From: Ragnar T. <rth...@gm...> - 2012-10-26 21:25:24
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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 |
From: Troels E. L. <tl...@gm...> - 2012-10-27 12:51:26
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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" <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 > > > ------------------------------------------------------------------------------ > WINDOWS 8 is here. > Millions of people. Your app in 30 days. > Visit The Windows 8 Center at Sourceforge for all your go to resources. > http://windows8center.sourceforge.net/ > join-generation-app-and-make-money-coding-fast/ > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > |