Coordinate File

From wiki.gromacs.org

GROMACS reads and writes several formats of coordinate file, including PDB, the GROMOS .gro file and .g96 file formats. Some of these formats can contain velocities, simulation box dimensions, or other data. In most cases, a run input file can also serve as a coordinate file for the purposes of GROMACS Utilities.

[edit] On the need for a .gro file

A common mistake of newcomers is to conclude that because the default output file format of (for example) pdb2gmx, editconf and mdrun is a .gro file that they need such a file for inputs to (for example) grompp, editconf, genion and mdrun. Careful inspection of the man pages for these utilities reveals that in the large majority of cases, any coordinate file format will do, and where exceptions apply these are reflected in the man page. So don't feel constrained!

[edit] Sources

Some ways of obtaining a coordinate file for the molecule(s) of interest are:

• Protein Data Bank
• Hetero-Compound Information Centre: Uppsala - information about hetero-compounds encountered in files from the Protein Data Bank (PDB), with each entry providing coordinate files (PDB and text files), visualisation files (Chime and VRML), dictionary files (X-PLOR/CNS, O, TNT), links to off-site databases and servers, and miscellaneous files and information.
• Construct yourself using molecule building software, e.g. SYBYL, PyMOL or Accelrys Discovery Studio
• PRODRG - sketch your small molecule in a simple text editor and coordinate / topology files are returned.

[edit] Note on using PyMOL

If you use (say) pdb2gmx to generate a topology and then use PyMOL to edit the conformation, atom re-ordering can occur in the exported coordinate file. This behaviour can be prevented, e.g. in the .pymolrc with

...
set retain_order,1
set pdb_retain_ids,1
...