[MMTK] bad lysine protonation

Konrad Hinsen hinsen at cnrs-orleans.fr
Fri Aug 29 07:43:38 UTC 2008


On 28.08.2008, at 02:39, Robert Jorissen wrote:

> 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.


As a quick fix to your problem, try the following script. It  
deactivates the identification of the protonation state, and you will  
get the most probable protonation state at pH 7 for each amino acid.

Konrad.


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

class MyPDBConfiguration(PDBConfiguration):
     def identifyProtonation(self):
         return

configuration = MyPDBConfiguration('1B2F.pdb')
configuration.peptide_chains[1][28].name = 'LYS'

chains = configuration.createPeptideChains()

protein = Protein(chains)

protein.writeToFile('protein_with_h.pdb')

--
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Konrad Hinsen
Centre de Biophysique Moléculaire, CNRS Orléans
Synchrotron Soleil - Division Expériences
Saint Aubin - BP 48
91192 Gif sur Yvette Cedex, France
Tel. +33-1 69 35 97 15
E-Mail: hinsen at cnrs-orleans.fr
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