VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Jun 11 2007 - 15:35:55 CDT

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
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