Building and Docking on CoreHPC

3D Ligand Building

Source the DOCK environment:

source /mnt/fac/CX900007_DS1/soft/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_folder_name] --bundle_size [bundle_size] --scheduler 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, 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 /mnt/fac/CX900007_DS1/soft/super_dock3r.sh