of the atom
         X,Y,Z   = Cartesian coordinates in angstrom
STOP
 
MMVELOCITY
NAME, VX, VY, VZ
         NAME    = The name of the atom.
         VX,VY,VZ= velocity in atomic unit, which is
                   2187691.2633 m/s.
STOP
 
QMVELOCITY
NAME, VX, VY, VZ
         NAME    = The name of the QM atom.
         VX,VY,VZ= velocity in atomic unit, which is
                   2187691.2633 m/s.
STOP
 
         MMVELOCITY and QMVELOCITY are required for
         restarting jobs, and should be copied together
         with COORDINATES from the *.trj file of a
         previous job.
 
PARAMETERS
NAME, MASS, Q, POL, SIGMA, EPSILON, SIGMA2, EPSILON2
         NAME    = The name of the atom.
         Q       = Force field charge (e) on the atom.
         POL     = Polarizability of the atom, in A**3
         SIGMA   = Lennard-Jones parameter in angstrom.
                   When LJSIGMA=0, input RMIN/2.
                   When LJSIGMA=1, input SIGMA.
         EPSILON = Lennard-Jones parameter in kcal/mol
         SIGMA2, EPSILON2
                 = the LJ parameters for select 1-4 cases
                   in CHARMM. Give zeros if not these.
 
         Give the same number of lines as specified in
         the COORDINATES section
STOP
 
QMMMREP
N, C1, Z1, C2, Z2, C3, Z3, C4, Z4
         N       = number of Gaussian type potentials.
                   currently only 4 is allowed.
         C1 - C4 = strength factor of the potential
         Z1 - Z4 = radial factor of the potential
 
         give the same number of lines as specified in
         the COORDINATES section
STOP
 
BOND
SERIAL#, ATOM1, ATOM2, BFC, R0
         SERIAL# = serial number of the bond.
                   this is only for notation purpose.
         ATOM1   = serial number in COORDINATES section
                   for the first atom in the bond.
         ATOM2   = same as ATOM1, but for the second atom.
         BFC     = bond force constant in kcal/mol/A**2.
                   note QuanPol uses E = BFC*(R-R0)**2.
         R0      = equilibrium bond length in angstrom.
STOP
 
ANGLE
SERIAL#, ATOM1, ATOM2, ATOM3, AFC, ANGLE0
         SERIAL# = serial number of the angle.
                   this is only for notation purpose.
         ATOM1   = serial number in COORDINATES section
                   for the first atom in the angle.
         ATOM2   = same as ATOM1, but for the second atom.
         ATOM3   = same as ATOM1, but for the third atom.
         AFC     = angle bending force constant in
                   kcal/mol/rad**2.
                   note QuanPol uses E = AFC*(A-A0)**2.
         ANGLE0  = equilibrium angle in degree.
STOP
 
STRBEND
SERIAL#, BOND1, BOND2, FC1, FC2
         SERIAL# = serial number of the angle.
                   Must be the same as in ANGLE section.
         BOND1   = serial number of the bond in the BOND
                   section for the first bond (atoms 1
                   and 2) in the angle.
         BOND2   = serial number of the bond in the BOND
                   section for the second bond (atoms 2
                   and 3) in the angle.
         FC1     = stretch-bend force constant in
                   kcal/mol/rad/angstrom, for BOND1
         FC2     = stretch-bend force constant in
                   kcal/mol/rad/angstrom, for BOND2
STOP
 
DIHROT
SERIAL#, ATOM1, ATOM2, ATOM3, ATOM4, VROT, N, GAMMA
         SERIAL# = serial number of the dihedral rotation
                   angle. This is only for notation
                   purpose.
         ATOM1   = serial number in COORDINATES section
                   for the first atom in the dihedral
                   rotation angle.
         ATOM2   = same as ATOM1, but for the second atom.
         ATOM3   = same as ATOM1, but for the third atom.
         ATOM4   = same as ATOM1, but for the fourth atom.
         VROT    = rotational barrier in kcal/mol
         N       = multiplicity, an integer.
         GAMMA   = the phase factor in degree.
STOP
 
DIHR3V
SERIAL#, ATOM1, ATOM2, ATOM3, ATOM4, VROT1, VROT2, VROT3
         Similar to DIHROT, but for MM2, MM3 and MMFF94
         style torsion potential.
         VROT1,2,3 are rotational barrier in kcal/mol
STOP
 
