Re: [AMBER] Measurement of distance between residues forming Hydrogen bond

From: Jason Swails <jason.swails.gmail.com>
Date: Tue, 1 Nov 2011 10:15:09 -0400

It may help to script it, but just take every donor and acceptor group and run it through the "distance" command in ptraj. An alternative is to use VMD to calculate the distances, but I am not comfortable enough with their scripting environment to know how to do it in batch.

HTH,
Jason

--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
On Nov 1, 2011, at 4:56 AM, Aditya Padhi <adi.uoh.gmail.com> wrote:
> Dear AMBER users,
>                We know that from VMD we can get all the possible hydrogen
> bonds as well as its associated percentage occupancy from a MD trajectory
> file. But I want to get the distance among the donor and acceptor for all
> the H-bonds obtained from the MD trajectories. I know that the default
> distance is 3 Angstrom and angle of 20 degrees.
>                 If any one can help in getting the distances for every
> donor-acceptor atoms throughout the simulation I would be grateful. If any
> coding is required for this purpose or any other suggestions are there,
> kindly let me know.
> 
> Thanks and regards
> Aditya.
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Received on Tue Nov 01 2011 - 07:30:05 PDT