<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">G'day<br><br>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.<br><br>Here is the script I used (comments removed and a PDB entry used):<br><br>#!/bin/env python<br><br>from MMTK import *<br>from MMTK.PDB import PDBConfiguration<br>from MMTK.Proteins import PeptideChain, Protein<br><br>configuration = PDBConfiguration('1B2F.pdb')<br><br>chains = configuration..createPeptideChains()<br><br>insulin = Protein(chains)<br><br>insulin.writeToFile('insulin_with_h.pdb')<br><br><br>Any comments as to what is going on would
be appreciated.<br><br>Rob Jorissen<br>Ludwig Institute for Cancer Research, Melbourne branch<br><br></td></tr></table><br>
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