Building and Docking on CoreHPC: Difference between revisions
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source /home/remote/jirwin3/ | source /home/remote/jirwin3/soft/dock385/DOCK3.8/env.sh | ||
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Revision as of 18:59, 8 September 2026
3D Ligand Building
Source the DOCK environment:
source /home/remote/jirwin3/soft/dock385/DOCK3.8/env.sh
Submit the building pipeline (Apptainer container, SLURM scheduler):
python $DOCK_INSTALL_PATH/zinc22-3d/submit/submit_building_docker.py --output_folder output --bundle_size 5 --skip_name_check --schedule slurm --container_software apptainer --container_path_or_name $DOCK_INSTALL_PATH/building_pipeline_oss.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:
bash /home/remote/jirwin3/fac/katiesoft/scripts/submit_docking.sh [sdi_file_name].sdi
```