ADL: membrane protein

Trevor Marshall Trevor at trevormarshall.com
Sun Jan 29 19:10:09 PST 2006


Sure, I can confirm that.
Take a look at our recent paper on 7-transmembrane GPCRs. 
You can find a copy at "Theoretical Biology and Medical Modelling" 
http://www.tbiomed.com/content/3/1/1

Download the fulltext PDF to see just what AutoDock can do with membrane
proteins. There is a library of membrane proteins and ligand models there
which you can download and look at how I handled these X and M atoms.

Sincerely
Trevor

-------------------------
Trevor G Marshall, PhD
Autoimmunity Research Foundation
-------------------------



At 09:09 AM 1/30/2006 +1100, Swarna Patra wrote:
>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/editCommand
s.py", 
>line 2439, in doit
>    babel.assignHybridization(mol.allAtoms)
>  File 
>"/net/biophys0/swarna/PMV/share/lib/python2.3/site-packages/PyBabel/atomTyp
es.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/atomTyp
es.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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