VMD-L Mailing List

From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Fri Nov 18 2005 - 10:51:09 CST

Dear John,
   The residue names are absolutely the same in the pdb and parm files.
In fact if I create a pdb from the parm and crd files (using ambpdb),
STRIDE calculates properly the secondary structure on that pdb. For sure
in this pdb the resname will be the same as in the parm file. Also, if I
load parm and crd files in vmd, then I do "atomselect top all",
"atomselect0 writepdb pdbfile", STRIDE represents SS correctly on the
pdbfile created. The only difference between the "parm crd" loading and
the "pdb" loading is the way vmd deals with the Me-S bond, that's why I
assumed in the first place that the problem should reside there.
   The error message that I get from STRIDE when I load the top and crd
files is " Too many atoms in residue RES". So, since vmd sends a pdb
file to STRIDE even if parm and crd are loaded, I suppose that this pdb
would look the same as the one created by "atomselect-writepdb" so the
problem doesnt make to much sense unless the pdb file sent to STRIDE is
different than that created by "atomselect-writepdb".
   Anyway, as I said ... the problem can be solved if loading a pdb file
instead of the parm file and for me that's fine (at least for now)...so
dont trouble yourself too much unless this will become a problem for
many other users .....
Cheers
vlad

John Stone wrote:

>Vlad,
> STRIDE is fed it's data directly from VMD, not from the original file.
>I thought about it some more this morning, and now I believe that your
>problem has nothing to do with the bonds at all, because the information
>that VMD sends to STRIDE is done by writing a new PDB file containing the
>structure from VMD's memory, executing STRIDE on it, and getting the results
>back. I wasn't thinking clearly when I suggested toggling that bond on/off.
>Toggling the bond on/off clearly won't make a difference since bonding
>information isn't provided in the PDB file that VMD generates before it
>calls STRIDE. Given this, its far more likely that STRIDE is sensitive to
>the residue names and that the PDB file you tried previously had a residue
>name recognized by STRIDE, and the parm file did not.
>Can you compare the residue names that were assigned
>in your PDB version versus what you get when you load directly from the
>AMBER parm file? I suspect STRIDE may be lost due to the residue naming...
>
>Let me know,
> John Stone
> vmd_at_ks.uiuc.edu
>
>On Fri, Nov 18, 2005 at 11:57:08AM +0100, Vlad Cojocaru wrote:
>
>
>>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/>
>>
>>
>>
>>
>
>
> 

-- 
          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/>