[MMTK] Length one peptides in PDB files

Peter mmtk at maubp.freeserve.co.uk
Thu Jan 19 17:20:36 CET 2006


I have been trying to load PDB file 1ATL, using either:

configuration = MMTK.PDB.PDBConfiguration(filename)
protein = MMTK.Proteins.Protein(configuration.createPeptideChains(model 
= "no_hydrogens"))

Or simply:

protein = MMTK.Proteins.Protein(filename, model="no_hydrogens")

Both fail as follows:

IOError: Database entry Groups/tyrosine_nt_ct_noh not found

Notice that chains C and D are length one (tyrosine with an associated 
metal complex):

PDBConfiguration('top500\\1atl.pdb'):
   Peptide chain A of length 200
   Peptide chain C of length 1
   Peptide chain B of length 200
   Peptide chain D of length 1
   2 SLE molecules
   2 ZN molecules
   2 CH3 molecules
   2 CA molecules
   159 HOH molecules

As the "chain" is only length one, this means that the tyrosine is both 
n-terminal and c-terminal - something the current MMTK database does not 
include.

Thank you

Peter




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