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.TH AUTODOCK 1 "Juli 23, 2007"
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.SH NAME
autodock \- docking of chemical ligands to protein receptors
.SH SYNOPSIS
.B autodock4
.RI [ options ]
.SH 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.
.PP
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.SH OPTIONS
.TP
.B \-p
.RI parameter_filename
.TP
.B \-l
.RI log_filename
.TP
.B \-o
Use old PDBQ format, charge q in columns 55-61
.TP
.B \-k
Keep original residue numbers
.TP
.B \-i
Ignore header-checking
.TP
.B \-t
Parse the PDBQ file to check torsions, then stop.
.TP
.B \-c < 
.RI command_file
Command mode, by file
.TP
.B \-c |
.RI control_program
Command mode, by control_program
.SH 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:
.br
gunzip *.map.gz
.br
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. 

.SH SEE ALSO
.BR autogrid (1),
.BR runAdt (1).
.br
http://autodock.scripps.edu
.br
http://autodock.scripps.edu/faqs-help/faq/what-is-the-command-line-to-start-autodock-4
.SH 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.
.SH 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.
.PP
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).