VMD-L Mailing List

From: fariba taghavi (faribataghavifariba_at_gmail.com)
Date: Thu Jun 28 2012 - 01:09:05 CDT

Dear Albert,
Actually you can not find this option directly in the VMD but, you can
use TLC to write a short code. My suggestion is to select oxygen atom
in the hole (for example by "atomselect" to choose oxygen atoms with
x^2+y^2+Z^2<=16, it is related to the shape of the hole) and then you
can get the number of your selected atoms.

Good Luck,
Fariba Taghavi
PhD Candidate in Physical Chemistry
Tarbiat Modares University

On 6/27/12, Albert <mailmd2011_at_gmail.com> wrote:
> hello:
>
> I've finished a MD and I would like to to make statistics for the
> water density in the 'hole' within the protein at specific region. I am
> wondering, is it possible for VMD to do so ? Does anybody have any
> suggestions? I've searched in the mailist and VMD plug-in/scripts pages,
> but didn't find anything related.
>
> thank you very much
> Albert
>