ADL: ADT, Hydrogens, and Free Radicals

Nicolas Sapay nicolas.sapay at
Fri Mar 26 01:37:31 PDT 2010


You can try to disable the hydrogen merging function fo ADT in 
File>Preferences>Modify Defaults>AutoDockTools, although it is not 
directly related to your problem. At worst, you can always modify the 
pdbqt file by hand. It is just a text file.


Kamikaze_Keeper a écrit :
> 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?
> Thanks,
> Brian (aka - Kamikaze_Keeper)
> Senior Research Associate
> The Ohio State University
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