Forcefield File
The Forcefield File is used to specify the atom types that will be used by EGAD Library. Any parameters that are specific to a type of atom (such as VDW parameters) are stored in this file. This file is parsed by the ForcefieldFile object.
Format
# # Comment Region # START atomtype torsion_type vdw_sigma vdw_well_depth vdw_radius ASP #comment ... END
- Comment Region
- The lines preceeding the START line are ignored by the Forcefield File parser. These lines do not have to start with #, or any other comment marker.
- START line
- Parsing begins at the START line, which is defined to be the first line with the word START as the first five characters. Leading whitespace is not allowed. Trailing characters (whitespace or otherwise) are ignored.
- Atomtype lines
- All of the relevant data is contained in multiple atomtype lines. Each atom type is given a unique line. Each parameter is separated by whitespace. Leading whitespace is ignored, but allowed. Atomtype lines are the only type of line allowed between the START and END lines of a Forcefield File.
- Atomtype: this is the name of the atom type as it will be referred to in both client code and other input files (such as the resparam file).
- Torsion Type: when calculating torsional corrections for the OPLS forcefield, atom types are compressed into a subset of the normal types. This column is often the same as the atom type, but some types can be mapped onto others as defined here.
- VDW Sigma: used when calculating Lennard Jones energies. This is the equilibrium radius of the atom type.
- VDW Well Depth: used when calculating Lennard Jones energies. This is the well depth of the atom type.
- VDW Radius: used for solvent-accessible surface area calculations. This is usually defined as simply half of the VDW sigma. A "probe" radius (usually 1.4 angstroms) is added to this number to produce the solvent-accessible surface for the atom.
- Atomic Solvation Parameter: not currently used by EGAD Library. This parameter is a holdover from the original EGAD program.
- Comment Region: any non-whitespace text found after the atomic solvation parameter is assumed to be comment and ignored.
- END line
- Parsing ends at the END line, which is defined to be the first parsed line with the word END as the first three characters. Leading whitespace is not allowed. Trailing characters (whitespace or otherwise) are ignored.
- Other Forcefield File Parameters
- The original EGAD had additional parameters at the end of the Forcefield File. These parameters were implementation specific and are not allowed in EGAD Library's Forcefield File. They will be ignored and may generate error messages or warnings in the future