VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Feb 27 2009 - 16:23:19 CST

Nick,
  VMD uses a simple distance-based bond search heuristic which can
make mistakes in some cases. I'd suggest that you try using one of
the new test versions of VMD 1.8.7 (rather than an older version) and
let us know if you still have trouble. If you do, then you might see
if running the autopsf plugin on your structure will assign correct
bonds even when the model is in a single molecule.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Feb 27, 2009 at 05:01:30PM -0500, Nikolay Simakov wrote:
> Hi,
>
> I have next problem. Then I load pdb file which has protein and lipids,
> vmd create bonds between protein and lipids and do not create bonds
> withing lipids. If I split protein and lipids into separate pdb files
> and then load them separately everything is fine.
>
> I am running vmd-1.8.6 under linux. I also try to downgrade and check is
> it working or not and found that 1.7.1 is doing good.
>
> Has anyone have similar problems?
>
> Nick 

-- 
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