How to dock in DOCK3.8: Difference between revisions

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* 3. super script:
* 3. super script:
export DOCKBASE=/wynton/group/bks/work/jji/DOCK
export WORKDIR=/wynton/home/shoichetlab/jji/work/p2
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
  <nowiki>
export k=$(basename $i .in)
export DOCKBASE=/wynton/group/bks/work/jji/DOCK
export WORKDIR=/wynton/home/shoichetlab/jji/work/p2
export DOCKFILES=$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"
</nowiki>
 
<nowiki>
 
for i in  sdi/*.in  ; do
        export k=$(basename $i .in)
echo k $k
echo k $k
export INPUT_SOURCE=$WORKDIR/$i
export INPUT_SOURCE=$WORKDIR/$i
export EXPORT_DEST=$WORKDIR/output/$k
export EXPORT_DEST=$WORKDIR/output/$k
$DOCKBASE/docking/submit/subdock.bash
$DOCKBASE/docking/submit/subdock.bash
done
done
</nowiki>


# 3a. to run for first time
# 3a. to run for first time

Revision as of 21:13, 28 January 2021

How to dock in DOCK 3.8.0

  • 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($1, 1, 12)}')
  • 3. super script:
export DOCKBASE=/wynton/group/bks/work/jji/DOCK
export WORKDIR=/wynton/home/shoichetlab/jji/work/p2
export DOCKFILES=$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/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.

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