How to dock in DOCK3.8: Difference between revisions
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* 3. super script: | * 3. super script: | ||
for i in sdi/*.in ; do | <nowiki> | ||
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 | |||
</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
- 3a. to run for first time
sh super
- 4. how to restart (to make sure complete, iterate until complete)
sh super
- 5. check which output is valid (and broken or incomplete output)
- 6. extract all blazing fast
- 7. extract mol2
more soon, under active development, Jan 28.