Supported formats

List of supported formats

This page list the supported formats in chemfiles, with a link to the format specification. For each format, it is also indicated whether they have some information to create a Topology, and if you can read them, write them or both using chemfiles.

The Extension column gives the extension used when trying to detect the format. If your file does not have this extension, you can also use the string in the Format column as a parameter to the Trajectory constructor to manually specify which format to use.

Format

Extension

Read

Write

Atoms names

Bonds

Amber NetCDF

.nc

CML

.cml

CSSR

.cssr

DCD

.dcd

GRO

.gro

LAMMPS 1

.lammpstrj

LAMMPS Data 2

mmCIF

.mmcif

MMTF

.mmtf

MOL2

.mol2

Molden

.molen

PDB

.pdb

SDF

.sdf

TNG

.tng

TRJ

.trj

TRR

.trr

Tinker

.arc

XTC

.xtc

XYZ

.xyz

1

LAMMPS format corresponds to trajectory files written by the LAMMPS dump command.

2

LAMMPS Data format corresponds to LAMMPS data files, as read by the LAMMPS read_data command.

Asking for a new format

If you want to use chemfiles with a format which is not yet implemented, you may easily add it by yourself if you know some C++. See the src/formats/XYZ.cpp file for example. The list of planned formats can be found here. If you can not find your favorite format in this list, you can open an issue with a description of the format, or even better a link to the format specification. If your format is in the list of formats supported by VMD, then you are lucky! It will be easy to add support for this format. Please open an issue on and provide a file example to test the plugin against it.