VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jun 24 2010 - 16:47:36 CDT

Hi,
  How are you generating your PSF? If you're doing any part of the PSF
generation using autopsf then the bond editing you're doing is being
ignored in favor of the bond pattern in the topology files autopsf
is using. If you're loading a PSF, editing it, and simply re-saving,
that ought to give you the intended result since VMD is agnostic
about what you do with manual bond editing.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Jun 24, 2010 at 10:27:20AM -0700, Rabab Toubar wrote:
> I have a protein with disulfide bonds that I want to reduce. When I was using VMD 1.8.6, I used the add/remove bonds to delete the disulfide, save coordinates and then psf generation and it was OK. Now I am using vmd 1.8.7 with the same molecule when I try to load the saved reduced molecule, I still can see the disulfides.
>
> I also tried to use the molefacture, but I get C-S-H-S-H bond instead of the expected two C-S-H pattern
>
> Any suggestions what could be wrong?
>
> Thanks
> Rabab Toubar
>
>
>
> 

-- 
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