[MMTK] PDB with several chains

Konrad Hinsen konrad.hinsen at cea.fr
Wed Mar 15 17:55:18 CET 2006


On Mar 14, 2006, at 1:01, vanitha at cs.wisc.edu wrote:

> Hi All:
> I'm working with the protein 1A0O (CHEY-BINDING DOMAIN OF CHEA IN  
> COMPLEX
> WITH CHEY) where chains A,C, E and G refer to Chey and B,D,F,H  
> refer to
> Chea. I'm trying to extract the ligand and the receptor from this PDB
> within MMTK so that I can do some docking refinements. Can one of  
> you take
> a look at my code that reads them in, and tell me if I'm missing
> something?

Something obvious you are missing is the addition of hydrogen  
positions. It takes just a small change:

                 protein1chains.append(PeptideChain(chain))

should be replaced by

                 protein1chains.append(chain.createPeptideChain())

Konrad.
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Konrad Hinsen
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