ADL: strange error for chloride atom

Zhenwei Lu luzhenw1 at msu.edu
Fri Mar 7 05:52:27 PST 2008


Thanks. However, In my case, the program cannot recognize the C-CL bond As 
shown from ADT display. I tried to build bond and failed. I think it is a 
bug because only CL does not work and F/Br is fine. Any suggestion to bypass 
this problem for running with chlorine atom? 

Thanks. 

Giulia Canevari writes: 

> 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 
>>
>> ________________________________________________
>> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list --- 
>>
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list --- 
> 
 


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




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