Difference between revisions of "How to dock in DOCK3.8"

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export SHRTCACHE=/scratch
export SHRTCACHE=/scratch
export LONGCACHE=/scratch
export LONGCACHE=/scratch
export QSUB_ARGS="-l s_rt=01:58:00 -l h_rt=02:00:00"
export QSUB_ARGS="-l s_rt=00:28:00 -l h_rt=00:30:00"

Revision as of 16:56, 24 February 2021

How to dock in DOCK 3.8.0

Differences from DOCK.3.7

DOCK 3.8.0 can be interrupted safely and restarted, which allows more flexibility when submitting docking jobs.

For example, you could set QSUB_ARGS="-l s_rt=00:05:00 -l h_rt=00:07:00" (or SBATCH_ARGS="--time=00:07:00") so that each docking job will only run for 5 minutes before being interrupted. The new subdock.bash script allows submitting the same set of jobs multiple times, until they are all complete. A more pragmatic choice might be "-l s_rt=00:28:00 -l h_rt=00:30:00" to get the benefit of faster scheduling on wynton in the short.q. Another advantage is that the job can be interrupted at any time on AWS and it will checkpoint and be restartable.

Running the Script

New subdock scripts are here:

$DOCKBASE/docking/submit/sge/subdock.bash $DOCKBASE/docking/submit/slurm/subdock.bash

subdock.bash requires a number of environmental variables to be passed as arguments.

Required Arguments


INPUT_SOURCE should be either:

a) A directory containing one or more db2.tgz files OR

b) A text file containing a list of paths to db2.tgz files

A db2.tgz file should be a tarred + gzipped archive (tar -czf archive.tgz) that contains one or more db2 or db2.gz files.

A job will be launched for each db2.tgz file in INPUT_SOURCE.


A directory on the NFS where you would like your docking output to end up. If the directory does not exist, the script will try to create it.


An NFS path to a DOCK binary executable (NOT a wrapper script).


An NFS path to the dockfiles (INDOCK, spheres, receptor files, grids, etc.) being used for this docking run. The dockfiles directory should be named uniquely, to avoid confusion with other dockfiles other users may be running.

Optional Arguments


The directory DOCK will perform it's work in. Files saved to this directory will be deleted once the docking job has concluded. By default this is /dev/shm.


The directory DOCK will store files that are shared between multiple docking jobs. Files saved to this directory (dockexec and dockfiles) will persist until they are deleted. By default this directory is /tmp.

Beware of using the default SHRTCACHE or LONGCACHE settings on large clusters.


Additional arguments to provide to slurm's sbatch, if using the slurm version of subdock.bash.


Additional arguments to provide to sge's qsub, if using the sge version of subdock.bash


BKS Example

export INPUT_SOURCE=example.in
export OUTPUT_DEST=output
export DOCKEXEC=$DOCKBASE/docking/DOCK/bin/dock64
export DOCKFILES=dockfiles.example
export SHRTCACHE=/dev/shm
export LONGCACHE=/tmp
export SBATCH_ARGS="--time=02:00:00"


Wynton Example

export INPUT_SOURCE=example.in
export OUTPUT_DEST=output
export DOCKEXEC=$DOCKBASE/docking/DOCK/bin/dock64
export DOCKFILES=dockfiles.example
export SHRTCACHE=/scratch
export LONGCACHE=/scratch
export QSUB_ARGS="-l s_rt=00:28:00 -l h_rt=00:30:00"


Example: Running a lot of docking jobs

  • 1. set up sdi files
mkdir sdi
export sdi=sdi
ls /wynton/group/bks/zinc-22/H19/H19P0??/*.db2.tgz > $sdi/h19p0.in
ls /wynton/group/bks/zinc-22/H19/H19P1??/*.db2.tgz > $sdi/h19p1.in
ls /wynton/group/bks/zinc-22/H19/H19P2??/*.db2.tgz > $sdi/h19p2.in
ls /wynton/group/bks/zinc-22/H19/H19P3??/*.db2.tgz > $sdi/h19p3.in
and so on
  • 2. set up INDOCK and dockfiles. rename dockfiles to dockfiles.$indockhash. On some nodes, the shasum command is called by sha1sum. Ultimately, renaming the dockfiles to a unique dockfiles is key.
indockhash=$(cat INDOCK | shasum | awk '{print substr($1, 1, 12)}')
  • 3. super script:
export DOCKBASE=/wynton/group/bks/work/jji/DOCK
export DOCKFILES=$WORKDIR/dockfiles.21751f1bb16b
export DOCKEXEC=$DOCKBASE/docking/DOCK/bin/dock64
#export SHRTCACHE=/dev/shm # default
export SHRTCACHE=/scratch
#export LONGCACHE=/scratch # default
export QSUB_ARGS="-l s_rt=00:28:00 -l h_rt=00:30:00 -l mem_free=2G"

for i in  sdi/*.in  ; do
        export k=$(basename $i .in)
	echo k $k
	export INPUT_SOURCE=$PWD/$i
	export EXPORT_DEST=$PWD/output/$k

  1. 3a. to run for first time
sh super
  1. 4. how to restart (to make sure complete, iterate until complete)
sh super
  1. 5. check which output is valid (and broken or incomplete output)
  1. 6. extract all blazing fast
  1. 7. extract mol2

more soon, under active development, Jan 28.