Building and Docking on CoreHPC: Difference between revisions
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(Created page with "3D LIGAND BUILDING: source /home/remote/jirwin3/fac/katiesoft/DOCK3.8/env.sh 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 sbatch building_array_job.sh find /path/to/building/output -maxdepth 2 -name "bundle.db2.tgz" > [sdi_file_name}.sdi DOCKING: in a...") |
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3D | == 3D Ligand Building == | ||
Source the DOCK environment: | |||
<syntaxhighlight lang="bash"> | |||
source /home/remote/jirwin3/fac/katiesoft/DOCK3.8/env.sh | source /home/remote/jirwin3/fac/katiesoft/DOCK3.8/env.sh | ||
</syntaxhighlight> | |||
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 | <syntaxhighlight lang="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 [smiles].smi | |||
</syntaxhighlight> | |||
Launch the array job: | |||
<syntaxhighlight lang="bash"> | |||
sbatch building_array_job.sh | sbatch building_array_job.sh | ||
</syntaxhighlight> | |||
Collect the built bundles into an SDI file: | |||
<syntaxhighlight lang="bash"> | |||
find /path/to/building/output -maxdepth 2 -name "bundle.db2.tgz" > [sdi_file_name].sdi | |||
</syntaxhighlight> | |||
== Docking == | |||
From a directory containing your dockfiles and the SDI file: | |||
<syntaxhighlight lang="bash"> | |||
bash /home/remote/jirwin3/fac/katiesoft/scripts/submit_docking.sh [sdi_file_name].sdi | bash /home/remote/jirwin3/fac/katiesoft/scripts/submit_docking.sh [sdi_file_name].sdi | ||
</syntaxhighlight> | |||
``` | |||
Latest revision as of 15:57, 13 August 2026
3D Ligand Building
Source the DOCK environment:
source /home/remote/jirwin3/fac/katiesoft/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
```