X-PLOR Format Datasets

Included in the EGO distribution is the utility program xpl2lis which converts data of X-PLOR-compatible data files to lis-files used by EGO. X-PLOR data files include:

1.

a .pdb (Brookhaven Protein Data Bank) file listing atom number, atom name, residue name, residue number, atom coordinates (x,y,z in units of angstroms), a friction coefficient and force constant,

2.

a .psf (protein structure file) file listing each atom type, partial charge and mass, as well as a specification of which atom pairs are bonded, which sets of atoms form dihedral bond angles, exclusion lists, etc. A .psf file is commonly created from a starting .pdb file by using the structure editing functions of the X-PLOR program.

3.

energy parameter file(s) which describe the bonded force parameters (such as certain hydrogen bond interactions, for example) as well as the van der Waals parameters for the different atom types. It is also possible for xpl2lis to use CHARMM parameter files.

The structure of .pdb, .psf and parameter files are further described in Appendix A of the EGO User Manual.