zerodivisionerror error in autodock

Question

[siadatielahesadat]

Hi, I used material studio and build selenium nanoparticle. I used autodock and dock nanoparticle with hsa. When input ligand I received this error:

Python 2.5.2 (r252:60911, Feb 21 2008, 13:11:45) [MSC v.1310 32 bit (Intel)] on win32
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IDLE 1.2.2      ==== No Subprocess ====
>>> adding gasteiger charges to  receptor
NanoSe3: :MOL2:Se and NanoSe3: :MOL2:Se have the same coordinates
ERROR *********************************************
Traceback (most recent call last):
  File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\ViewerFramework\VF.py", line 898, in tryto
    result = command( *args, **kw )
  File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\autotorsCommands.py", line 1008, in doit
    initLPO4(mol, cleanup=cleanup)
  File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\autotorsCommands.py", line 292, in initLPO4
    root=root, outputfilename=outputfilename, cleanup=cleanup)
  File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 1019, in __init__
    detect_bonds_between_cycles=detect_bonds_between_cycles)
  File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 768, in __init__
    delete_single_nonstd_residues=False)
  File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 143, in __init__
    self.addCharges(mol, charges_to_add)
  File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 229, in addCharges
    chargeCalculator.addCharges(mol.allAtoms)
  File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\MolKit\chargeCalculator.py", line 80, in addCharges
    babel.assignHybridization(atoms)
  File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\PyBabel\atomTypes.py", line 137, in assignHybridization
    self.valence_two()
  File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\PyBabel\atomTypes.py", line 266, in valence_two
    angle1 = bond_angle(k.coords, a.coords, l.coords)
  File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\PyBabel\util.py", line 47, in bond_angle
    raise ZeroDivisionError("Input used:", a, b, c)
ZeroDivisionError: ('Input used:', [-3.7719999999999998, -9.9429999999999996, -5.774], [-3.7719999999999998, -9.9429999999999996, -5.774], [-3.7719999999999998, -9.9429999999999996, -5.774])

[zorbax]

Your error is raised because the SD of the angles provided is equal to zero.