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 Post subject: Negative Engery but not seeing ligand binding
PostPosted: Thu Jan 15, 2015 3:46 pm 

Joined: Tue Jan 13, 2015 2:12 pm
Posts: 4
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


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 Post subject: Re: Negative Engery but not seeing ligand binding
PostPosted: Thu Jan 15, 2015 5:59 pm 

Joined: Wed Oct 29, 2008 2:24 pm
Posts: 203
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.


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 Post subject: Re: Negative Engery but not seeing ligand binding
PostPosted: Thu Jan 15, 2015 6:05 pm 

Joined: Tue Jan 13, 2015 2:12 pm
Posts: 4
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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