[gmx-users] .XYZ file format to .gro format
Dr. K N Naresh, Post-Doctoral Fellow, Biosciences, SSSIHL
knnaresh at sssihl.edu.in
Wed Oct 18 22:04:30 CEST 2017
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.
On 18-Oct-2017 8:53 PM, "Justin Lemkul" <jalemkul at vt.edu> wrote:
> 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.
> 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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