Ligand preparation - 20170424: Difference between revisions
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"/nfs/scratch/A/xyz/protomer/qsub-mr-map.sh" -s $BUILD_ENVIRONMENT \ | "/nfs/scratch/A/xyz/protomer/qsub-mr-map.sh" -s $BUILD_ENVIRONMENT \ | ||
-l 300 $1 $DOCKBASE/ligand/generate/build_database_ligand.sh | -l 300 $1 $DOCKBASE/ligand/generate/build_database_ligand.sh | ||
If you have any trouble using this (which the procedure used to build ZINC between July 14, 2016 and Nov 14, 2016 (ongoing), | |||
please contact me. I would be happy to help debug, as it will help us to make this procedure more robust. | |||
[[Category:Curator]] | [[Category:Curator]] | ||
Revision as of 18:01, 14 November 2016
set up environment: jchem mitools, DOCK3.7, ZINC, corina
source /nfs/soft/jchem/current/env.csh source /nfs/soft/mitools/env.csh source /nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/env.csh deactivate source /nfs/soft/www/apps/zinc15/envs/edge/env.csh source /nfs/soft/corina/current/env.csh setenv EMBED_PROTOMERS_3D_EXE $DOCKBASE/ligand/3D/embed3d_corina.sh setenv ZINC_CONFIG_ENV admin setenv ZINC_CONFIG_SETUP_SKIP blueprints
step 2. csh cmd mysmiles.ism
# put any change in the BUILD_ENVIRONMENT source /nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/env.csh source /nfs/soft/corina/current/env.csh setenv EMBED_PROTOMERS_3D_EXE $DOCKBASE/ligand/3D/embed3d_corina.sh setenv BUILD_ENVIRONMENT /nfs/home/xyz/bin/dockenvNS.sh # /nfs/soft/tools/utils/qsub-slice/qsub-mr-meta -tc 10 -L 100000 --map-instance-script \ "/nfs/scratch/A/xyz/protomer/qsub-mr-map.sh" -s $BUILD_ENVIRONMENT \ -l 300 $1 $DOCKBASE/ligand/generate/build_database_ligand.sh
If you have any trouble using this (which the procedure used to build ZINC between July 14, 2016 and Nov 14, 2016 (ongoing), please contact me. I would be happy to help debug, as it will help us to make this procedure more robust.