autodock - 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.
- -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).