How to dock in DOCK3.8

Revision as of 19:04, 28 January 2021 by Frodo (talk | contribs) (asdf)
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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/
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($1, 1, 12)}')
  • 3. super script:
export DOCKBASE=/wynton/group/bks/work/jji/DOCK
export WORKDIR=/wynton/home/shoichetlab/jji/work/p2
export DOCKFILES=$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

sh super