To quote from the official
website:
AutoDock is a suite of automated docking tools. It is
designed to predict how small molecules, such as substrates or drug
candidates, bind to a receptor of known 3D structure.
AutoDock actually consists of three separate programs:
- AutoDock performs the docking of
the ligand to a set of grids describing the target protein
- AutoGrid pre-calculates these grids
- AutoTors sets up which bonds will
be treated as rotatable in the ligand.
AutoDock has been widely used and there are many examples of its successful
application in the literature (see
References). It is very fast, provides high quality predictions of
ligand conformations, and good correlations between predicted inhibition
constants and experimental ones.
For a more complete list, see the official AutoDock homepage and click on
"capabilities".
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2. Where is
"Autodock" located and how do I access it?
The present version of AutoDock is 3.05, which is the latest as of
October 2005. According to the webpage, version 4 is available.
Before you can access AutoDock, you need to read our license
agreement and sign a statement that you have done so and will abide by
it. See the last section for details.
The AutoDock program is located in the directory
/opt/autodock
To access it, you have to either
include this directory in your path:
export PATH='/opt/autodock/bin/sun.SunOS_5.5:'$PATH
export AUTODOCK_UTI=/opt/autodock/share
export PATH=$AUTODOCK_UTI':'$PATH
or (preferably) use the usepackage facility:
use autodock305
Of course, these settings may be included in your
setup files, so you don't have to type them each time you run
AutoDock.
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3. How do I run
"Autodock"?
The usage of AutoDock is explained in the User's Manual which is available for download in html, postscript, and pdf formats.
Input files for Autodock are in a PDBQS format for the macromolecule and in a PDBQ format for the ligand molecule. Autodock comes with additional ultilities such as mol2topdqs and addsol to convert other formats (such as mol2). For details, please check the documentation.
Assuming that we have input files ligand.pdbq and macro.pdbqs, we need to make a Grid Parameter file (gpf) and a Docking Parameter file (dpf) which can be created using the mkgpf3 and mkdpf3 programs. Both are part of the Autodock distribution:
% mkgpf3 ligand.pdbq macro.pdbqs
% mkdpf3 ligand.pdbq macro.pdbqs
This produces input files for autogrid3 and autodock3, which are called macro.gpf and ligand.macro.dpf. Both files might have to be edited manually before being used. The main part of an Autodock run then consists in calls to autogrid3 (for calculating a grid map) and autodock2 (for docking):
% autogrid3 -p macro.gpf -l macro.glg
% autodock3 -p ligand.macro.dpf -l ligand.macro.dlg
The -l option is used to specify log files, whereas the -p defines the input. Various other output files will be produced, someof which can be used to inspect the docking result graphically. Other utilities such as get-docked are supplied to perform the necessary conversions.
The usage of Autodock is quite complex, and the outline here cannot replace the study of the manual. A postscript version of the latter may be found in /opt/autodock/doc.
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4. Can I run AutoDock in
parallel?
No. At this point, AutoDock is a serial program.
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5. How do I set up
and run an AutoDock batch job?
Production jobs are submitted on the SunFire systems via the
GridEngine, which is a load-balancing software. To obtain details, read our
GridEngine FAQ.
The following sample submission script can be used as a guideline. Since Autodock is serial, it is very basic. Just replace the items in curly brackets by the proper entries for your run. File name definitions for the ligand and macromolecule are assumed to be without "extensions".
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6. Where can I get
further help?
AutoDock is a complex software package, and requires practice
to be used efficiently. In this FAQ we can not explain its use in any
detail. Complete documentation for the program is available in the form of
the
User's Manual, which is an absolute must-have if you want to use this
program. It is available at the official AutoDock website. This website is also your
number-one address if you have questions about the program or encounter
problems. They feature a useful FAQ and even a few movies.
HPCVL also provide user support in the case of technical problems. Contact us here, we might be able to help,
or pass you on to someone who can.
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7. How is AutoDock
licensed?
AutoDock is obtainable free of charge for academic
research users only from the Scripps Research Institute. To obtain
your own copy, go here.
The distributors of AutoDock require their users to sign a User's
Agreement, and HPCVL has done so. Our license agreement covers only
academic researchers that are HPCVL members, explicitly excluding any
commercial or contract usage. Like with other software, HPCVL requires
users who want to use AutoDock, to read the license agreement, and sign a
statement that they have done so and will abide by its terms. The license
agreement can be downloaded here . Please also download the
statement , sign it and return it to us. You will then be included in a
Unix user group that has access to the AutoDock executables.
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