[MMTK] about reading pdb files

Hua Wong wong at ebgm.jussieu.fr
Thu Jun 10 09:45:45 CEST 2004

I would like to have a bit more information on the way PDB coordinate are read within mmtk.protein.

My problem is that when reading a complete PDB file, there is no problem, but edited pdb files don't seem to work so well.

What I mean is, I have 336 residues e.g.
I need only a part of the coordinate to be treated by mmtk.Protein, so I use an editor to get rid of coordinate I don't need. But the way my scripts run afterward puzzles me...

If I get rid of coordinate at the end 60-336 (doesn't change the order of the atoms coordinate) it seems to pass

If I get rid of coordinate at the beginning of the file (1-20) I get multiple errors
Traceback (most recent call last):
  File "/home/pif/wong/exercices/scripts/inertiaxis5", line 16, in ?
    protein = Protein(sys.argv[1])
  File "/home/pif/wong/Softwares/MMTK/lib/python2.2/site-packages/MMTK/Proteins.py", line 564, in __init__
    items = conf.createPeptideChains(model)
  File "/home/pif/wong/Softwares/MMTK/lib/python2.2/site-packages/MMTK/PDB.py", line 170, in createPeptideChains
    chain = apply(Proteins.PeptideChain, (chain,), properties)
  File "/home/pif/wong/Softwares/MMTK/lib/python2.2/site-packages/MMTK/Proteins.py", line 243, in __init__
    self._setupChain(circular, properties, conf)
  File "/home/pif/wong/Softwares/MMTK/lib/python2.2/site-packages/MMTK/Biopolymers.py", line 79, in _setupChain
  File "/home/pif/wong/Softwares/MMTK/lib/python2.2/site-packages/MMTK/PDB.py", line 33, in applyTo
    setResidueConfiguration(residue, self[i], pdbmap[0], altmap)
  File "/home/pif/wong/Softwares/MMTK/lib/python2.2/site-packages/MMTK/PDB.py", line 313, in setResidueConfiguration
    raise IOError, 'Atom '+atom.name+' of PDB residue ' + \
IOError: Atom O1 of PDB residue LEU not found in residue Leu of object .Leu23
I tried using pdb2gmx from GROMACS package to obtain a correctly numbered pdb coordinate (starting from 1) but it doesn't work.

Is there something I should check in my pdb files? And else, is there some settings I should tweak in order to load pdb smmothly?


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