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3.1.4 The Format of Parameter Files

In 1995, the parameter file format was completely redone to accomodate the addition of the AMBER potential, see AMBERPARM. The new format is free field and allows patterns to be supplied for parameters in order to reduce the size of the file and to allow for default parameters to handle molecules which have not been seen before.

For the bond length, bond angle, torsion angle, and improper torsion parameters, CONGEN stores a patterns to match the atom types along with the relevant force field parameters. When the programs needs to calculate the energy of any internal coordinate, it goes sequentially through the patterns, and upon finding the first pattern which matches the atom types of the internal coordinate with the highest “specificity”, it uses the corresponding parameters. In this context, “specificity” means the sum of the specificities of each atom type pattern. The specificity of an atom type pattern is 0 if it's a complete wildcard, “*”; 0.5 if any wildcards are present, and 1.0 if there are no wildcards at all. This scheme allows parameters to be specified in different levels of generality, with specific parameters taking precedence over general ones.

In the case of hydrogen bond and non-bonded interactions, all the possible combinations of atom types are computed, and tables for the parameters are constructed. Patterns are used to match against the atom types when the tables are computed.

Parameters are stored as strings with the first character being either “S” or “P”, which means string or pattern, respectively. If a pattern is a string, then the program does a simple string comparison; otherwise, a wildcard match is used, see Interpretation of Atom Selection Tokens. CONGEN checks the patterns you specify to see whether a pattern or string has been specified.

Parameter files can be read in either text or binary format. For text files, the version can be set using the VERSION keyword on the READ PARAMETER command. The default value of 2 specifies the old format. The new version is specified by using a value of 3. For binary files, the header record indicates which version of parameter file is being read.