[gmx-users] Hydrogen bond occupancy

[Mark Abraham]

Hi,

On Wed, Apr 5, 2017 at 1:09 PM Neha Gupta <nehaphysics17 at gmail.com> wrote:

> 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.
>

Sounds like it. Visualizing your trajectory would be an obvious stage in
understanding what is happening. There's no particular reason to expect two
different approximate model physics to agree with each other, unless
they've been already shown to have good agreement.


> 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?
>

It means that one bond has a higher propensity to persist than another.
Only you can put that in context.

Mark


>
> 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 <018-471%2045%2039>
> > 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
> > --
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