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Autodock on Biowulf
autodock

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 was developed at the Scripps Research Institute in San Diego.

Autodock on Biowulf is intended for large-scale Autodock processing. Since the program is single-threaded, a single job cannot be parallelized over multiple processors. The best reason to run Autodock on the Biowulf cluster would be to run large numbers of Autodock jobs with different parameters or input files simultaneously.

It is not recommended that the Autodock-related graphics tools be run on the Biowulf cluster.

The Autodock Vina program (/usr/local/bin/vina) is also available on the Biowulf cluster. AutoDock Vina is a new program for drug discovery, molecular docking and virtual screening, offering multi-core capability, high performance and enhanced accuracy and ease of use

Submitting a single Autodock batch job

Set up a job script along the following lines:

#!/bin/bash
#
#this file is Myjob.sh
#
#PBS -N Autodock
#PBS -m be
#PBS -k oe
#

cd $PBS_O_WORKDIR
autodock4 -p myfile.dpf -l myfile.dlg 

Submit this job:

qsub -l nodes=1 Myjob.sh
Submitting a swarm of Autodock jobs

Set up a swarm command file with a single line for each Autodock command. e.g.

--------file myswarm.cmd---------------
autodock4 -p /data/user/mydir/lig1.macro.dpf -l /data/user/mydir/llig1.log
autodock4 -p /data/user/mydir/llig2.macro.dpf -l /data/user/mydir/llig2.log
autodock4 -p /data/user/mydir/llig3.macro.dpf -l /data/user/mydir/llig3.log
autodock4 -p /data/user/mydir/llig4.macro.dpf -l /data/user/mydir/llig4.log
[...]

If each autodock command requires less than 1 GB of RAM, submit this swarm of jobs with a command like:

swarm -f myswarm.cmd
If each autodock command requires more than 1 GB of RAM, submit with
swarm -g # -f myswarm.cmd
where '#' is the number of Gigabytes required by each autodock command. See the swarm web page for more information about swarm options.

It may be more convenient to separate the files for each autodock run into individual directories. In this case, the swarm command file could be set up as follows:

--------file myswarm.cmd---------------
cd /data/user/mydir1; autodock4 -p lig1.macro.dpf -l llig1.log
cd /data/user/mydir2; autodock4 -p lig2.macro.dpf -l llig2.log
cd /data/user/mydir3; autodock4 -p lig3.macro.dpf -l llig3.log
Documentation

Autodock website.
Autodock Vina website
Autodock Vina manual
Autodock User Guide
Autodock Tutorials