From: Axel Kohlmeyer (
Date: Wed Aug 18 2010 - 04:01:00 CDT

On Wed, Aug 18, 2010 at 2:14 AM, deepti nayar <> wrote:
> Hi all
> I want to find out the residues that are interacting with water in a
> trajectory. Is there any script for this in vmd?

you don't need a script for that. _all_ residues are. always!

i suspect, however, that the question that you want to ask
is not actually the one from above. you probably wanted to
ask which residues interact less strongly than a specific
energy cutoff value with water. remember how long-ranging
coulomb interactions are!

if that is the case, the answer is no and yes. VMD itself
is a viewer and as such has _no_ idea of the physics
of the model that you are simulating and thus cannot
give you an answer to that kind of question. it can, however,
generate inputs for a custom simulation (or single point
energy evaluation) e.g. via the namdenergy plugin and
return that result.

i suggest you rethink your question and then look up
the plugin and namd documentation to see how to proceed.


> -

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.