ADL: ADT, Hydrogens, and Free Radicals

Kamikaze_Keeper brian.rivera at
Thu Mar 25 09:16:53 PDT 2010

Good afternoon!

I'm new to AutoDock, but I have an issue that I am hoping someone could
provide some help on.

I have succeeded in completing a run using a hydroxylamine-containing ligand
to a particular macromolecule. Now, I am trying to dock the corresponding
nitroxide as a ligand to the same macromolecule. Unfortunately, ADT does not
like the charge-bearing free oxygen, and automatically returns the ligand to
the nitroxide configuration by adding a hydrogen atom.

Is there a way to remove this added hydrogen atom or override ADT in order
to maintain the nitroxide state?

Brian (aka - Kamikaze_Keeper)
Senior Research Associate
The Ohio State University
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