VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jun 13 2007 - 03:01:10 CDT

Hi,
  I don't know of one off hand, and I don't have time to write one
for you, but I don't expect that it would be too difficult. Give it
a try and see how you do. If you can at least get started on it others
should be able to help you tune it up and finish it.

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Jun 12, 2007 at 02:58:36PM +0100, Kailee wrote:
> 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
> > 

-- 
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