VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Nov 16 2005 - 15:39:11 CST

Vlad,
  How about temporarily taking out the bond that confuses stride using the
Mouse->Add/Remove Bonds feature. Once removed, you could then use sscache
to get stride to build 2ndary struct for all of your timesteps, or if you just
need one good one, just call 'mol ssrecalc top'. Once you've got STRIDE
doing what you need, you can put the bond back, and things should be ok then.
This is obviously an annoying hack, but until someone comes up with a better
free/open source secondary structure determination package, I don't have
any better suggestions. That said, if anyone knows of something better,
I'm all ears.

  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Nov 16, 2005 at 12:14:47PM +0100, Vlad Cojocaru wrote:
> Dear vmd users,
> In my protein I have a metal ion that has five coordinations, one of
> them being a CYS residue. For AMBER, I built a new residue RES by
> creating a bond between the S atom of CYS and the metal ion. If I load
> into vmd the AMBER topology together with the AMBER coordinates files,
> the bond S-Me is drawn but STRIDE fails to calculate the secondary
> structure complaining that there are too many atoms in the unusual
> residue. If I load a pdb file of the protein, the S-Me bond is not drawn
> and STRIDE calculates the secondary struucture properly. This is not
> really nice because I am not able to create NewCartoon representations
> for my molecule unless I convert all amber trajectories to multiple pdb
> files (which of course I dont want).
> The question is ... Is there a way I can make STRIDE recognize my
> unusual residue as regular protein residue so that I can represent the
> secondary structure of the protein without converting AMBER trajectories
> to multiple pdb files?
>
>
> Thank you very much in advance
>
> Best wishes
> vlad
>
>
> Dr. Vlad Cojocaru
> EML Research gGmbH
> Molecular and Cellular Modeling Group
> Villa Bosch
> Schloss-Wolfsbrunnenweg 33
> 69118 Heidelberg
> Germany
> Phone: +49-6221-533266
> Fax: +49-6221-533298
> e-mail: Vlad.Cojocaru_at_eml-r.villa-bosch.de
> <mailto:Vlad.Cojocaru_at_eml-r.villa-bosch.de>
> Additional info: my home page
> <http://projects.villa-bosch.de/mcm/people/cojocaru/>
>
> 

-- 
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