[MMTK] PDB with several chains

[vanitha@cs.wisc.edu]

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?
Here is the code and the output :-


Code:-

from MMTK import *
from MMTK.PDB import PDBConfiguration
from MMTK.Proteins import PeptideChain, Protein

# First we read the two PDB files.
configuration = PDBConfiguration('1A0O.pdb')

protein1chains = []
protein2chains = []

i = 0
for chain in configuration.peptide_chains:
        if i%2 == 0:
                protein1chains.append(PeptideChain(chain))
        else:
                protein2chains.append(PeptideChain(chain))
        i = i + 1

Protein1 = Protein(protein1chains)
Protein2 = Protein(protein2chains)

Output:-

Warning: Some atoms in a protein have undefined positions.
Warning: Some atoms in a protein have undefined positions.
4
4

Thanks in advance,

- Vanitha