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 Post subject: ligand stuck?
PostPosted: Wed Oct 21, 2015 12:26 am 

Joined: Mon Jun 15, 2015 7:30 pm
Posts: 1
I uploaded a ligand but there seems to be a problem with the setup- it says "done" but there is no date and no 3D structure. I set up a couple of dockings with it anyway and they currently say "waiting /0". There is nothing else running. I tried two different parameters for ligand setup and both have the issue, but am using MMF/ PM6 now (which is the one I would like to use).

 Post subject: Re: ligand stuck?
PostPosted: Fri Oct 23, 2015 9:16 am 

Joined: Wed Oct 29, 2008 2:24 pm
Posts: 207
For very large ligands with high number of rotatable bonds a good input structure is crucial for further calculations. Without that the semiempirical charge calculation will fail. So you should either not choose PM6 or upload an X-ray ligands to avoid the problem.

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