This is a short help 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 our installation of the software.
AutoDock actually consists of three separate programs:
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".
Location of the program and setup
The present version of AutoDock is 4.2.5, which is the latest as of early 2014.
The AutoDock program is located in the directory /opt/autodock. To access it, you have to do a setup using the usepackage facility:
Of course, this may be included in your setup files (probably .bash_profile), so you don't have to type them each time you run AutoDock.
Running From a Command Line
The usage of AutoDock is explained in the User's Manual which is available for download.
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 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.
Note: AutoDock does not have parallel capabilities at this point. As a result you won't get a considerable speedup for an individual run on a parallel system as compared with, say, a desktop machine. However, a parallel machine allows the simultaneous execution of multiple instances of this software.
Submitting AutoDock Jobs
Production jobs are submitted via the Grid Engine Scheduler. To obtain details, read our Scheduler Help File. A sample script looks like this:
#!/bin/bash #$ -S /bin/bash #$ -q abaqus.q #$ -l qname=abaqus.q #$ -V #$ -cwd #$ -M email@example.com #$ -m be #$ -o STD.out #$ -e STD.err
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".
NAMD is free for non-commercial use, but it is licensed. As with other licensed software, we ask our users to read through the license agreement that exists between the University of Illinois and HPCVL, and to sign a statement that they agree to abide by the terms of the license. The main issue in the NAMD case is that usage has to non-commercial.
Once we have received the signed statement (FAX to (613) 533-2015 or scan/email to firstname.lastname@example.org), we will enter the user to a Unix group namd which enables access to the software.
NAMD requires practice to be used efficiently. We cannot explain it use in any detail here, but