Hi Matej,
Thanks for your suggestion. I got the output of hbond data through the
following in VMD main menu:
Extensions > Analysis > Hydrogen bonds > Detailed hbond data.
It is a file detailing the no. of h-bonds, donar atoms, acceptor atoms and
percentage occupancy.
All the options I have tried show the hydrogen bonds present in the entire
sequence. I want to see the real-time hydrogen bond formation between two
residues. Is there any option for the same?
Regards,
On Wed, Oct 14, 2015 at 12:36 PM, Repic Matej <matej.repic.epfl.ch> wrote:
> Hi Abhipriya,
>
> I am not exactly sure what you mean by "detailed output of the hbond
> data", but I guess this should help you out:
>
> In VMD do the following:
>
> Graphical Representations window > Draw style tab > Drawing Method > HBonds
> Graphical Representations window > Trajectory tab > Update Selection Every
> Frame
>
> Best,
>
>
> ------------------------------------------------------
> Dr. Matej Repic
> Ecole Polytechnique Fédérale de Lausanne
> Laboratory of Computational Chemistry and Biochemistry
> SB - ISIC LCBC
> BCH 4108
> CH - 1015 Lausanne
> ------------------------------------------------------
>
>
>
>
>
>
>
> On 10/14/15, 08:21, "Abhipriya K" <abhipriya0406.gmail.com> wrote:
>
> >Dear Amber users,
> >
> >I am analyzing my simulation results using Visual Molecular Dynamics
> >program. I am able to generate the detailed output file of the hbond data.
> >But, I want to visualize the real-time hydrogen bond formation between two
> >residues/atoms. Is there any option for doing the same using VMD?
> >
> >Any suggestions/help is highly appreciated.
> >
> >Many thanks,
> >--
> >Abhipriya
> >Junior Research Fellow
> >National Institute for Research in Reproductive Health (ICMR)
> >J.M. Street, Parel, Mumbai 400012
> >INDIA
> >_______________________________________________
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> >http://lists.ambermd.org/mailman/listinfo/amber
>
>
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>
--
Abhipriya
Junior Research Fellow
National Institute for Research in Reproductive Health (ICMR)
J.M. Street, Parel, Mumbai 400012
INDIA
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Received on Wed Oct 14 2015 - 01:00:02 PDT
