[gmx-users] Number of H bonds formed between ligand and amino acid residues

[Amali Guruge]

Thank you very much for the answer. How we identify residues involving in H
bonds? In index file do we have to specify them?

On Tue, Jun 28, 2016 at 11:45 AM, Subhomoi Borkotoky <subhomoy.bk at gmail.com>
wrote:

> Hello,
>
> Please use the "hbond"  utility in gromacs.
>
> gmx hbond [-f [<.xtc/.trr/...>]] [-s [<.tpr/.tpb/...>]] [-n
> [<.ndx>]][-num [<.xvg>]
>
>
> On Tue, Jun 28, 2016 at 11:24 AM, Amali Guruge <amaligg2010 at gmail.com>
> wrote:
>
> > Dear Gromacs users,
> >
> > I carried out 20 ns long MD simulation for my receptor-ligand complex
> using
> > Gromacs software. Now I want to calculate number of hydrogen bonds formed
> > in the ligand and receptor corresponding to the residue number. Can
> anyone
> > help me?
> >
> >
> > Thank you.
> > --
> > 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.
> >
>
>
>
> --
> Yours Sincerely,
> --------------------------
> SUBHOMOI BORKOTOKY,
> Centre for Bioinformatics
> Pondicherry University
> Pondicherry,INDIA.
>
> Alternate Email: subhomoi at mails.bicpu.edu.in
> --
> 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.
>