How to dock in DOCK3.8

From DISI
Revision as of 19:04, 28 January 2021 by Frodo (talk | contribs) (asdf)
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to navigation Jump to search

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
sh super