ADL: prepare_ligand4py fails on quaternary nitrogen atoms

Bennion, Brian bennion1 at
Mon Dec 8 16:35:14 PST 2014

Thank you for the quick reply.
The work path I am following uses a pdb file containing all hydrogen atoms that has been subjected to energy minimization. -l somefile.pdb is then called.  An error is given stating that only 6 of 23 atoms were written.  So I explicitly select the quaternary nitrogen as root with -R 4 (the atom index).
This allows all but six atoms to be converted.  These six atoms are a complete branch from the quaternary nitrogen atom.

Which method do want to me to send the file?


From: autodock-bounces at [autodock-bounces at] on behalf of Stefano Forli [forli at]
Sent: Monday, December 08, 2014 4:28 PM
To: autodock at
Subject: Re: ADL: prepare_ligand4py fails on quaternary nitrogen atoms

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
> ________________________________________________
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  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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