---
name: "autodock4"
section: "1"
platform: "linux"
package: "autodock"
version: "4.2.6-9"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/autodock4"
---

# autodock4(1)

docking of chemical ligands to protein receptors

## NAME

autodock - docking of chemical ligands to protein receptors

## SYNOPSIS

**autodock4** \[*options*\]

## DESCRIPTION

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.

## OPTIONS

- **-p**

  parameter\_filename

- **-l**

  log\_filename

- **-o**

  Use old PDBQ format, charge q in columns 55-61

- **-k**

  Keep original residue numbers

- **-i**

  Ignore header-checking

- **-t**

  Parse the PDBQ file to check torsions, then stop.

- **-c \<**

  command\_file Command mode, by file

- **-c \|**

  control\_program Command mode, by control\_program

## EXAMPLE

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.

## SEE ALSO

**autogrid**(1), **runAdt**(1).\
 http://autodock.scripps.edu\
 http://autodock.scripps.edu/faqs-help/faq/what-is-the-command-line-to-start-autodock-4

## LICENSE

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 http://autodock.scripps.edu/downloads.

## AUTHOR

The most prominent author of the version 4 of autodock is G. Morris \<garrett@scripps.edu\>. See the AUTHORS file in /usr/share/doc/autodock for details.

This manual page was written by Steffen Moeller \<moeller@debian.org\>, for the Debian project (but may be used by others and is hopefully adopted by the upstream developers).