How to dock in DOCK3.8

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

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

EXPORT_DEST

EXPORT_DEST should be 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.

DOCKEXEC

DOCKEXEC should be an NFS path to a DOCK binary executable (NOT a wrapper script).

DOCKFILES

DOCKFILES should be 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

SHRTCACHE

SHRTCACHE is 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.

LONGCACHE

LONGCACHE is 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.

SBATCH_ARGS

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

QSUB_ARGS

Optional arguments 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/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

bash
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 $k
	export INPUT_SOURCE=$WORKDIR/$i
	export EXPORT_DEST=$WORKDIR/output/$k
	$DOCKBASE/docking/submit/sge/subdock.bash
done

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.