ADL: Automated conversion of PDB to useful PDBQT files

Paul Reginato paullouisreginato at
Fri Jun 28 14:41:35 PDT 2013

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,

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