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Negative Engery but not seeing ligand binding
https://www.dockingserver.com/forum/viewtopic.php?f=5&t=129
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Author:  PREACT_Shanmugam [ Thu Jan 15, 2015 3:46 pm ]
Post subject:  Negative Engery but not seeing ligand binding

On one of my dockings, I have a negative binding energy, but no residues are identified and on the "gallery" I do not see my ligand or interacting residues.

Any suggestions?

Thanks

Author:  bikadi [ Thu Jan 15, 2015 5:59 pm ]
Post subject:  Re: Negative Engery but not seeing ligand binding

What do you see on the geometry tab? Do you see your ligand in a binding pocket? A small negative energy but no interacting residues could mean a wrongly selected simulation box where ligands have only weak, distant WdV interactions.

Author:  PREACT_Shanmugam [ Thu Jan 15, 2015 6:05 pm ]
Post subject:  Re: Negative Engery but not seeing ligand binding

On geometry, I see only the protein. No interacting chains and no ligand. I will try your suggestion to refine the box.

Thank you!

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