VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jun 09 2009 - 14:55:44 CDT

Akemi,
  Try running Extensions->Modeling->Automatic PSF Builder and
have it generate a PSF for your structure. I think that will cure
your problem, as it will define bonds explicitly, allowing VMD to
skip the simplistic distance-based bond determination heuristic.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Jun 09, 2009 at 11:01:09AM -0700, Akemi Matsuno-Yagi wrote:
> Hi,
>
> I have a problem that is similar to what was reported earlier:
>
> http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/13173.html
>
> In my case, it is a pdb file I created using molecular modeling
> software. It contains 2 protein subunits. Each one displays
> without any problem. However, when the two files are combined
> into one pdb, vmd cannot create the bonds all the way through. I
> understand this has to do with the distance-based bond search
> heuristic vmd employs.
>
> Could someone please confirm that my pdb file is suffering this
> issue? The file is at:
>
> http://www.toracat.org/work/testCD.pdb
>
> Thank you in advance.
>
> Akemi
> --
> =========================================
> Akemi Matsuno-Yagi, Ph.D.
> The Scripps Research Institute
> Dept of Molecular & Experimental Medicine
> 10550 N. Torrey Pines Rd., MEM256
> La Jolla, CA 92037
> email: ayagi <at> scripps.edu
> ========================================= 

-- 
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