[gmx-users] .XYZ file format to .gro format
jalemkul at vt.edu
Wed Oct 18 17:22:35 CEST 2017
On 10/18/17 11:01 AM, Nagasree Garapati wrote:
> 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.
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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