Topology

Table of supported topology parsers and the attributes read

Format

Description

Attributes read

Attributes guessed

CONFIG

DL_Poly CONFIG file

names

masses, types

CRD

CHARMM CARD file

names, resnames, tempfactors

masses, types

DATA

LAMMPS data file

angles, bonds, charges, dihedrals, impropers

DMS

DESRES Molecular Structure file

atomnums, bonds, chainIDs, charges, names, resnames

types

GMS

GAMESS file

atomiccharges, names

masses, types

GRO

GROMACS structure file

names, resnames

masses, types

GSD

HOOMD GSD file

angles, bonds, charges, dihedrals, impropers, names, radii, resnames

HISTORY

DL_Poly HISTORY file

names

masses, types

IN, FHIAIMS

FHI-aims input file

elements, names

masses, types

LAMMPSDUMP

LAMMPS ascii dump file

masses

MMTF

MMTF file

altLocs, bonds, charges, icodes, models, names, occupancies, resnames, tempfactors

masses

MOL2

Tripos MOL2 file

bonds, charges, elements, names, resnames

masses

PDB, ENT

Standard PDB file

altLocs, chainIDs, elements, icodes, names, occupancies, record_types, resnames, tempfactors

masses, types

PDBQT

PDBQT file

altLocs, chainIDs, charges, icodes, names, occupancies, record_types, resnames, tempfactors

masses

PQR

PQR file

charges, icodes, names, radii, record_types, resnames

masses, types

PSF

CHARMM, NAMD, or XPLOR PSF file

angles, bonds, charges, dihedrals, impropers, names, resnames

TOP, PRMTOP, PARM7

AMBER topology file

angles, bonds, charges, dihedrals, impropers, names, resnames, type_indices

TPR

GROMACS run topology file

angles, bonds, chainIDs, charges, dihedrals, elements, impropers, molnums, moltypes, names, resnames

TXYZ, ARC

Tinker file

bonds, elements, names

masses

XML

HOOMD XML file

angles, bonds, charges, dihedrals, impropers, radii

XPDB

Extended PDB file

altLocs, chainIDs, icodes, names, occupancies, record_types, resnames, tempfactors

masses, types

XYZ

XYZ file

elements, names

masses, types