Topology Statement

The topology statement consists of information about “residues" that combine to form a particular macromolecule. The data include descriptions of atoms, assignments of covalent bonds (connectivity), bond angles, and other information. The information provided by the topology statement is used by the segment statement and the patch statement to generate the molecular structure.

X-PLOR, like many other macromolecular mechanics/dynamics packages, can use a classification scheme that employs chemical atom types. This system of atom classification makes force fields transferable between groups that are almost equivalent and thereby allows one definition to work for all or almost all instances of that type of atom. The specific atom classifications can be arbitrarily defined by the user. The parameters of chemical atom types are given in the parameter statement (Section 3.2.1). Electric charges are specified on an individual atom basis, since they are less transferable than stereochemical parameters. For historical reasons, atomic masses may also be specified on an individual atom basis, but there exists the mass statement outside the residue statement that assigns default atomic masses on a basis of chemical atom type. Apart from the type-based parameter retrieval, X-PLOR also provides atom-based parameter statements (Section 3.2), which allow one to specify any parameter on a per-atom basis.