ADL: How to define the known atom in the ligand for docking?

Ngo Duc Tri ngoductri at gmail.com
Wed Jun 10 08:52:09 PDT 2009


Dear Autodock Experts,
I'm new with the program so forgive me if my question is noob.
I am trying to dock the ligand to my structure. I know clearly the active
site (Ser) of my protein and the atom in the ligand where the active Ser
will bind to.
However, the results showed that this Ser always bind to another active
group in my ligand. So my question is how to tell Autodock specifically
choose one atom in the ligand.
Thank you so much for your advices!
My best regards,
TriNgo,
Sungkyunkwan University, Korea


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