[MMTK] about reading pdb files
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)
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, 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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