.. -*- coding: utf-8 -*- .. _TOP-format: ======================================== TOP, PRMTOP, PARM7 (AMBER topology) ======================================== .. include:: classes/TOP.txt 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. .. table:: Attributes parsed from AMBER keywords +----------------------------+----------------------+ | AMBER flag | MDAnalysis attribute | +----------------------------+----------------------+ | ATOM_NAME | names | +----------------------------+----------------------+ | CHARGE | charges | +----------------------------+----------------------+ | ATOMIC_NUMBER | elements | +----------------------------+----------------------+ | MASS | masses | +----------------------------+----------------------+ | BONDS_INC_HYDROGEN | bonds | | BONDS_WITHOUT_HYDROGEN | | +----------------------------+----------------------+ | ANGLES_INC_HYDROGEN | angles | | ANGLES_WITHOUT_HYDROGEN | | +----------------------------+----------------------+ | DIHEDRALS_INC_HYDROGEN | dihedrals / improper | | DIHEDRALS_WITHOUT_HYDROGEN | | +----------------------------+----------------------+ | 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". .. _`PARM parameter/topology file specification`: http://ambermd.org/formats.html#topology