ADL: ADT bug ?

Ruth Huey rhuey at scripps.edu
Wed May 28 17:37:52 PDT 2008


Hi,
(1) Only the side chains of the designated residues are allowed to be 
flexible. Thus for a flexible Thr residue, at most 4 atoms would be 
written in the flexible file.
(2) The receptor file for prepare_flexreceptor4.py needs to be in 
".pdbqt" format.  You can use ADT or prepare_receptor4.py to  convert 
your pdb file to pdbqt.

         Ruth


  
Amor A. San Juan wrote:
> 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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>
>   



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