VMD-L Mailing List

From: ban arn (ban.arn_at_gmail.com)
Date: Fri Jun 18 2010 - 08:18:23 CDT

Dear Alex

I am really sorry reposting more than once.

Because the sent mail has been bounced back to me.

I would like to calculate non-polar interaction around say 4A or 5A of the
ligand over the trajectories.

I cann't mention atom selection syntax for specifc residues because i have
used biased MD in my simulations.

Kindly advice.

Many Thanks
Balaji.

On Fri, Jun 18, 2010 at 2:10 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> 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.
>
> thanks,
> axel.
>
> > Many Thanks
> > Balaji
> >
> >
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com
> http://sites.google.com/site/akohlmey/
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
>
>