VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Aug 05 2011 - 16:28:17 CDT

Hi,
  If you're having trouble using atom selections, please check
the VMD User's Guide to make sure your syntax is correct, and
double-check what you're selecting by using those selections
on a representation in the graphics window, so you can actually
see what your selection is getting. That should be helpful in
solving your problem. Your selections below have the "@" character
in them, this might potentially cause trouble, so you'll want to
see if that character needs to be escaped or not.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Aug 03, 2011 at 07:11:05PM +0630, subrata paul wrote:
> ---------- Forwarded message ----------
> From: subrata paul <paul.subrata34_at_gmail.com>
> Date: Thu, Jul 28, 2011 at 1:49 PM
> Subject: hbond analysis
> To: majordomo_at_ks.uiuc.edu
>
> Dear Sir,
> I have done my simulation in amber10 with a disscharide (glycam force
> field) and water .Now i want to calculate hbond in VMD,
> But I am facing problem in selection 1 and selection2.
>
> How I select selection1 for disscharide (1GA0GA)?
> I tryed with 1GA_at_O2 ,0GA_at_O2, but it is not working. How to solve the
> problem?
> for selection 2 how I select water molecule??
>
> thanking you
> subrata
> IITGuwahati 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/       Fax: 217-244-6078