as well as position. Because these files are sometimes used to describe macromolecular assemblies or molecules represented in explicit solvent, they can grow very large and are often compressed. Some tools, such as Jmol and KiNG, can read PDB files in gzipped format. The wwPDB maintains the specifications of the PDB file format and its XML alternative, PDBML. There was a fairly major change in PDB format specification (to version 3.0) in August 2007, and a remediation of many file problems in the existing database. The typical file extension for a PDB file is .pdb, although some older files use .ent or .brk. Some molecular modeling tools write nonstandard PDB-style files that adapt the basic format to their own needs. GROMACS format The GROMACS file format family was created for use with the molecular simulation software package GROMACS. It closely resembles the PDB format but was designed for storing output from molecular dynamics simulations, so it allows for additional numerical precision and optionally retains information about particle velocity as well as position at a given point in the simulation trajectory. It does not allow for the storage of connectivity information, which in GROMACS is obtained from separate molecule and system topology files. The typical file extension for a GROMACS file is .gro. CHARMM format The CHARMM molecular dynamics package can read and write a number of standard chemical and biochemical file formats; however, the CARD (coordinate) and PSF (protein structure file) are largely unique to CHARMM. The CARD format is fixed-column-width, resembles the PDB format, and is used exclusively for storing atomic coordinates. The PSF file contains atomic connectivity information (which describes atomic bonds) and is required before beginning a simulation. The typical file extensions used are .crd and .psf respectively. GSD format The General Simulation Data (GSD) file format created for efficient reading / writing of generic particle simulations, primarily - but not restricted to - those from HOOMD-blue. The package also contains a python module that reads and writes hoomd schema gsd files with an easy to use syntax. Ghemical file format The Ghemical software can use OpenBabel to import and export a number of file formats. However, by default, it uses the GPR format. This file is composed of several parts, separated by a tag (!Header, !Info, !Atoms, !Bonds, !Coord, !PartialCharges and !End). The proposed MIME type for this format is application/x-ghemical. SYBYL Line Notation SYBYL Line