[MMTK] Creating universe with heme in PDB file

Hyuntae Na htna at hotmail.com
Tue Jan 17 02:53:32 UTC 2012





Hi all, Could you help me to make a universe that has a protein with a heme that is connected to the protein. I use 1A6G for my study. The pdb file has a protein and a heme, and they are connected together. If I use "MMTK.Proteins.Protein(pdbFile)" to generate a protein structure, it remove water and heme, but take only protein part. I need a molecule of the pdb file, where both protein and heme are connected as described in the pdb file. Can you help me to generate it? I tried to use "MMTK.PDB.PDBConfiguration" as follows: config = MMTK.PDB.PDBConfiguration('1A6G.pdb');
univ = MMTK.InfiniteUniverse();
univ.addObject(config.createAll()); And, the call "config.createAll()" throw following errors: Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "C:\Python27\lib\site-packages\MMTK\PDB.py", line 428, in createAll
    molecules = self.createMolecules(molecule_names, permit_undefined)
  File "C:\Python27\lib\site-packages\MMTK\PDB.py", line 368, in createMolecules
    setConfiguration(m, [molecule])
  File "C:\Python27\lib\site-packages\MMTK\PDB.py", line 534, in setConfiguration
    pdbmap[i], altmap, atom_map)
  File "C:\Python27\lib\site-packages\MMTK\PDB.py", line 497, in setResidueConfiguration
    pdbmap[0] + ' of object ' + object.fullName())
IOError: Atom NA of PDB residue HEM not found in residue HEM of object heme Thank you. Best regards,
-- Hyuntae 		 	   		  
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