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.
