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AutoDock

Please note: The FAQ pages at the HPCVL website are continuously being revised. Some pages might pertain to an older configuration of the system. Please let us know if you encounter problems or inaccuracies, and we will correct the entries.

This is a short "Frequently Asked Questions" file on the AutoDock suite of automated docking tools. This software allows the prediction of how small molecules bind to a receptor site of known structure. Since AutoDock is a rather sophisticated set of tools, this FAQ cannot replace the manual. It is rather meant as a starting point for using AutoDock, and to answer questions that are specific to the installation of the software at HPCVL. 

What is "AutoDock"?

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:

  1. AutoDock performs the docking of the ligand to a set of grids describing the target protein
  2. AutoGrid pre-calculates these grids
  3. 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".

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.

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 asmol2topdqs 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 themkgpf3 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 andligand.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.

Can I run AutoDock in parallel?

No. At this point, AutoDock is a serial program.

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.

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".

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.

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 users, 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.