VMD-L Mailing List

From: Anna Modzelewska (amodzelewska_at_iimcb.gov.pl)
Date: Thu Jan 12 2006 - 06:23:56 CST

Great!
My ligand has 173 atoms defined with ATOM cards.
I use VMD mainly on Windows, but we have installed it also on Linux
computer. So your help with Stride on Linux will be very apreciated too.

Thank you!
Anna

----- Original Message -----
From: "John Stone" <johns_at_ks.uiuc.edu>
To: "Vlad Cojocaru" <Vlad.Cojocaru_at_eml-r.villa-bosch.de>
Cc: "Anna Modzelewska" <amodzelewska_at_iimcb.gov.pl>; "VMD list"
<vmd-l_at_ks.uiuc.edu>
Sent: Wednesday, January 11, 2006 4:58 PM
Subject: Re: vmd-l: secondary structure's display - problem

>
> 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
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078