VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Oct 30 2002 - 10:37:02 CST

Hi,
  You can do distance-based atom selections in VMD using the
"within" atom selection keyword. There are some examples of how to
do this in the VMD user's guide here:
  http://www.ks.uiuc.edu/Research/vmd/vmd-1.7.1/ug/node86.html#5239

Let us know if you need more help.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Oct 29, 2002 at 09:22:48AM +0530, Y. U. Sasidhar wrote:
> Hi,
> I am using vmd ( 1.7.x ) on both windows and red hat linux 7.1 or higher to
> visualize gromacs trajectories of peptides in water.
> I want to detect simultaneous hydrogen bonding of i+4 NH and i CO with water
> molecule. If I can display waters within 2.6 A of NH && CO I might be able
> to do that. How do I do this in vmd.
> regards,
> Sasidhar
>
> 

-- 
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