[MMTK] bad lysine protonation

[Robert Jorissen]

G'day

I have tried out one of the test scripts from the MMTK web site to read in a protein structure, add hydrogen atoms and then write out a PDB file. However, the lysine sidechain seems to be neutral rather than charged - two hydrogen atoms are added to an apparently sp2 sidechain nitrogen. I also noticed this on another protein that I was working with, so it is not restricted to this particular PDB file.

Here is the script I used (comments removed and a PDB entry used):

#!/bin/env python

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

configuration = PDBConfiguration('1B2F.pdb')

chains = configuration.createPeptideChains()

insulin = Protein(chains)

insulin.writeToFile('insulin_with_h.pdb')


Any comments as to what is going on would be appreciated.

Rob Jorissen
Ludwig Institute for Cancer Research, Melbourne branch




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