VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Dec 03 2010 - 12:08:59 CST

Hi,
  You could probably adapt that script to do what you want, but
it'll be best to write your own script because that old one uses
some outdated atom selection features that aren't part of the
current version of VMD. Let us know if you have specific questions
about this.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Nov 30, 2010 at 10:11:58AM +0330, leila karami wrote:
> Dear John Stone
>
> thanks for your attention.
>
> You didn't answer me about my first question (I want to know the
> percentage of existence of each water mediated hydrogen bonds between
> protein and dna during my trajectory. Can I use bridging_waters.tcl in
> VMD. is it true? In following web page, (in HOW IT WORKS section)there are
> Something like that about me:
> http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/bridging_waters/.).
>
> --
>
> Leila Karami
> Ph.D. student of Physical Chemistry
> K.N. Toosi University of Technology
> Theoretical Physical Chemistry Group 

-- 
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