ADL: Prepare all parameters

Sargis Dallakyan sargis at scripps.edu
Mon Jan 28 11:11:24 PST 2008


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


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