VMD-L Mailing List

From: bora erdemli (boraerdemli_at_yahoo.com)
Date: Tue Aug 24 2004 - 06:52:50 CDT

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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> Email: johns_at_ks.uiuc.edu Phone:
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>

                
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