ADL: membrane protein

Swarna Patra swarna at physics.usyd.edu.au
Sun Jan 29 14:09:28 PST 2006


Hi
Can anyone clarify me that is it possible to handle membrane protein in ADT? I 
am attaching a .pdb file which contains the protein and membrane DMPC. I have 
loaded the molecule through grid read macromolecule and I get the following 
error.
>>> ERROR ************************************************
Traceback (most recent call last):
  File 
"/net/biophys0/swarna/PMV/share/lib/python2.3/site-packages/ViewerFramework/VF.py", 
line 582, in tryto
    result = apply( command, args, kw )
  File 
"/net/biophys0/swarna/PMV/share/lib/python2.3/site-packages/Pmv/editCommands.py", 
line 2439, in doit
    babel.assignHybridization(mol.allAtoms)
  File 
"/net/biophys0/swarna/PMV/share/lib/python2.3/site-packages/PyBabel/atomTypes.py", 
line 127, in assignHybridization
    a.babel_atomic_number = self.get_atomic_number(a.babel_type)
  File 
"/net/biophys0/swarna/PMV/share/lib/python2.3/site-packages/PyBabel/atomTypes.py", 
line 100, in get_atomic_number
    return babel_elements[name]['num']
KeyError: 'H1'
charges on carbons unchanged

I request if anyone knows please have a look and let me know what needs to be 
done.
regards
swarna
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