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PostPosted: Fri Jul 04, 2014 3:37 pm 
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Joined: Fri Jul 04, 2014 3:26 pm
Posts: 1
Hello !

We have prepared a protein with an other software (that add the charges as we want) and we would like to keep theses charges so we tried with -C option which is supposed to preserve all input charges. However prepare_receptor4 did not convert our molecule in pdbqt and display this error :

prepare_receptor4.py -v -r protein.mol2 -A none -C
set verbose to True
set receptor_filename to protein.mol2
set repairs to none
do not add charges
read protein.mol2
setting up RPO with mode= automatic and outputfilename= None
charges_to_add= None
delete_single_nonstd_residues= None
Traceback (most recent call last):
File "/usr/lib/python2.7/dist-packages/AutoDockTools/Utilities24/prepare_receptor4.py", line 179, in <module>
dict=dictionary)
File "/usr/lib/python2.7/dist-packages/AutoDockTools/MoleculePreparation.py", line 546, in __init__
version=version, delete_single_nonstd_residues=delete_single_nonstd_residues)
File "/usr/lib/python2.7/dist-packages/AutoDockTools/MoleculePreparation.py", line 140, in __init__
self.addCharges(mol, charges_to_add)
File "/usr/lib/python2.7/dist-packages/AutoDockTools/MoleculePreparation.py", line 212, in addCharges
mol.chains.residues.atoms))
File "/usr/lib/python2.7/dist-packages/AutoDockTools/MoleculePreparation.py", line 211, in <lambda>
len_zero_charges = len(filter(lambda x: x.charge==0,
File "/usr/lib/python2.7/dist-packages/MolKit/molecule.py", line 407, in __getattr__
return self._charges[self.chargeSet]
KeyError: None

Do you have any idea of what can trigger this problem ?

Thanks a lot for your help !


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