[gmx-users] .XYZ file format to .gro format

Justin Lemkul jalemkul at vt.edu
Wed Oct 18 17:22:35 CEST 2017

On 10/18/17 11:01 AM, Nagasree Garapati wrote:
> Hi
> I have structure of a molecule in .xyz format, is there an option similar to pdb2gmx in gromacs to convert .xyz file to .gro files?
Format conversion is done with editconf or trjconv; the fact that one 
gets a coordinate file at the end of pdb2gmx is actually somewhat of a 
side effect of producing a topology. One should not view pdb2gmx as a 
format conversion tool.

To answer your question though, no, GROMACS tools do not deal with XYZ 
coordinates, largely because different programs produce different files 
called XYZ and I don't know of a uniform convention for them. But both 
.pdb and .gro have fixed file formats that are very easy to write using 
your favorite scripting language (Perl, Python, etc).




Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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