ADL: strange error for chloride atom

Zhenwei Lu luzhenw1 at msu.edu
Thu Mar 6 13:43:48 PST 2008


Dear All: 

    I am a newcomer and want some help about one strange problem. I tried to 
prepare ligand using ADT. the ligand contains one benzen ring with two 
chlorine atom. It keeps going wrong from the begining. However, When I 
substitute CL with either F or Br, it works OK. Although I still have 
trouble with ADT, I can get it done using prepare_ligand4.py. Here is the 
error message. Any suggestion will be appreciated. 

  setting PYTHONHOME environment
Traceback (most recent call last):
 File "./prepare_ligand4.py", line 185, in <module>
   inactivate_all_torsions=inactivate_all_torsions)
 File 
"/opt/MGLTools-1.5.0/MGLToolsPckgs/AutoDockTools/MoleculePreparation.py", 
line 925, in __init__
   limit_torsions=limit_torsions)
 File 
"/opt/MGLTools-1.5.0/MGLToolsPckgs/AutoDockTools/MoleculePreparation.py", 
line 681, in __init__
   delete_single_nonstd_residues=False)
 File 
"/opt/MGLTools-1.5.0/MGLToolsPckgs/AutoDockTools/MoleculePreparation.py", 
line 130, in __init__
   self.addCharges(mol, charges_to_add)
 File 
"/opt/MGLTools-1.5.0/MGLToolsPckgs/AutoDockTools/MoleculePreparation.py", 
line 218, in addCharges
   chargeCalculator.addCharges(mol.allAtoms)
 File "/opt/MGLTools-1.5.0/MGLToolsPckgs/MolKit/chargeCalculator.py", line 
80, in addCharges
   babel.assignHybridization(atoms)
 File "/opt/MGLTools-1.5.0/MGLToolsPckgs/PyBabel/atomTypes.py", line 136, in 
assignHybridization
   self.valence_two()
 File "/opt/MGLTools-1.5.0/MGLToolsPckgs/PyBabel/atomTypes.py", line 262, in 
valence_two
   angle1 = bond_angle(k.coords, a.coords, l.coords)
 File "/opt/MGLTools-1.5.0/MGLToolsPckgs/PyBabel/util.py", line 48, in 
bond_angle
   (a[2] - b[2]) * (c[2] - b[2]) ) / dist
ZeroDivisionError: float division 


Zhenwei Lu
Graduate Student
Biochemistry & Molecular Biology
313 Biochemistry building
Tel: 517-353-8786
Email: luzhenw1 at msu.edu



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