From: Anna Modzelewska (amodzelewska_at_iimcb.gov.pl)
Date: Wed Jan 11 2006 - 09:03:28 CST

Dear Vlad,
thank you for the answer.
The error that I get is "to many atoms in residue (ligand name)", my ligand
is not linked to the protein and it is defined with ATOM cards.
I use VMD on Windows XP.
I'm not familiar with compiling. Could you please tell me where can I find
the stride.h file and how to compile it?
I guess after compiling the program, I just have to overwrite the
stride_win32.exe file in the vmd directory?

Anna

----- Original Message -----
From: "Vlad Cojocaru" <Vlad.Cojocaru_at_eml-r.villa-bosch.de>
To: "Anna Modzelewska" <amodzelewska_at_iimcb.gov.pl>
Cc: "VMD list" <vmd-l_at_ks.uiuc.edu>
Sent: Tuesday, January 10, 2006 6:08 PM
Subject: Re: vmd-l: secondary structure's display - problem

> 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/
>