From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Aug 24 2004 - 09:58:04 CDT

You can use a "within" selection to find waters that
are located within a specified distance of your interface region.
If you have an atom selection that represents the interface region,
you'd write a selection like this, replacing "interface selection" with
the appropriate text:
  water within 5 of (interface selection)

Let us know if you need more help.

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Aug 24, 2004 at 04:52:50AM -0700, bora erdemli wrote:
> Hi,
> first of all I would like to thank you for your
> attention. After asking the question, I looked into
> the VMD tutorial and came across with the measure
> hbond command and I wrote a script that can monitor
> the H bonds.
>
> Now I am looking for a another script that finds the
> water molecules in the interface,which is the protein
> - protein interaction interface, during simulation.
>
> Do you have any suggestion?
>
> thank you in advance....
>
> Sabri Bora Erdemli
> Computational Science and Engineering
> Koc University
> Turkey
>
> --- John Stone <johns_at_ks.uiuc.edu> wrote:
>
> >
> > Hi,
> > I assume that what you mean by "monitor" is to
> > generate a list
> > of the H-bonds for each timestep over the course of
> > an MD trajectory?
> > If so, there isn't such a script available yet, but
> > it should be very
> > easy to write a script that uses the 'measure
> > hbonds' command to determine
> > H bonds for each timestep. Let us know if you need
> > help writing the script.
> > I'd suggest that you try the "measure hbonds"
> > command by hand first in order
> > to familiarize yourself with it.
> >
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Wed, Aug 18, 2004 at 06:59:56AM -0700, bora
> > erdemli wrote:
> > > I wonder if there is a script which can monitor H
> > > bonds between selected atoms or residues during
> > the
> > > simulation ? I mean by using trajectory and psf
> > files
> > > of course...
> > >
> > > thank you in advence...
> > >
> > > sabri Bora Erdemli
> > > Computational Science and Engineering
> > > Koc University
> > > Turkey
> > >
> > >
> > >
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> >
>
>
>
>
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-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349              
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078