DIHBND
SERIAL#, ATOM1, ATOM2, ATOM3, ATOM4, DBFC, DIHB0
         SERIAL# = serial number of the dihedral bending
                   (improper torsion) angle. this is only
                   for notation purpose.
         ATOM1   = serial number in COORDINATES section
                   for the first atom in the dihedral
                   bending angle.
         ATOM2   = same as ATOM1, but for the second atom.
         ATOM3   = same as ATOM1, but for the third atom.
         ATOM4   = same as ATOM1, but for the fourth atom.
         DBFC    = dihedral bending force constant in
                   kcal/mol/rad**2
         DIHB0   = equilibrium dihedral bending angle in
                   degree.
STOP
 
CMAP
SERIAL#, ATOM1, ATOM2, ATOM3, ATOM4, ATOM5, ITYPE
         SERIAL# = serial number of the CHARMM correction
                   map phi,psi couples. this is only
                   for notation purpose.
         ATOM1   = serial number in COORDINATES section
                   for the first atom in the phi angle
                   (the carbonyl carbon of an amino acid
                   residue) of the peptide backbone in a
                   phi,psi couple.
         ATOM2   = serial number in COORDINATES section
                   for the second atom in the phi angle
                   (peptide N atom) of a phi,psi couple.
                   this is the first atom of the psi angle.
         ATOM3   = serial number in COORDINATES section
                   for the third atom in the phi angle
                   (the alpha C atom) of a phi,psi couple.
                   this is the 2nd atom of the psi angle.
         ATOM4   = serial number in COORDINATES section
                   for the fourth atom in the phi angle
                   (a carbonyl carbon) of a phi,psi couple.
                   this is the third atom of the psi angle.
         ATOM5   = serial number in COORDINATES section
                   for the fourth atom in the psi angle
                   (the next peptide N atom).
         ITYPE   = specifies the map potential a phi,psi
                   couple belongs to.
                 =1 alanine map (all except for pro/gly)
                 =2 proline map
                 =3 glycine map
STOP
 
When $FFPDB is given, CMAP is automatically generated for
restart jobs, via $FFDATA input.  The CMAP group could be,
but should not be, input by a user.
 
WAGGING
SERIAL#, ATOM2, ATOM3, ATOM4, ATOM1, WFC
         SERIAL# = serial number of the wagging angle.
                   this is only for notation purpose.
         ATOM2   = serial number in COORDINATES section
                   for the second atom in the wagging
                   angle.
         ATOM3   = same as ATOM2, but for the third atom.
         ATOM4   = same as ATOM2, but for the fourth atom.
         ATOM1   = same as ATOM2, but for the first atom.
         WFC     = wagging force constant kcal/mol/rad**2
STOP
 
MMTYPE
NATOM
N01 N02 N03 ... N18 N19 N20
N21 N22 N23 ... N(NATOM)
         NATOM   = total number of atoms in MMTYPE
                   section.  This must be accurate and
                   occupy a line.
         N(I)    = atom type in force field such as
                   MMFF94.  In MMFF94, there are 95
                   types of atoms.  Each line must have
                   exactly 20 atoms except for the last
                   line, which may have 1-20 atoms.  A
                   line should not exceed 79 characters
                   (including space).  The MMTYPE section
                   is always generated by using LOUT=1.
                   If 0 is seen, one can manually change
                   0 to a real MMFF94 type.  For example,
                   one can change the heme bound Oxygen
                   atom to MMFF94 type 6.  A real type
                   number is required when the LJ
                   potential is needed.
STOP
 
MMFFLJ
NMMTP
I,J,RIJ,EPSIJ,   I,J,RIJ,EPSIJ,   I,J,RIJ,EPSIJ
         NMMTP   = total number of types in MMFFLJ
                   section.  This must be accurate and
                   occupy a line.
         I, J    = atom types in force field such as
                   MMFF94.  In MMFF94, there are 95
                   types of atoms.  J must be equal to
                   or greater than I.
         RIJ     = the minimum Lennard-Jones energy
                   distance (angstrom) between two atoms
                   of type I and type J.
         EPSIJ   = the well depth (kcal/mol) of the LJ
                   term between two atoms of type I and
                   type J.  Each line must have 1, 2, or
                   3 sets, and cannot exceed 79 characters
                   (including space).  The MMFFLJ section
                   is always generated by using LOUT=1.
STOP
 
Use a $END line to end $FFDATA or $FFDATB.