Building and Docking on CoreHPC

3D Ligand Building

Source the DOCK environment:

source /home/remote/jirwin3/fac/katiesoft/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

```