VMD-L Mailing List

From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Fri Nov 18 2005 - 04:57:08 CST

Dear John,
   Thanks a lot for the suggestions .. However it seems that they do not
solve the problem since the bond is present in the amber topology file,
no matter if I graphically remove it in VMD, and I guess STRIDE tries to
calculate the SS from the original file (correct me if I am wrong). Of
course a provisional solution could be to load a pdb file instead of the
topology file and then load the trajectory onto this pdb file .....
However, it would be nice if this problem will be eventually solved...
Best wishes
vlad

John Stone wrote:

>Vlad,
> How about temporarily taking out the bond that confuses stride using the
>Mouse->Add/Remove Bonds feature. Once removed, you could then use sscache
>to get stride to build 2ndary struct for all of your timesteps, or if you just
>need one good one, just call 'mol ssrecalc top'. Once you've got STRIDE
>doing what you need, you can put the bond back, and things should be ok then.
>This is obviously an annoying hack, but until someone comes up with a better
>free/open source secondary structure determination package, I don't have
>any better suggestions. That said, if anyone knows of something better,
>I'm all ears.
>
> John Stone
> vmd_at_ks.uiuc.edu
>
>On Wed, Nov 16, 2005 at 12:14:47PM +0100, Vlad Cojocaru wrote:
>
>
>>Dear vmd users,
>> In my protein I have a metal ion that has five coordinations, one of
>>them being a CYS residue. For AMBER, I built a new residue RES by
>>creating a bond between the S atom of CYS and the metal ion. If I load
>>into vmd the AMBER topology together with the AMBER coordinates files,
>>the bond S-Me is drawn but STRIDE fails to calculate the secondary
>>structure complaining that there are too many atoms in the unusual
>>residue. If I load a pdb file of the protein, the S-Me bond is not drawn
>>and STRIDE calculates the secondary struucture properly. This is not
>>really nice because I am not able to create NewCartoon representations
>>for my molecule unless I convert all amber trajectories to multiple pdb
>>files (which of course I dont want).
>> The question is ... Is there a way I can make STRIDE recognize my
>>unusual residue as regular protein residue so that I can represent the
>>secondary structure of the protein without converting AMBER trajectories
>>to multiple pdb files?
>>
>>
>>Thank you very much in advance
>>
>>Best wishes
>>vlad
>>
>>
>> Dr. Vlad Cojocaru
>> EML Research gGmbH
>> Molecular and Cellular Modeling Group
>> Villa Bosch
>> Schloss-Wolfsbrunnenweg 33
>> 69118 Heidelberg
>> Germany
>> Phone: +49-6221-533266
>> Fax: +49-6221-533298
>> e-mail: Vlad.Cojocaru_at_eml-r.villa-bosch.de
>> <mailto:Vlad.Cojocaru_at_eml-r.villa-bosch.de>
>> Additional info: my home page
>> <http://projects.villa-bosch.de/mcm/people/cojocaru/>
>>
>>
>>
>>
>
>
> 

-- 
          Dr. Vlad Cojocaru
          EML Research gGmbH
          Molecular and Cellular Modeling Group
          Villa Bosch
          Schloss-Wolfsbrunnenweg 33
          69118 Heidelberg
          Germany
          Phone: +49-6221-533266
          Fax: +49-6221-533298
          e-mail: Vlad.Cojocaru_at_eml-r.villa-bosch.de
          <mailto:Vlad.Cojocaru_at_eml-r.villa-bosch.de>
          Additional info: my home page
          <http://projects.villa-bosch.de/mcm/people/cojocaru/>