[AMBER] Glutathione with disufide-bond

From: <german.erlenkamp.pharmazie.uni-halle.de>
Date: Fri, 02 Dec 2011 16:08:07 +0100

Dear Amber-Users,

I have a problem with a glutathione connected to my protein over
a disulfide-bond.
I've created a parameter file for the glutamic-acid part of the
glutathione, and loaded it into leap.
Loading the protein works also, but when I want to save the prmtop and
inpcrd files, I'll receive this error-message:
         Building topology.
         Building atom parameters.
         Building bond parameters.
         Could not find bond parameter for: C - N3
         Building angle parameters.
         Could not find angle parameter: O - C - N3
         Could not find angle parameter: C - N3 - H
         Could not find angle parameter: C - N3 - H
         Could not find angle parameter: C - N3 - H
         Could not find angle parameter: C - N3 - CT
         Could not find angle parameter: CT - C - N3
         Building proper torsion parameters.
          ** No torsion terms for O-C-N3-H
          ** No torsion terms for O-C-N3-H
          ** No torsion terms for O-C-N3-H
          ** No torsion terms for O-C-N3-CT
          ** No torsion terms for CT-C-N3-H
          ** No torsion terms for CT-C-N3-H
          ** No torsion terms for CT-C-N3-H
          ** No torsion terms for CT-C-N3-CT
         Building improper torsion parameters.
         total 1093 improper torsions applied
         Building H-Bond parameters.
         Parameter file was not saved.

So I would say, that there is something wrong with my parameter file.

My question is:

        - Is it OK to create a parameter file just for the glutamic-acid
          part, or do I have to create it for the whole glutadione?
        
Best regards,

German
-- 
German Erlenkamp
Institut fuer Pharmazeutische Chemie
Martin-Luther-Universitaet Halle	
Wolfgang-Langenbeck-Str.4
06120 Halle/ Saale
E-Mail:	german.erlenkamp.pharmazie.uni-halle.de
Phone: (49)345 - 55 25 194
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Dec 02 2011 - 07:30:04 PST
Custom Search