Building and Docking on CoreHPC: Difference between revisions

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<syntaxhighlight lang="bash">
<syntaxhighlight lang="bash">
source /home/remote/jirwin3/fac/katiesoft/env.sh
source /mnt/fac/CX900007_DS1/soft/DOCK3.8/env.sh
</syntaxhighlight>
</syntaxhighlight>


Line 27: Line 27:
== Docking ==
== Docking ==


From a directory containing your dockfiles and the SDI file:
From a directory containing your dockfiles and the SDI file, set the environment variables:


<syntaxhighlight lang="bash">
<syntaxhighlight lang="bash">
bash /home/remote/jirwin3/fac/katiesoft/scripts/submit_docking.sh [sdi_file_name].sdi
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]
</syntaxhighlight>
 
Then run the docking script:
 
<syntaxhighlight lang="bash">
bash /mnt/fac/CX900007_DS1/soft/super_dock3r.sh
</syntaxhighlight>
</syntaxhighlight>
```

Revision as of 19:28, 10 September 2026

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 --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, 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
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