VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Jun 18 2010 - 08:25:36 CDT

On Fri, 2010-06-18 at 14:18 +0100, ban arn wrote:
> Dear Alex
>
> I am really sorry reposting more than once.
>
> Because the sent mail has been bounced back to me.

you are subscribed to the list, right?
why should you *not* receive what is sent to it?

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

please explain what do you mean by "calculate"
and define what would be a "non-polar interaction".

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

i don't see what that would have to do with the polarity.

> Kindly advice.

sorry, but i cannot advise if i cannot understand
the question. perhaps somebody else can...

axel.

> 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.
>
> 

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