AutoDock

Description

From the AutoDock 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 4 actually consists of two main programs: autodock performs the docking of the ligand to a set of grids describing the target protein; autogrid pre-calculates these grids. In addition to using them for docking, the atomic affinity grids can be visualised. This can help, for example, to guide organic synthetic chemists design better binders.

Version

  • 4.2.3

Authorized Users

  • CIRCE account holders
  • SC account holders

Platforms

  • CIRCE cluster
  • SC cluster

Modules

AutoDock requires the following module file to run:

  • apps/autodock/4.2.3

Running AutoDock on CIRCE/SC

The AutoDock user guide is essential to understanding the application and making the most of it. The guide and this page should help you to get started with your simulations. Please refer to the Documentation section for a link to the guide.

  • Note on CIRCE: Make sure to run your jobs from your $WORK directory!
  • Note: Scripts are provided as examples only. Your SLURM executables, tools, and options may vary from the example below. For help on submitting jobs to the queue, see our SLURM User’s Guide.

Distributed Parallel

If, for example, you have an AutoDock input file named autodock.pdb, you would set up a submit script like this:

  • The script below (for testing, name it “autodock-test.sh”) can be copied into your job directory (the folder with your input files) and modified so that you can submit batch processes to the queue. For help on submitting jobs to the queue, see our SLURM User’s Guide. Scripts are provided as examples only. Your SLURM executables, tools, and options will vary.
#!/bin/bash
#
#SBATCH --comment=autodock-test
#SBATCH --ntasks=4
#SBATCH --job-name=autodock-test
#SBATCH --output=output.%j.autodock-test
#SBATCH --time=01:00:00

#### SLURM 4 processor AutoDock test to run for 1 hour.

module purge
module load apps/autogrid/4.2.3
module load apps/autodock/4.2.3

mpirun autogrid4 autodock.pdb
mpirun autodock4 autodock.pdb

 
Next, you can change to your job’s directory, and run the sbatch command to submit the job:

[user@login0 ~]$ cd my/jobdir
[user@login0 jobdir]$ sbatch ./autodock-test.sh
  • You can view the status of your job with the “squeue -u <username>” command

Documentation

Home Page, User Guides, and Manuals

More Job Information

See the following for more detailed job submission information:

Reporting Bugs

Report bugs with AutoDock to the IT Help Desk: rc-help@usf.edu