Building and Docking on CoreHPC

1. DOCK 3.8 — 3D Ligand Building & Docking

Workflow for building 3D ligands from a SMILES file and running docking on CoreHPC (SLURM).

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1. 1. 1. 3D Ligand Building

Source the DOCK environment:

```bash source /home/remote/jirwin3/fac/katiesoft/DOCK3.8/env.sh ```

Submit the building pipeline (Apptainer container, SLURM scheduler):

```bash 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 5HT2C_actives.smi ```

Launch the array job:

```bash sbatch building_array_job.sh ```

Collect the built bundles into an SDI file:

```bash find /path/to/building/output -maxdepth 2 -name "bundle.db2.tgz" > [sdi_file_name].sdi ```

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1. 1. 2. Docking

From a directory containing your dockfiles and the SDI file:

```bash bash /home/remote/jirwin3/fac/katiesoft/scripts/submit_docking.sh [sdi_file_name].sdi ```