VMD-L Mailing List

From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Tue Jan 10 2006 - 11:08:43 CST

Dear Anna,
  What error do you get in the console upon running STRIDE? Is the
ligand defined with ATOM cards or with HETATM cards??? Is your ligand
coordinated anyhow to one of the protein residues?
  Just trying to guess ... if your ligand is defined with ATOM cards and
if you get an error message that sounds like "to many atoms in residue
...." then you should just compile STRIDE yourself with increasing the
number of maximum atoms in a standard residue (standard means defined
with ATOM cards) by changing the line 43 of stride.h file prior to
compilation...
   But first .. tell us the error that you get and then maybe we can
help more ...

vlad

Anna Modzelewska wrote:

> Hi,
> I have problem with STRIDE. In my model I have two proteins and a
> ligand. When I load the whole model into the VMD it doesn't recognize
> the secondary structure. However when I load the proteins and the
> ligand as two separate files it does. The same behavior I observed in
> the model containing 5 proteins, and ATP. It's strange because STRIDE
> recognize the sec. str. even when protein has non-standard residues
> for which I had to define the topology by myself. Once it finds in the
> pdb file a residue that is not a part of protein or membrane it
> doesn't do anything.
> It's not funny to cut the files and load them separately each time
> when I need to see the secondary structure or to use the new-cartoon
> graphic representation.
> Is there any way to resolve this problem?
>
> Thanks for any advises
> Anna
>
>
> ************************************************************************
> Anna Modzelewska, M.Sc. amodzelewska_at_iimcb.gov.pl
> <mailto:amodzelewska_at_iimcb.gov.pl>
> International Institute of Molecular and Cell Biology
> http://www.iimcb.gov.pl/
> Trojdena 4, 02-109 Warsaw, Poland
> phone: +48 22 5970721 fax: +48 22 5970715
> ************************************************************************
>
> 

-- 
Dr. Vlad Cojocaru
EML Research gGmbH
Molecular and Cellular Modeling Group
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg, Germany
Phone: +49-6221-533266
Fax: +49-6221-533298
e-mail: Vlad.Cojocaru_at_eml-r.villa-bosch.de
http://projects.villa-bosch.de/mcm/people/cojocaru/