ADL: (re)scoring with AutoDock4.2

Stefano Forli forli at
Wed Oct 28 15:37:07 PDT 2020

Hi Bruno,

take a look at the "epdb" keyword in the AutoDock user manual.
You will need to have maps for each complex, for which you will have to automate the preparation and calculation steps.

Your workflow should include the following steps using the scripts available in the AutoDockTools/Utilities24 directory:

  - prepare ligand PDBQT (
  - prepare receptor PDBQT (, possibly with "-U" option)
  - prepare GPF (, with "-y" and "-I" options)
  - calculate grids (autogrid4)
  - prepare DPF (, with the "-e" option)

You will need other tools to extract the ligand from your PDB complexes, and a reasonable amount of scripting will be required to get it to work.
Keep an eye on co-factors, if present, since they're going to be thrown away by the receptor preparation script)
Hope this helps,


On 10/28/20 3:00 PM, Bruno De Almeida Piscelli wrote:
> Hi all,
> I have multiple ligand-protein complexes (about 450) and want only to score
> them using AutoDock4.2, skipping the docking part. Does anyone know how to
> do it in an automated way?
> Thanks in advance.
> Best,
> Bruno
> ________________________________________________
> --- ADL: AutoDock List  --- ---


  Stefano Forli, PhD

  Assistant Professor
  Dept. of Integrative Structural
  and Computational Biology, MB-112A
  Scripps Research
  10550  North Torrey Pines Road
  La Jolla,  CA 92037-1000,  USA.

     tel: +1 (858)784-2055
     email: forli at

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