Difference between revisions of "Zinc22 restart wynton"

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I have used 28m and 30m cutoffs so jobs run in the fast queue.  
 
I have used 28m and 30m cutoffs so jobs run in the fast queue.  
 
If you are willing to wait for the slower queues, you can set this number higher. e.g. 2 hours.  
 
If you are willing to wait for the slower queues, you can set this number higher. e.g. 2 hours.  
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== resubmit stage ==
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== check which done, which not done ==
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== ready to do combine?  ==
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ls -1d h*/[0-9]* > dirlist
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$DOCKBASE/analysis/extract_all_blazing_fast.py dirlist extract_all.txt 30
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sort -n -k 22 extract_all.txt > extract_all.sort.uniq.txt
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python getposes_blazing_faster.py ./ extract_all.txt 100 poses.mol2 test.mol2.gz
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[[Category:ZINC22]]
 
[[Category:ZINC22]]
 
[[Category:DOCK22]]
 
[[Category:DOCK22]]

Latest revision as of 21:46, 18 January 2021

This is a temporary page describing how to use DOCK 3.8 restartable on Wynton.

  • prepare your grids as usual
  • copy from /wynton/group/bks/work/jji/p1/super
  • rename your dockfiles to dockfiles.${indockhash} where
 indockhash=$(cat INDOCK | shasum | awk '{print substr($1, 1, 12)}')
  • create sdi files for the tranches you want to run. copy and edit how4
  • update super to refer to your situation
sh super
  • this will launch dock jobs

I have used 28m and 30m cutoffs so jobs run in the fast queue. If you are willing to wait for the slower queues, you can set this number higher. e.g. 2 hours.

resubmit stage

check which done, which not done

ready to do combine?

ls -1d h*/[0-9]* > dirlist
$DOCKBASE/analysis/extract_all_blazing_fast.py dirlist extract_all.txt 30 
sort -n -k 22 extract_all.txt > extract_all.sort.uniq.txt
python getposes_blazing_faster.py ./ extract_all.txt 100 poses.mol2 test.mol2.gz