ADL: How should I prepare the Ligand PDBQT file with ADT for a single metal ion?

Stefano Forli forli at
Mon Sep 27 14:19:39 PDT 2010

Hi Jian,

AutoDock is designed and tuned to work with small molecules. Working with single atoms is 
an 'exotic' usage of the software, but it's also rather trivial, in principle, not having 
torsions or orientations to be evaluated.

Therefore, the docked position of your atom *should be* the absolute lowest value of the 
Mg map calculated with AutoGrid.

You can use ADT to load and visualize that map.

Hope this helps,


Jian Huang wrote:
> Dear ADT developers and Dockers,
> I have been trying to use ADT and Autodock to dock a single metal ion (mecury ion) in the active site of a protein. However, I get lots of errors from ADT when I try to enter the mecury ion as a ligand in PDB format. I am guessing this is because ADT expects to find some bonds in the ligand. How should I prepare the Ligand PDBQT file with ADT for a single metal ion? Is it possible to dock a single metal ion using Autodock? 
> Does anyone in the comunity have experience in this situation? 
> I would be very grateful if anyone can help me with this.
> Thanks in advance.
> Jian Huang
> School of Life Science and Technology
> University of Electronic Science and Technology of China
> Chengdu, 610054 P. R. China
> Phone: +86-28-83208232, Fax: +86-28-83208238
> ________________________________________________
> --- ADL: AutoDock List  --- ---

  Stefano Forli, PhD

  Research Associate
  Olson Molecular Graphics Laboratory
  Dept. Molecular Biology,  MB-112
  The Scripps Research Institute
  10550  North Torrey Pines Road
  La Jolla,  CA 92037-1000,  USA.

     tel: (858) 784-2055
     fax: (858) 784-2860
     email: forli at

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