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autodock4

Langue: en

Version: Juli 23, 2007 (debian - 07/07/09)

Section: 1 (Commandes utilisateur)

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).

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