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The text format for the parameter file begins with a title, see Syntactic Glossary, followed by a set of free field commands, and terminating with the end of the file or an END statement. The purpose of the commands is to fill the various parameter arrays. The commands are described below:
BOND repeat(word word) FORCe real DISTance real
The BOND command adds bond parameters. The bond energy term for one bond is given by
E_b = k_b (b - b_0)^2
where k_b is the force constant and b_0 is the equilibrium bond length.
The force constant is given by the FORCE keyword and the equilibrium bond length is given by the DISTANCE keyword. Each pair of words is treated as a separate entry in the bond parameter arrays, so it is possible to specify the same parameters for many bonds.
{ANGLE} repeat(word word word) FORCe real ANGLE real
{THETA}
The ANGLE command adds angle parameters. The angle energy term is given by
E_t = k_t (t - t_0)^2
where k_t is the force constant, t is the bond angle, and t_0 is the equilibrium angle. Bond angles are defined over triplets of atoms. The force constant is given by the FORCE keyword and the equilibrium angle is given by the ANGLE keyword. Each triplet of words is treated as a separate entry in the angle parameter arrays, so it is possible to specify the same parameters for many angles.
{TORSION} repeat(word word word word) repeat(torsion-term)
{PHI }
torsion-term ::= TERM FORCe real PHASe real PERIod real
MULTiplicity int END
The TORSION command adds torsion angle parameters. The torsion angle term has the following form
E_phi = sum_i k_phi_i (1 + cos(n_i phi + delta_i))
where i is over all the terms for one torsion angle, k_(phi_i) is the force constant for the i-th term, m_i is the multiplicity for the i-th term, n_i is the periodicity of the i-th term, delta_i is the phase for the i-th term, and phi is the current value of the torsion angle.
Torsion angles are defined over quadrulets of atoms, and there can be multiple terms per torsion angle so that complex torsions can be established. Each term is specified by strings beginning with TERM and ending with END. The force constant for each term is given by the FORCE keyword. The phase is given by the PHASE keyword. The periodicity is given by the PERIOD keyword, and limited to values of 1, 2, 3, 4, and 6. The multiplicity is given by the MULTIPLICITY keyword, and is most useful in using the AMBER force field, see AMBERPARM. At least one term must be specified for a torsion angle. Each quadruplet of words is treated as a separate entry in the torsion parameter arrays, so it is possible to specify the same parameters for many torsions.
{IMPROPER} repeat(word word word word) FORCe real improper-term
{IMPHI }
improper-term ::= {PHASe real PERIod real}
{MIN real }
The IMPROPER command adds improper torsion parameters. If the dihedral form of improper torsion is selected, the improper torsion term use the torsion angle term given above. If the harmonic form of the improper torsion is selected, then the improper torsion energy term is given by
E_i = k_i (phi_i - phi_i_0)^2
where k_i is the force constant, phi_i is the improper torsion, and phi_i_0 is the equilibrium improper torsion. Improper torsions are defined over quadruplets of atoms. The force constant is given by the FORCE keyword. If the dihedral form of the energy is used, then the phase and period are given by the PHASE and PERIOD keywords, respectively. The multiplicity is set to 1. If the harmonic form is used, then the equilibrium improper torsion angle is given by the MIN keyword. Each quadruplet of words is treated as a separate entry in the improper torsion parameter arrays, so it is possible to specify the same parameters for many improper torsions.
HBOND repeat(word word) {EMIN real RMIN real }
{CREPulsive real CATTractive real}
The HBOND command adds hydrogen bond parameters. The form of the hydrogen bond term is given by
E_hb = (C_r / r^12 - C_a / r^10) cos^4(theta_HB)
There are two different ways to calculate hydrogen bond energies. The form in the old CHARMM potential uses the distance between the heavy atom attached to the donor hydrogen and the acceptor, and angular term based on the heavy atom donor, donor hydrogen, acceptor angle. The form used by the AMBER potential uses the distance between the hydrogen and the acceptor, and no angle term. The DEFAULT command described below allows you to switch from one form to the other.
