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PostPosted: Fri Sep 12, 2014 8:22 pm 
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Joined: Fri Sep 12, 2014 8:01 pm
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I tried to prepare my small molecule for docking by prepare_ligand4.py in such a manner:
Code:
 prepare_ligand4.py -l Ac-lAla-CAM.mol2 -v -o dock/Ac-lAla-CAM.pdbqt -p C.2,C.3,C.ar,H,N.am,N.pl3,O.2,O.3

Ac-lAla-CAM.mol2 is my small molecule; this file contain partial charges calculated with MOPAC and I want to preserve these charges. But I have this error:
Code:
set verbose to  True
set outputfilename to  dock/Ac-lAla-CAM.pdbqt
preserve initial charges on  C.2,C.3,C.ar,H,N.am,N.pl3,O.2,O.3,
read  Ac-lAla-CAM.mol2
Traceback (most recent call last):
  File "/home/domain/mgi/progs/mgltools_1.5.6/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_ligand4.py", line 191, in <module>
    ats = mol.allAtoms.get(lambda x: x.autodock_element==t)
  File "/home/domain/mgi/progs/mgltools_1.5.6/MGLToolsPckgs/MolKit/tree.py", line 622, in get
    result = filter(selectionString, self.data)
  File "/home/domain/mgi/progs/mgltools_1.5.6/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_ligand4.py", line 188, in <lambda>
    ats = mol.allAtoms.get(lambda x: x.autodock_element==t)
  File "/home/domain/mgi/progs/mgltools_1.5.6/MGLToolsPckgs/MolKit/molecule.py", line 411, in __getattr__
    raise AttributeError('member %s not found'%member)
AttributeError: member autodock_element not found


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