How to dock in DOCK3.8

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How to dock in DOCK 3.8.0

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 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.


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

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/
ls /wynton/group/bks/zinc-22/H19/H19P1??/*.db2.tgz > $sdi/
ls /wynton/group/bks/zinc-22/H19/H19P2??/*.db2.tgz > $sdi/
ls /wynton/group/bks/zinc-22/H19/H19P3??/*.db2.tgz > $sdi/
and so on
  • 2. set up INDOCK and dockfiles. rename dockfiles to dockfiles.$indockhash
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.