Zinc22 restart wynton: Difference between revisions
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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. | ||
== resubmit stage == | |||
== check which done, which not done == | |||
== ready to do combine? == | |||
ls -1d h*/[0-9]* > dirlist | |||
$DOCKBASE/analysis/extract_all_blazing_fast.py dirlist extract_all.txt 30 | |||
sort -n -k 22 extract_all.txt > extract_all.sort.uniq.txt | |||
python getposes_blazing_faster.py ./ extract_all.txt 100 poses.mol2 test.mol2.gz | |||
[[Category:ZINC22]] | [[Category:ZINC22]] | ||
[[Category:DOCK22]] | [[Category:DOCK22]] | ||
Latest revision as of 05:46, 19 January 2021
This is a temporary page describing how to use DOCK 3.8 restartable on Wynton.
- prepare your grids as usual
- copy from /wynton/group/bks/work/jji/p1/super
- rename your dockfiles to dockfiles.${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