Hi.
Did you try using the selection 1 and selection 2 boxes of Hydrogen
bonds plugin of VMD? They should do what you what. Also If you already
know the residues for which you want to calculate the hbonds, I don't
think updating the selection every frame would be of any use.
If you want to visualize the h-bonds, you can do what Matej suggested
but select residues in the graphical representations like "resid 5".
Regards,
Amin.
On 2015-10-14 13:25, Abhipriya K wrote:
> 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 _______________________________________________ AMBER mailing list AMBER@ambermd.org
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Received on Wed Oct 14 2015 - 02:00:02 PDT
