Topology and Parameter Files

This section describes the most important parameter and topology files that are distributed with X-PLOR. A pair of parameter and topology files represents a force field or empirical energy function. Force fields are supplied for proteins, nucleic acids, carbohydrates, and lipids, as well as a number of other biological molecules. All parameter files represent polar hydrogens (i.e., hydrogens that can form hydrogen bonds) explicitly, whereas aliphatic hydrogens are either explicitly included or implicitly modeled by appropriate modification of the heavy-atom van der Waals parameters. A number of specialized force fields are available for X-ray crystallographic or NMR-spectroscopic structure determination. All parameter and topology files can be found in the “toppar" directory.