There are two ways to specify the two coefficients. They may be specified directly using CREPULSIVE to specify the first coefficient, and CATTRACTIVE for the second. The second way is to specify the minimum energy, keyword EMIN, and minimum energy distance, keyword RMIN, and CONGEN will compute the coefficients for you.
The pairs of words in each command specifies pairs of atom type patterns to be used for setting the coefficients. The first pattern in the pair gives the atoms types for the donor, being heavy atom or hydrogen. The second pattern gives the acceptor.
The actual process of setting hydrogen bond parameters is complicated by the requirement for constructing a table of hydrogen bond codes so that hydrogen bond codes can be looked up rapidly. Pseudocode for the operation is as follows:
For Ih = 1 to Number of Hydrogen bond patterns
For I = 1 to Number of Atom Types (NATC)
If atom_type(I) matches pattern(1,Ih)
For J = 1 to NATC
If atom_type(J) matches pattern(2,Ih)
HBCODE = I*NATC+J-1
if (HBCODE is not in current list of HB codes)
add new HBCODE and coefficients.
fi
fi
done
fi
done
done
{NBOND } repeat(word) [EMIN real ]
{NONBONDED} [RADIUS real ]
[ALPHa real ]
[NEFF real ]
[CREPulsive real ]
[CATTractive real]
The NBOND command adds non-bonded energy parameters. The nonbonded energy function is
Enb = A/r^12 - B/r^6
Non-bonded energy parameters are specified only by atom types, and mixed parameters are specified using the combination rules in the CHARMM paper, see Introduction, for the reference.
In each NBOND command, the words are atom type codes. The options have the following meanings:
The parameters can be specified in three different ways; by the 6-12 coefficients (CREPULSIVE and CATTRACTIVE, by minimum energy (EMIN) and radius (RADIUS), or by radius (RADIUS), number of effective electrons (NEFF), and polarizabilities (ALPHA). The program does not check if you overspecify options, so pick one method and use it consistently.
DEFAULT [IMPRoper [COSIne ] [NOSYmmetry] END]
[HARMonic] [SYMMetry ]
[HBOND [H-A] END]
[D-A]
[NBOND [VDW14 real] [EL14 real] [HBEXclude] END]
[HBINclude]
The DEFAULT command is used to set defaults which pertain how some of energy terms are calculated. These defaults are set in the parameter file because the parameters are developed as an integrated whole. Settings in the DEFAULT command are an integral part of any parameter file.
From the syntax, it can be seen that there are three different energy terms to which these defaults can apply. The IMPROPER options control the following aspects of the improper torsion energy:
The HBOND default options control which distance is used in the hydrogen bond energy. If D-A is specified, the distance is calculated between the heavy atom donor and the acceptor, and the angular term is included. In addition, the parameterization is done based on the heavy atom donor and acceptor. This is the CHARMM form. If H-A is specified, the distance is calculated between the hydrogen and the acceptor, and no angular term is included. The parameterization is done based on the hydrogen and the acceptor. The default is D-A
The NBOND default options control scaling for 1-4 interactions and the inclusion of van der Waals energies for hydrogen bond pairs. 1-4 interactions are non-bonded interactions of atoms connected by three bonds (see Nbxmod, for more information). The VDW14 keyword sets the scale factor for the van der Waals energy of 1-4 interactions. The EL14 keyword sets the scale factor for 1-4 electrostatic interactions. The default is 1.0 for both of these scale factors. In the AMBER potential, they are set to 0.5. The HBINCLUDE keyword specifies that van der Waals interactions will be calculated for atoms involved in hydrogen bonds. This is the default. The HBEXLCUDE keyword specifies that van der Waals interactions will be turned off for all possible atom pairs specified as possible hydrogen bonds. This is the default for the AMBER potential. Warning: you must ensure that the hydrogen bond distance cutoff is positive when this option is in use. Otherwise, it is possible to generate infinite energies if a charged hydrogen and its acceptor get too close together.
PRINT [ON ]
[OFF]
The PRINT command turns on the echoing of commands in the parameter file and the display of all non-bonded parameters. It is useful for debugging. It is off by default.
END