autodock4 (1)

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.

-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

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.

autogrid(1), runAdt(1).

http://autodock.scripps.edu

http://autodock.scripps.edu/faqs-help/faq/what-is-the-command-line-to-start-autodock-4

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.

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).