autodock(1) docking of chemical ligands to protein receptors


autodock4 [options]


AutoDock perfoms the automated docking of chemical compounds to proteins, i.e. it predicts how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.

The AutoDockSuite consists of two main programs of which AutoDock performs the docking of the ligand to a set of grids describing the target protein and AutoGrid pre-calculates these grids.


Use old PDBQ format, charge q in columns 55-61
Keep original residue numbers
Ignore header-checking
Parse the PDBQ file to check torsions, then stop.
-c <
command_file Command mode, by file
-c |
control_program Command mode, by control_program


On Debian, the directory /usr/share/doc/autodock offers examples to run. Change to that directory and unpack (as root) the gzipped map files, then execute AutoDock as shown below:
gunzip *.map.gz
autodock4 -p 1pgp.dpf -l /tmp/1pgp.dlg

The interpretation of results is aided by the AutoDockTools suite. Please also inspect the tutorials offered online.


This software is made available under the terms of the GNU Public License version 2 or later. This implies that this software may be redistributed if the source is made available. It would however help the future development of the AutoDockSuite if you register yourself at


The most prominent author of the version 4 of autodock is G. Morris <[email protected]>. See the AUTHORS file in /usr/share/doc/autodock for details.

This manual page was written by Steffen Moeller <[email protected]>, for the Debian project (but may be used by others and is hopefully adopted by the upstream developers).