Syntax TOPOLOGY INITIALIZE
APPEND SELECT ... END XPLOR
The TOPOLOGY command sentence INITIALIZES the topology library (sets the number of TOPOLOGY residues to 0) or APPENDS new reasidues to already existing ones. If the name of the APPENDING residue matches with the last one in the library then the last one is replaced by the new one.
The newly created TOPOLOGY library residue(s) contain(s) the complete residue description (ATOM NAME, CLASS, partial atomic CHARGE, cartesian (shifted to origin) and INTERNAL COORDINATES, the covalent BOND, DIHEDRAL and IMPROPER angle lists). The required information is extracted form the availabe data attached to the SELECTED residues. More than one residue can be APPENDED with a single TOPOLOGY APPEND sentence.
The XPLOR turns on the XPLOR mode, so that the created residues in the topology library will have no terms (BOND, DIHEDRALS, IMPROPERS) relating to the previous residue in the sequence. By default, the XPLOR mode is turned off, so that ATOM NAMES from the previous residue are preceeded by a hyphen '-'.