ADL: strange error for chloride atom

Giulia Canevari giulia.canevari at gmail.com
Fri Mar 7 01:47:27 PST 2008


Hi!

I had the same error message when i tried to use prepare_ligand4.py with a
ligand with an unbound ion  (in my case it was  Na). After removing it all
went well.

Giulia


2008/3/6, Zhenwei Lu <luzhenw1 at msu.edu>:
>
> 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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>


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