The force field (.ff) file

All the lines beginning with “#” are considered as commentaries.

The file consists of a number of sections; each beginning with a keyword. Each new keyword means the end of the old section and beginning of the new section corresponding to this keyword. The order of section must be kept. All energies are given in $kJ/mol$, distances in $\AA$, and angles in degrees.

• begin_definitions

  < an orbitrary number of lines >

  end_definitions

  This optional section is optional. It contains list of atom types with their masses, and a number of directives.

  Directives:

  FACTORS <fudge_LJ> <fudge_Q>

  This defines scaling factors for 1-4 Lennard-Jones and electrostatic interactions

  No_UB : do not include Urey-Bradley term even if they are present

  SKIP_ABS : skip writing angles and torsions into .mmol file parameters for which are not found.

  Other lines are in the form:

  <atom type> <mass> [ commentary ]

  These lines determine masses for atom types, which will be written in the mmol file. If masses of atoms are not determined in this section, the values of masses will be guessed from the first letters of the atom type names.

• BONDS

  Contains parameters for covalent bonds. Each line consists of four or six parameters. The first two parameters are the force field atom types. The third parameter is the force constant $k$ of the harmonic potential (4) and the fourth parameter is the equilibrium distance $r_0$. The presence of 5-th and 6-th parameters means that the corresponding bond should be described by a Morse potential, they have a sense of $D$ and $\rho$ parameters of the Morse potential (5) correspondingly.

• ANGLES

  Contains parameters for covalent bonds. Each line consists of 5 or 7 parameters. The first three parameters are the force field atom types. The fourth parameter is the equilibrium angle, the 5th parameter is the force constant $k$. The 6-th and 7-th parameters are optional, if they are present, they define the Urey-Bradley (UB) potential which is in fact a distance-dependent harmonic potential between 1st and 3rd atoms. The equilibrium distance for UB potential is given as a 6-th parameter and the force constant as a 7-th. makemol puts the UB term into the “bond” section of the .mmol file.

• TORSIONS

  Contains parameters for torsion potentials of “standard” type (7). Each line consists of 7 parameters, the first four define the force field atom types, and parameters from 5-th to 7-th are $\Delta$, $K_\phi$ and $M$ correspondingly.

  This section allows definition of multiple torsions and wildcards (denotes as “X”). The wildcards can be used only for the 1st and 4-th atoms in the list. The following rules are applied. If an explicit torsion (without wildcards) is specified, lines with wildcards matching this torsion are ignored. If lines with explicit torsions are repeated for the same set of atom types, they define multiple torsions, that is the total torsion potential is a sum of several terms of type (7).

• NONBONDED

  Contains Lennard-Jones parameters for non-bonded interactions. Each line consists of 3 or 5 parameters. The first parameter is the force field atom type. The second and third parameters are $\sigma$ and $\varepsilon$ of the Lennard-Jones potential. If the 4-th and 5-th parameters are present, they define $\sigma$ and $\varepsilon$ parameters for 1-4 Lennard-Jones interactions.

• PAR14

  Defines list of special LJ parameters for atom pairs involved in 1-4 interactions. Each line contains 4 parameters, the forst two defines two atom types, and the next two defines Sigma and Epsilon for LJ interactions between atoms of this pair when they atoms are 1-4 neighbours.

• LJ_PAIRS

  Defines Lennard-Jones parameters for cross-interactions which overwrite combination rules. Each line contains 4 parameters: two first defines atom types, the 3rd defines LJ sigma parameter and the 4-th define LJ Epsilon parameter. Content of this section is not used in generation of .mmol files, but it is used during molecular dynamics run if parameter Piar_list FF_file <value> is present in the md input file.

• END

  The last line of the file