What is the atom name of EFP.ligand:A:EFP999?
Can you check your pdb file? Do you rename them before running the plugin?
Den 26/10/2012 23.26 skrev "Ragnar Thomsen" <rthoms...@gmail.com>:
> I have a problem when running the autodock plugin for PyMOL. I followed the
> tutorial at http://www.pymolwiki.org/index.php/Autodock_plugin.
> When I prepare the ligand I get the following error output:
>
> Batch: /usr/lib/python2.7/site-
> packages/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_ligand4.py -l
> /home/ragnar/pymol/EFP.ligand.pdb -o /home/ragnar/pymol/EFP.pdbqt -A
> checkhydrogens
> swig/python detected a memory leak of type 'BHtree *', no destructor found.
> Traceback (most recent call last):
> File "/usr/lib/python2.7/site-
> packages/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_ligand4.py", line
> 207, in <module>
> if a.coords!=coord_dict[a]: bad_list.append(a)
> KeyError: <Atom instance> EFP.ligand:A:EFP999:HN
>
> Software versions:
> PyMOL 1.5.0.1
> mgltools 1.5.4
> autodock/autogrid 4.2.3
> audodock vina 1.1.2
>
> Any help appreciated...
>
> Regards,
> Rthomsen
>
>
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join-generation-app-and-make-money-coding-fast/
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