Building and Docking on Cluster 7: Difference between revisions
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(Created page with "== 3D Ligand Building == Source the DOCK environment: <syntaxhighlight lang="bash"> source /nfs/software/dock/versions/dock385/env.sh </syntaxhighlight> Submit the building pipeline (Apptainer container, SLURM scheduler): <syntaxhighlight lang="bash"> python $DOCK_INSTALL_PATH/zinc22-3d/submit/submit_building_docker.py --output_folder [output_folder_name] --bundle_size [bundle_size] --scheduler slurm --container_software apptainer --container_path_or_name $DOCK_INSTA...") |
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python $DOCK_INSTALL_PATH/zinc22-3d/submit/submit_building_docker.py --output_folder [output_folder_name] --bundle_size [bundle_size] --scheduler slurm --container_software apptainer --container_path_or_name $DOCK_INSTALL_PATH/ | python $DOCK_INSTALL_PATH/zinc22-3d/submit/submit_building_docker.py --output_folder [output_folder_name] --bundle_size [bundle_size] --scheduler slurm --container_software apptainer --container_path_or_name $DOCK_INSTALL_PATH/building_pipeline.sif [smiles].smi | ||
</syntaxhighlight> | </syntaxhighlight> | ||
Latest revision as of 21:56, 15 September 2026
3D Ligand Building
Source the DOCK environment:
source /nfs/software/dock/versions/dock385/env.sh
Submit the building pipeline (Apptainer container, SLURM scheduler):
python $DOCK_INSTALL_PATH/zinc22-3d/submit/submit_building_docker.py --output_folder [output_folder_name] --bundle_size [bundle_size] --scheduler slurm --container_software apptainer --container_path_or_name $DOCK_INSTALL_PATH/building_pipeline.sif [smiles].smi
Launch the array job:
sbatch building_array_job.sh
Collect the built bundles into an SDI file:
find /path/to/building/output -maxdepth 2 -name "bundle.db2.tgz" > [sdi_file_name].sdi
Docking
From a directory containing your dockfiles and the SDI file, set the environment variables:
export MOLECULES_DIR_TO_BIND=[outermost folder containing the molecules to dock]
export DOCKFILES=[path to your dockfiles]
export INPUT_FOLDER=[the folder containing your .sdi file(s)]
export OUTPUT_FOLDER=[where you want the output]
Then run the docking script:
bash /nfs/software/dock/versions/dock385/super_dock3r.sh