VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Sep 28 2009 - 14:16:12 CDT

On Mon, 2009-09-28 at 13:53 -0400, Katherine Parra wrote:
> Dear VMD users:

dear katherine,

> I'm trying to get H bonds between my protein and the solvent during a
> trajectory. What I;m getting so far is a number of bonds.

how do you do that?

> Is there any way to identify these H bonds between the two specified
> sections of the protein during the trajectory?

the measure hbonds command will provide you with three lists of
atom indices, i.e. those of the h-bond donors, acceptors, and
hydrogens, respectively. if you first create a map of all residues
or whatever else you are looking for, you can used the lindex command
to access that information. example for a map of residue names:

set all [atomselect top all]
set resnamemap [$all get resname]

...and then within your analysis, assuming that you store the
atom indices in variables $id, $ia, $ih you can use

   lindex $resnamemap $id

to access the residue name for the atom with the index $id.
this can obviously extended to all kinds of atom properties.

cheers,
   axel.

> What I mean by identify is to get a list of the residues involved.
> Thanks.
> Katherine. 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com 
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.