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

[Justin Lemkul]

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

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

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