Stereochemical parameters and molecular topology

All molecular modeling programs generally need to know what are the atoms in all residue types, what are the atom pairs that are covalently bonded to each other (i.e., molecular topology), and what are the ideal bond lengths, angles, dihedral angles, and improper dihedral angles (i.e., internal coordinates and stereochemical restraints). For a given MODEL, these data are constructed mostly from information in the residue topology and parameter libraries. This section describes the commands for reading and writing parameter and residue topology libraries, and for generating, patching, and mutating molecular topology.