ADL: Prepare all parameters

Jack Shultz jackygrahamez at gmail.com
Mon Jan 28 11:34:20 PST 2008


Great one other thing, may be trivial, certain pdb files will generate PDBQT
with a substring "model1", any idea what is going on there?

C:\Program Files\MGLTools
1.4.6\MGLToolsPckgs\AutoDockTools\Utilities24>prepare_all4.py
-l nsc2559.mol2 -r 1txe.pdb
01/28/2008  02:21 PM            65,315 1txe_model1.pdbqt
01/28/2008  02:21 PM             3,669 nsc2559.pdbqt
               3 File(s)         69,819 bytes
               0 Dir(s)  18,727,534,592 bytes free


On Jan 28, 2008 2:11 PM, Sargis Dallakyan <sargis at scripps.edu> wrote:

> Jack Shultz wrote:
> > There may be an easier way. Not sure if I've handled the tors
> properly...
> > I managed to get the basic functionality of prepare_ligand4,
> > prepare_receptor4 and prepare_gpf4...still trying to get prepare_dpf4
> >
> > Here is the command line that works on the script bellow
> > pythonsh prepare_all4.py -l nsc19892.mol2 -r 1tfw.pdb
> > http://hydrogenathome.org/prepare_all4.py.txt
> >
> > When I try to include the code for prepare_dpf in this script
> > http://hydrogenathome.org/prepare_all4_with_dpf.py.txt
> >
> > I get these errors
> > Traceback (most recent call last):
> >   File "prepare_all4.py", line 460, in ?
> >     dm.set_ligand(ligand_filename)
> >   File "prepare_all4.py", line 75, in set_ligand
> >     self.dpo['ndihe']['value'] = self.ligand.parser.keys.count("BRANCH")
> > AttributeError: Mol2Parser instance has no attribute 'keys'
>
> ligand_filename in dm.set_ligand(ligand_filename) should be pdbqt (mol2
> won't
> work). AD4LigandPreparation is using outputfilename = None, that results
> in
> .pdbqt file created. If you pass os.path.splitext
> (ligand_filename)[0]+'.pdbqt'
> to set_ligand instead of ligand_filename, it should do the job.
>
> I'm getting parameter_list is not defined when I use pdbqt file as an
> input
> ligand. After adding parameter_list=local_search_list4 to
> prepare_all4_with_dpf.py it was able to generate dpf.
>
> -Sargis
>  ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>


More information about the autodock mailing list