From: Axel Kohlmeyer (
Date: Fri Jun 18 2010 - 08:10:23 CDT

On Fri, 2010-06-18 at 12:53 +0100, ban arn wrote:
> Dear All

dear balaji,

is it possible that you can give people some time to
respond before reposting? reposting is *really* annoying
and waiting an hour and then another half hour is hardly
sufficient, when the majority of people that tend to
respond are in a different time zone. please show some
consideration. thanks.

> I am interested in calculating the residues that are involved in
> hydrobhoic interaction with ligand over the trajectories. Is it is
> possible in VMD.

there is a lot that can be done in VMD and some even
that you would find hard to imagine, but first of all
your question is ill defined: what do you mean by
"hydrophobic interaction"? VMD has no real knowledge
of chemistry, but it has flexible means to compute
items that you can put into its atom selection syntax.

> Kindly advice.

kindly provide more concise questions.


> Many Thanks
> Balaji

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