ADL: Automated conversion of PDB to useful PDBQT files

Oleg Trott trott at
Fri Jun 28 14:54:19 PDT 2013

This is correct, except that Vina doesn't really care about
partial/Gasteiger charges.

ADT has a script called "" (Google it) that should
do what you want. OpenBabel may also be able to convert PDB to PDBQT.
In either case, double-check that the hydrogens are getting added

On Fri, Jun 28, 2013 at 2:41 PM, Paul Reginato
<paullouisreginato at> wrote:
> Hi there,
> The way I've come to understand it, Autodock vina requires PDBQT files that
> contain Gasteiger charges, polar hydrogens, partial charges, and a torsion
> tree for flexible ligands. I normally produce these from normal PDB files
> using AutdoDock Tools. However, I'm now wanting to process so many proteins
> and ligands that automation of the process is required. Is there a way I
> can produce useful PDBQT files (ie containing all the required info) in an
> automated way using the UNIX command line so that I can then dock them? I'm
> hoping to write a Python script that can do all this for me.
> Many thanks,
> Paul
> ________________________________________________
> --- ADL: AutoDock List  --- ---

Oleg Trott, Ph.D. (Columbia University)

Staff Scientist in the Olson Lab
The Scripps Research Institute

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