Format overview

MDAnalysis can read topology or coordinate information from a wide variety of file formats. The emphasis is on formats used in popular simulation packages. By default, MDAnalysis figures out formats by looking at the extension, unless the format is explicitly specified with the format or topology_format keywords.

Below is a table of formats in MDAnalysis, and which information can be read from them. A topology file supplies the list of atoms in the system, their connectivity and possibly additional information such as B-factors, partial charges, etc. The details depend on the file format and not every topology file provides all (or even any) additional data.

Important

File formats are complicated and not always well defined. MDAnalysis tries to follow published standards but this can sometimes surprise users. It is highly recommended that you read the page for your data file format instead of assuming certain behaviour. If you encounter problems with a file format, please get in touch with us.

As a minimum, all topology parsers will provide atom ids, atom types, masses, resids, resnums, and segids. They will also assign all Atoms to Residues and all Residues to Segments. For systems without residues and segments, this results in there being a single Residue and Segment to which all Atoms belong. See Topology attributes for more topology attributes.

Often when data is not provided by a file, it will be guessed based on other data in the file. In this scenario, MDAnalysis will issue a warning. See Guessing for more information.

If a trajectory is loaded without time information, MDAnalysis will set a default timestep of 1.0 ps, where the first frame starts at 0.0 ps. In order to change these, pass the following optional arguments to Universe:

• dt: the timestep

• time_offset: the starting time from which to calculate the time of each frame

Table of all supported formats in MDAnalysis

File type	Description	Topology	Coordinates	Read	Write
ARC	Tinker file	✓	✓	✓
CHEMFILES	use readers from chemfiles library		✓	✓	✓
CONFIG	DL_Poly CONFIG file	✓	✓	✓
COOR	NAMD binary restart file		✓	✓	✓
CRD	CHARMM CARD file	✓	✓	✓	✓
CRDBOX	AMBER ASCII trajectories		✓	✓
DATA	LAMMPS data file	✓	✓	✓	✓
DCD	CHARMM, NAMD, or LAMMPS binary trajectory		✓	✓	✓
DMS	DESRES Molecular Structure file	✓	✓	✓
ENT	Standard PDB file	✓	✓	✓	✓
FHIAIMS	FHI-aims input file	✓	✓	✓	✓
GMS	GAMESS file	✓	✓	✓
GRO	GROMACS structure file	✓	✓	✓	✓
GSD	HOOMD GSD file	✓	✓	✓
HISTORY	DL_Poly HISTORY file	✓	✓	✓
IN	FHI-aims input file	✓	✓	✓	✓
INPCRD	AMBER restart file		✓	✓
ITP	GROMACS portable topology file	✓		✓
LAMMPS	a LAMMPS DCD trajectory		✓	✓	✓
LAMMPSDUMP	LAMMPS ascii dump file	✓	✓	✓
MDCRD	AMBER ASCII trajectories		✓	✓
MMTF	MMTF file	✓	✓	✓
MOL2	Tripos MOL2 file	✓	✓	✓	✓
NAMDBIN	NAMD binary restart file		✓	✓	✓
NC	AMBER NETCDF format		✓	✓
NCDF	AMBER NETCDF format		✓	✓	✓
PARM7	AMBER topology file	✓		✓
PARMED	ParmEd Structure	✓	✓	✓	✓
PDB	Standard PDB file	✓	✓	✓	✓
PDBQT	PDBQT file	✓	✓	✓	✓
PQR	PQR file	✓	✓	✓	✓
PRMTOP	AMBER topology file	✓		✓
PSF	CHARMM, NAMD, or XPLOR PSF file	✓		✓
RESTRT	AMBER restart file		✓	✓
TOP	AMBER topology file	✓		✓
TPR	GROMACS run topology file	✓		✓
TRJ	AMBER ASCII trajectories		✓	✓
TRR	GROMACS TRR trajectory		✓	✓	✓
TRZ	IBIsCO or YASP binary trajectory		✓	✓	✓
TXYZ	Tinker file	✓	✓	✓
XML	HOOMD XML file	✓		✓
XPDB	Extended PDB file	✓	✓	✓
XTC	GROMACS compressed trajectory		✓	✓	✓
XYZ	XYZ file	✓	✓	✓	✓

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, bfactors, bonds, charges, icodes, models, names, occupancies, resnames	masses
MOL2	Tripos MOL2 file	bonds, charges, names, resnames	masses
PARMED	ParmEd Structure	altLocs, angles, bonds, chainIDs, charges, cmaps, dihedrals, elements, epsilon14s, epsilons, gbscreens, impropers, names, nbindices, occupancies, resnames, rmin14s, rmins, solventradii, tempfactors, ureybradleys
PDB, ENT	Standard PDB file	altLocs, bonds, chainIDs, elements, icodes, names, occupancies, record_types, resnames, tempfactors	masses, types
PDBQT	PDBQT file	altLocs, 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	elements
TPR	GROMACS run topology file	angles, bonds, charges, dihedrals, impropers, molnums, moltypes, names, resnames
TXYZ, ARC	Tinker file	bonds, names	masses
XML	HOOMD XML file	angles, bonds, charges, dihedrals, impropers, radii
XPDB	Extended PDB file	altLocs, bonds, chainIDs, icodes, names, occupancies, record_types, resnames, tempfactors	masses, types
XYZ	XYZ file	elements, names	masses, types

Coordinates

Table of supported coordinate readers and the information read

File type	Description	Velocities	Forces
ARC	Tinker file
CHEMFILES	use readers from chemfiles library
CONFIG	DL_Poly CONFIG file	✓
COOR	NAMD binary restart file
CRD	CHARMM CARD file
CRDBOX	AMBER ASCII trajectories
DATA	LAMMPS data file	✓
DCD	CHARMM, NAMD, or LAMMPS binary trajectory
DMS	DESRES Molecular Structure file	✓
ENT	Standard PDB file
FHIAIMS	FHI-aims input file	✓
GMS	GAMESS file
GRO	GROMACS structure file	✓
GSD	HOOMD GSD file
HISTORY	DL_Poly HISTORY file	✓
IN	FHI-aims input file	✓
INPCRD	AMBER restart file
LAMMPS	a LAMMPS DCD trajectory
LAMMPSDUMP	LAMMPS ascii dump file
MDCRD	AMBER ASCII trajectories
MMTF	MMTF file
MOL2	Tripos MOL2 file
NAMDBIN	NAMD binary restart file
NC	AMBER NETCDF format	✓	✓
NCDF	AMBER NETCDF format	✓	✓
PARMED	ParmEd Structure
PDB	Standard PDB file
PDBQT	PDBQT file
PQR	PQR file
RESTRT	AMBER restart file
TRJ	AMBER ASCII trajectories
TRR	GROMACS TRR trajectory	✓	✓
TRZ	IBIsCO or YASP binary trajectory	✓
TXYZ	Tinker file
XPDB	Extended PDB file
XTC	GROMACS compressed trajectory
XYZ	XYZ file