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PostPosted: Tue May 15, 2012 7:06 am 
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Joined: Mon Apr 23, 2012 2:58 pm
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Hi!
I am trying to use pymol autodock plugin (developed by Dr. Daniel Seeliger) to dock my ligand. When I generate ligand pdbqt file, it always fails, although the protein file is ok.
And the log says:

"Traceback (most recent call last):
File "/home/autodock/MGLTools-1.5.4/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_ligand4.py", line 207, in <module>
if a.coords!=coord_dict[a]: bad_list.append(a)
KeyError: <Atom instance> mybl.ligand:A:BLD800:H02".

Who can help me?

Thank you.


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PostPosted: Fri Sep 21, 2012 9:01 pm 
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Micromolar User
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Joined: Fri Sep 21, 2012 3:25 am
Posts: 40
Location: Mexico
I don't want to be mean but have you written to the developer of the plugin?

Other than that, the error could be due to two things (as far as I can tell):

1) You have no such path installed. That is, have you installed the Autodock Tools? If so, have you indicated the right path to the plugin?

2) There is a chain, atom number and atom ID there. Have you check that that atom is right, that is, that it makes sense for the molecule?

Best regards.


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