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

[Dr. K N Naresh, Post-Doctoral Fellow, Biosciences, SSSIHL]

As Justin pointed out in GROMACS per se we can't convert .xyz to .gro file.

On 19-Oct-2017 1:32 AM, "Dr. K N Naresh, Post-Doctoral Fellow, Biosciences,
SSSIHL" <knnaresh at sssihl.edu.in> wrote:

I can think of an option

If it is a small molecule, .xyz can be converted to .pdb using 'OpenBabel'.
And .gro file can be generated for the .pdb using PRODRG server online. I
guess even directly using the .xyz file, PRODRG can generate .gro file.

Best

Naresh

On 18-Oct-2017 8:53 PM, "Justin Lemkul" <jalemkul at vt.edu> wrote:

>
>
> 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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