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The tags and placement of data for each of the classes is given below:
Class Property of Placement Tags
BOND Bond Use first atom Tags for atoms separated by
dashes.
ANGLE Angles Use middle atom As for bonds.
TORSION Torsion angles Use second atom As for bonds.
IMPROPER Improper Use first atom As for bonds.
torsion angles
HBOND Hydrogen bonds Use donor atom The tag for the donor
atom is concatenated
with a string giving its
segment id, residue
name, and residue id.
ATOM Atom Itself See below
The placement gives the atom which is used to determine which residue the data belongs to. The tag for an atom is specified by the third word of the command. If nothing is specified or if IUPAC is specified, the tag for an atom is its IUPAC name as given in the residue topology file. PARM specifies that the atom type name as given in the parameter file should be used.