TOP, PRMTOP, PARM7 (AMBER topology)

Topology parser

MDAnalysis.topology.TOPParser.TOPParser

AMBER specification

Note

The Amber charge is converted to electron charges as used in MDAnalysis and other packages. To get back Amber charges, multiply by 18.2223.

Attributes parsed from AMBER keywords

AMBER flag	MDAnalysis attribute
ATOM_NAME	names
CHARGE	charges
ATOMIC_NUMBER	elements
MASS	masses
BONDS_INC_HYDROGEN BONDS_WITHOUT_HYDROGEN	bonds
ANGLES_INC_HYDROGEN ANGLES_WITHOUT_HYDROGEN	angles
DIHEDRALS_INC_HYDROGEN DIHEDRALS_WITHOUT_HYDROGEN	dihedrals / improper
ATOM_TYPE_INDEX	type_indices
AMBER_ATOM_TYPE	types
RESIDUE_LABEL	resnames
RESIDUE_POINTER	residues

Developer notes

The format is defined in PARM parameter/topology file specification. The reader tries to detect if it is a newer (AMBER 12?) file format by looking for the flag “ATOMIC_NUMBER”.