ADL: prepare_ligand4py fails on quaternary nitrogen atoms

Stefano Forli forli at
Mon Dec 8 16:28:59 PST 2014

it would be helpful if you could provide an example of such molecules and a description of 
what the specific issue is (e.g. unrecognized rotatable bonds, misplaced hydrogens, etc...).

Without a well-defined structure it is hard to help, but a general advice for peculiar 
molecular structures is to add hydrogens using tools that are more sophisticated than 
AutoDockTools (that's known to have problems with some nitrogen-containing structures), 
then generate the PDBQT file with the scripts or the graphical interface.


On 12/08/2014 04:24 PM, Bennion, Brian wrote:
> ________________________________
> Hello,
> I am wondering if there is a way to help recognize and properly prepare ligands for docking when they contain a quaternary nitrogen in which two bonds are part of a 6 member ring.
> Brian
> ________________________________________________
> --- ADL: AutoDock List  --- ---

  Stefano Forli, PhD

  Staff Scientist
  Molecular Graphics Laboratory
  Dept. of Integrative Structural
   and Computational Biology, MB-112F
  The Scripps Research Institute
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  La Jolla,  CA 92037-1000,  USA.

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