The AMBER interface may be used to generate parmameter/topology and coordinate files for use with the AMBER suite of programs. The same interface may be used to read coordinate output files from AMBER back into Wit!P. The AMBER interface assumes that appropriate atom types and partial atomic charges have been assigned to all atoms of the molecular system for which a parameter/topology file is to be generated.
Description of menu options:
frcmod <modFFparams> : <modFFparams> defines the file containing the "modified force field parameters". Parameters defined in this file take precedence over parameters define in the regular force field parameter file. The environment variable WNP_AMBER_FRCMOD defines the default modified parameter. The use of a modified parameter file may be suppressed by setting <modFFparams> to -none.
parameters <FFparams> : <FFparams> defines the file containing the "regular force field parameters". Parameters in this file may be overwritten by parameters from the modified force field parameter file. The environment variable WNP_AMBER_PARAM defines the defualt regular parameter file. The use of a regular parameter file may be suppressed by setting <FFparams> to -none.
read crd <coordinates> <molecule> : updates the coordinates of <molecule> with the coordinate values read from the coordinates file <coordinates>. The number of xyz coordinate triplets in <coordinates> must match the number of atoms in <molecule>. The order of the xyz coordinate triplets in <coordinates> must correspond to the order of the atoms in <molecule>.
write crd <coordinates> <molecule> : write the coordinates of all atoms in <molecule> to the file <coordinates> in AMBER coordinate file format.
write prmtop <prmtopfile> <molecule> : write a parameter/topology file for the molecule specified by <molecule> to the file <prmtopfile>. If there are missing parameter definitions, they will be reported in the message box. No output file will be produced for systems with missing parameter definitions (with the exception of missing parameters for "improper" dihedrals, which are reported, and set to 0).
end : return from Amber interface menu.
Implementation Details:
The write prmtop command will generate an improper dihedral term in the output file for each planar atom in the molecule with three bonds. Atoms are planar, if they have a non-zero value of the out-of-plane flag ("oopflag"). If no matching parameter can be found for an improper dihedral term, the parameter is reported as "missing", and a force constant of zero will be used for this energy term. This differs from the treatment of all other energy terms, where a missing parameter constitutes a fatal error, leading to the non-production of an output file.
If multiple defintions of a parameter are found in the parameter definition files (<FFparams> and <modFFparams>) the following priority rules are applied to decide which parameter value will be used:
bond stretch and angle bend parameters : Within a file, the first definition is used. If the parameter is defined in both parameter definition files, the definition from the modified parameter file takes precedence.
masses : Within a file, the last definition is used. Definitions from the modified parameter file take precedence over definitions from the regular parameter file.
non-bonded parameters : Within a file, the last definition is used. Definitions from the modified parameter file take precedence over definitions from the regular parameter file. Explicit definitions take precedence over implicit (via non-bonded eqivalence) definitions, i.e. an explicit definition will not be overwritten by a later "equivalent" definition.
dihedral parameters : Within a file, the last exact definition is used. Subsequent wild-card definitions will be added to multiple dihedral terms, provided that they do not collide with an exact definition for the same frequency. Wild cards from the modified parameter file are not mixed with exact parameters form the regular parameter files, but will be mixed with wild-card definitions from the regular file. Within a file, earlier wild-card definitions take precedence over later ones.
improper dihedral parameters : The third atom type in the defintion must match the atom type of the central atom. Wild-cards are allowed only for the three atoms bonded to the central atom. The order of the three bonded atoms is arbitrary. The parameter using the least number of wild-cards will be used. For matches with the same number of wild cards, earlier definitions within a file take precedence over later ones. Definitions in the modified file take precedence over definitions in the regualr file.
H-bond parameters : are currently not used.