Molecular Docking Server

ligand stuck?
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Author:  ogretmenlab [ Wed Oct 21, 2015 12:26 am ]
Post subject:  ligand stuck?

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).

Author:  bikadi [ Fri Oct 23, 2015 9:16 am ]
Post subject:  Re: ligand stuck?

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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