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PostPosted: Tue Dec 10, 2013 7:00 am 
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Joined: Wed Aug 01, 2012 1:50 pm
Posts: 2
Hi

I try use Raccoon to convert multiple mol2 files to pdbqt for autodock vina screening. there always came out the following error message for some molecules, any idea how to fix this issue?

<type 'exceptions.ZeroDivisionError'> Exception in Tk callback
Function: <function openLigandDir at 0x1dad1b8> (type: <type 'function'>)
Args: ()
Traceback (innermost last):
../MGLTools-1.5.7rc1/lib/python2.7/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in __call__
return apply(self.func, args)
File "raccoon.py", line 1694, in openLigandDir
openLigand(ligFiles)
File "raccoon.py", line 1248, in openLigand
openMultiMol2(filename)
File "raccoon.py", line 1283, in openMultiMol2
if genPDBQT(ligFile, output_file):
File "raccoon.py", line 1532, in genPDBQT
attach_nonbonded_fragments=attach_nonbonded_fragments)
File "/home/EMIC/MGLTools-1.5.7rc1/MGLToolsPckgs/AutoDockTools/MoleculePreparation.py", line 1019, in __init__
detect_bonds_between_cycles=detect_bonds_between_cycles)
File "/home/EMIC/MGLTools-1.5.7rc1/MGLToolsPckgs/AutoDockTools/MoleculePreparation.py", line 779, in __init__
detectAll=self.detect_bonds_between_cycles)
File "/home/EMIC/MGLTools-1.5.7rc1/MGLToolsPckgs/AutoDockTools/MoleculePreparation.py", line 1798, in __init__
self.__classifyBonds(molecule.allAtoms, allow_guanidinium_torsions)
File "/home/EMIC/MGLTools-1.5.7rc1/MGLToolsPckgs/AutoDockTools/MoleculePreparation.py", line 1836, in __classifyBonds
dict =self.dict = ADBC.classify(mol.allAtoms.bonds[0])
File "/home/EMIC/MGLTools-1.5.7rc1/MGLToolsPckgs/AutoDockTools/AutoDockBondClassifier.py", line 58, in classify
rotatables = self.d['rotatable'].select(bonds)
File "/home/EMIC/MGLTools-1.5.7rc1/MGLToolsPckgs/MolKit/bondSelector.py", line 535, in select
rotatable = BondOrderBondSelector().select(bnds,1)
File "/home/EMIC/MGLTools-1.5.7rc1/MGLToolsPckgs/MolKit/bondSelector.py", line 512, in select
bo.assignBondOrder(allAts, allAts.bonds[0], rf)
File "/home/EMIC/MGLTools-1.5.7rc1/MGLToolsPckgs/PyBabel/bo.py", line 82, in assignBondOrder
self.assign_bond_order2(atoms, bonds, rings)
File "/home/EMIC/MGLTools-1.5.7rc1/MGLToolsPckgs/PyBabel/bo.py", line 185, in assign_bond_order2
self.process_5_ring(ring)
File "/home/EMIC/MGLTools-1.5.7rc1/MGLToolsPckgs/PyBabel/bo.py", line 395, in process_5_ring
atoms[3].coords,atoms[4].coords)
File "/home/EMIC/MGLTools-1.5.7rc1/MGLToolsPckgs/PyBabel/util.py", line 78, in torsion_angle
n = 1.0 / math.sqrt( q[0]*q[0] + q[1]*q[1] + q[2]*q[2] )
<type 'exceptions.ZeroDivisionError'>: float division by zero


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