VMD-L Mailing List

From: Kailee (kaileeamber_at_googlemail.com)
Date: Tue Jun 12 2007 - 08:58:36 CDT

Dear John,

Thank you for your reply. As I am not very skilled with tcl script, can I
ask is there any similar scripts written by others that I can modify from?

Thank you.
Best regards,
Kailee

On 6/11/07, John Stone <johns_at_ks.uiuc.edu> wrote:
>
>
> Hi,
> You could do this using a script combining the output of
> the "measure contacts" commands with your own code to update
> the per-atom Beta field per-collision. You can probably get
> "measure contacts" to do the hard part of the work, after which you
> will just need to shuffle the output to the beta fields of the affected
> atoms.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Mon, Jun 11, 2007 at 06:10:30PM +0100, Kailee wrote:
> > Dear all,
> >
> > I want to analyse a trajectory file from AMBER (.mdcrd), which is a MD
> > simulation of some gas molecules diffusing into a protein. Is there any
> way
> > to calculate the number of times each protein atom collides with the gas
> > molecules, and then store the number of collisions for each protein atom
> in
> > the B-factor of the PDB file so that I can visualise the structure in
> VMD?
> >
> > Thank you for any suggestions.
> >
> > Best regards,
> > Kailee
>
> --
> 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
>