Torsion Parameter File
The Torsion Parameter File is used to specify the Fourier constants required by the OPLS torsional correction energy term. It is a mapping of a set of four atom types to three Fourier constants for every plausible dihedral angle in a protein. Many combinations are excluded because they are unlikely to be found in the context of a protein. Also, each dihedral type should only be listed once; the reverse order can (and will) be inferred. Repeat entries will be ignored. This file is parsed by the TorsionFile object.
Format
# # Comment Region # START atom1 atom2 atom3 atom4 k1 k2 k3 #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.
- Torsion Parameter lines
- All of the relevant data is contained in multiple torsion parameter lines. Each dihedral type is given a unique line. Each parameter is separated by whitespace. Leading whitespace is ignored, but allowed. Torsion parameter lines are the only type of line allowed between the START and END lines of a Torsion Parameter File.
- Atom Type Entries : the first four entries on this line refer to the atom types of each atom along the dihedral bond. So long as they are ordered properly relative to one another, it does not matter if they are listed in the forward or reverse direction.
- Fourier Constants : Each dihedral type is associated with three Fourier constants that are used to calculate the torsional correction for the OPLS forcefield.
- Comment Region: any non-whitespace text found after the three Fourier constants 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.