Difference between revisions of "How to dock in DOCK3.8"

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  done
 
  done
  
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# 3a. to run for first time
 
  sh super
 
  sh super
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# 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.

Revision as of 19:10, 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.