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" <knnar...@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" <jalem...@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 > > -- > > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support > /Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.