ADL: Fresh Autodock install ligand input error

David M. Carter david.carter3 at mail.mcgill.ca
Fri May 2 07:22:10 PDT 2008


Hi All,

 

I thought I might speed up my docking experiments by installing Autodock on
the fastest machine that our lab just acquired.  It's running Ubuntu 8.0 and
I installed MGLTools 1.5.1 along with Autodock4 and Autogrid4.  After
acquiring the libraries that weren't preinstalled on the machine ADT opened
smoothly with no errors.  However, when I try to input a ligand, I get the
following error in the Python Shell (See below).  After this error I can't
prepare the ligand as is required for the docking experiments.  Can anyone
interpret this and help me solve this issue so that I might proceed?  It
worked fine on the slower computer which ran MGL tools 1.4.6.  I thought
that may have been the problem so I uninstalled MGLTools 1.5.1 and installed
1.4.6, but this didn't resolve the issue.

 

Many Thanks,

 

David Carter

 

IDLE 1.1.2      ==== No Subprocess ====

>>> adding gasteiger charges to peptide

ERROR *********************************************

Traceback (most recent call last):

  File "/home/coulton/MGLTools-1.4.6/MGLToolsPckgs/ViewerFramework/VF.py",
line 714, in tryto

    result = apply( command, args, kw )

  File
"/home/coulton/MGLTools-1.4.6/MGLToolsPckgs/AutoDockTools/autotorsCommands.p
y", line 754, in doit

    initLPO4(mol, cleanup=cleanup)

  File
"/home/coulton/MGLTools-1.4.6/MGLToolsPckgs/AutoDockTools/autotorsCommands.p
y", line 286, in initLPO4

    root=root, outputfilename=outputfilename, cleanup=cleanup)

  File
"/home/coulton/MGLTools-1.4.6/MGLToolsPckgs/AutoDockTools/MoleculePreparatio
n.py", line 920, in __init__

    limit_torsions=limit_torsions)

  File
"/home/coulton/MGLTools-1.4.6/MGLToolsPckgs/AutoDockTools/MoleculePreparatio
n.py", line 676, in __init__

    delete_single_nonstd_residues=False)

  File
"/home/coulton/MGLTools-1.4.6/MGLToolsPckgs/AutoDockTools/MoleculePreparatio
n.py", line 128, in __init__

    self.addCharges(mol, charges_to_add)

  File
"/home/coulton/MGLTools-1.4.6/MGLToolsPckgs/AutoDockTools/MoleculePreparatio
n.py", line 216, in addCharges

    chargeCalculator.addCharges(mol.allAtoms)

  File
"/home/coulton/MGLTools-1.4.6/MGLToolsPckgs/MolKit/chargeCalculator.py",
line 80, in addCharges

    babel.assignHybridization(atoms)

  File "/home/coulton/MGLTools-1.4.6/MGLToolsPckgs/PyBabel/atomTypes.py",
line 136, in assignHybridization

    self.valence_two()

  File "/home/coulton/MGLTools-1.4.6/MGLToolsPckgs/PyBabel/atomTypes.py",
line 262, in valence_two

    angle1 = bond_angle(k.coords, a.coords, l.coords)

  File "/home/coulton/MGLTools-1.4.6/MGLToolsPckgs/PyBabel/util.py", line
46, in bond_angle

    cos_theta = ( (a[0] - b[0]) * (c[0] - b[0]) +

ZeroDivisionError: float division



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