[gmx-users] COMMAND IN HBOND

[Neha Gupta]

Hi,


Thank you for the reply.

Actually, we get the number of hydrogen bonds in .xvg file using

gmx hbond -s prd.tpr -f prd.xtc -n index.ndx -num hbnum.xvg
.

Can we generate an output file similar to that, which prints the bonding
residues of protein and ligand?


Thanks,
Neha



On Fri, Mar 24, 2017 at 8:05 PM, Erik Marklund <erik.marklund at kemi.uu.se>
wrote:

> Dear Neha,
>
> Gromacs doesn’t offer that much in terms of viewing. This sounds more like
> a PyMol/VMD/Other question.
>
> Kind regards,
> Erik
> ______________________________________________
> Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
> Department of Chemistry – BMC, Uppsala University
> +46 (0)18 471 4539
> erik.marklund at kemi.uu.se<mailto:erik.marklund at kemi.uu.se>
>
> On 24 Mar 2017, at 14:33, Neha Gupta <nehaphysics17 at gmail.com<mailto:
> nehaphysics17 at gmail.com>> wrote:
>
> Hi gromacs users,
>
> What is the command to view the residues of protein and atoms of ligand
> involved in hydrogen bond?
>
> Thanks,
> Neha
> --
> 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-request at gromacs.org<mailto:gmx-users-request@
> 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-request at gromacs.org.