Ligand preparation - 20170424

From DISI
Revision as of 15:28, 12 April 2017 by TBalius (talk | contribs)
Jump to navigation Jump to search
The printable version is no longer supported and may have rendering errors. Please update your browser bookmarks and please use the default browser print function instead.

3 ways to build ligands:

1. Source the environment and run the stand-alone script:

  source /nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/env.sh
  sh $DOCKBASE/ligand/generate/build_database_ligand.sh mysmiles.smi


2. Source the environment and submit jobs:

  a. put these commands in cmd file:
     setenv DOCKBASE /nfs/soft/dock/versions/dock37/DOCK-3.7-trunk 
     setenv BUILD_ENVIRONMENT /nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/env.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 100 $1 $DOCKBASE/ligand/generate/build_database_ligand.sh
  b. run the script:
     csh cmd mysmiles.smi


3.



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.