VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jan 11 2006 - 09:58:28 CST

Hi,
  I can certainly compile a Windows Stride with the increased limit if that
will solve Anna's problem...

  John

On Wed, Jan 11, 2006 at 04:25:01PM +0100, Vlad Cojocaru wrote:
> 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/
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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