ADL: ADT bug ?

Amor A. San Juan amorasj at bii.a-star.edu.sg
Mon May 26 22:56:28 PDT 2008


Hi,

I noticed that ADT in PMV parse residue atoms when implemented in the
recepter preparation. For example, only few atoms of residue Thr were in
the *_flex.pdbqt output. This is due to ADT bug I presume. In effect,
input flex residues are not sensible and so the output from dlg as well.

I try to use manually the ADT script prepare_flexreceptor4.py in order to
prepare the protein flex residues. But error flags showed up:

Hope anybody can give suggestion/help.

Thanks,
Amor

[biiamor at hilbert flex_test]$ pythonsh
/HOME01/BII/biiamor/MGLTools-1.4.6/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_flexreceptor4.py
-r 1IPB.pdb -s THR205 -x test.pdb
setting PYTHONHOME environment
Traceback (most recent call last):
  File
"/HOME01/BII/biiamor/MGLTools-1.4.6/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_flexreceptor4.py",
line 127, in ?
    non_rotatable_bonds=all_bnds)
  File
"/HOME01/BII/biiamor/MGLTools-1.4.6/MGLToolsPckgs/AutoDockTools/MoleculePreparation.py",
line 2201, in __init__
    self.write_flex(flex_residues, flexres_filename)
  File
"/HOME01/BII/biiamor/MGLTools-1.4.6/MGLToolsPckgs/AutoDockTools/MoleculePreparation.py",
line 2241, in write_flex
    self.writeResidue(res, outfileptr)
  File
"/HOME01/BII/biiamor/MGLTools-1.4.6/MGLToolsPckgs/AutoDockTools/MoleculePreparation.py",
line 2327, in writeResidue
    self.writeSubtree(outfileptr, at, at2)
  File
"/HOME01/BII/biiamor/MGLTools-1.4.6/MGLToolsPckgs/AutoDockTools/MoleculePreparation.py",
line 2344, in writeSubtree
    charge = startAtom.charge
  File
"/HOME01/BII/biiamor/MGLTools-1.4.6/MGLToolsPckgs/MolKit/molecule.py",
line 385, in __getattr__
    return self._charges[self.chargeSet]
KeyError




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