May call multiple times. Default is read from topology file and may be residue-specific. Default is read from topology file and may be residue-specific. Patches make small modifications to the structure of residues such as converting one to a terminus, changing the protonation state, or creating disulphide bonds between a pair of residues. Provide translations from atom names found in PDB files to proper atom names read in from topology definition files.
Calculation is based on internal coordinate hints contained in toplogy definition files.