[PyMOL] Help with autodock plugin for PyMOL

[Ragnar T. <rth...@gm...>]

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