VMD-L Mailing List

From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Wed Jan 11 2006 - 09:25:01 CST

Dear Anna,
   So, I was right in guessing your problem ... However I am afraid that
I have no experience whatsoever with compiling in Windows .... On linux
I could help you to fix this ... but on Windows maybe somebody else can
give you a hint .... But the problem is clear .. you need to increase
the maximum number of atoms in standard or non-standard (depending
whether your ligand comes with ATOM or HETATM cards) residues in
stride.h. For linux I believe those numbers are set to 75 and 200
respectively in the stride.h used for compiling the stride executable
delievered with vmd, but again no idea about windows.... sorry

vlad

Anna Modzelewska wrote:

> 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/
>>
>
> 

-- 
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/