VMD-L Mailing List

From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Wed Nov 16 2005 - 05:14:47 CST

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/>