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
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
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.cmdIf each autodock command requires more than 1 GB of RAM, submit with
swarm -g # -f myswarm.cmdwhere '#' 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