[gmx-users] Hydrogen bond occupancy

[Neha Gupta]

Hi,

Thank you for the reply.

However, I don't get the same bonds as obtained through docking.  Those
hydrogen bonds have vanished, I presume during the simulation duration of
2ns.

The bonding takes place with different protein residues. One donor -
acceptor has higher percentage (29%)  and the other has very less
percentage (0.05%)

Can someone tell me what does it mean?

Thanks,
Neha





On Wed, Apr 5, 2017 at 1:34 PM, Erik Marklund <erik.marklund at kemi.uu.se>
wrote:

> Dear Neha,
>
> What fraction of the time the ligand hydrogen bonds to whatever it
> interacts with.
>
> 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 5 Apr 2017, at 10:00, Neha Gupta <nehaphysics17 at gmail.com<mailto:
> nehaphysics17 at gmail.com>> wrote:
>
> Hi gromacs users,
>
> What is meant by Hydrogen bond occupancy in protein ligand simulations?
>
> What information do we extract from % of hydrogen bond occupancy?
>
> 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.