Difference between revisions of "Ligand preparation - 20170424"

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== 3 ways to build ligands: ==
 
== 3 ways to build ligands: ==
  
1. Run the stand-alone script:
+
1. Source the environment and run the stand-alone script:
 
    
 
    
 
   source /nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/env.sh
 
   source /nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/env.sh
  $DOCKBASE/ligand/generate/build_database_ligand.sh
 
  
 +
  $DOCKBASE/ligand/generate/build_database_ligand.sh mysmiles.sh
  
2. Submit jobs:
 
  
  setenv DOCKBASE /nfs/soft/dock/versions/dock37/DOCK-3.7-trunk
+
2. Source the environment and submit jobs:
  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 \
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   a. put these commands in cmd file:
  "/nfs/scratch/A/xyz/protomer/qsub-mr-map.sh" -s $BUILD_ENVIRONMENT \
 
  -l 100 $1 $DOCKBASE/ligand/generate/build_database_ligand.sh
 
  
 +
      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.
  
  

Revision as of 22:54, 10 April 2017

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
  $DOCKBASE/ligand/generate/build_database_ligand.sh mysmiles.sh


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.