Building and Docking on CoreHPC: Difference between revisions

From DISI
Jump to navigation Jump to search
mNo edit summary
mNo edit summary
Tag: Manual revert
 
(2 intermediate revisions by the same user not shown)
Line 27: Line 27:
== Docking ==
== Docking ==


From a directory containing your dockfiles and the SDI file, set the environment variables:
Run this from your working directory, which must contain your dockfiles and a subdirectory named 'sdi' holding your SDI file:
 
<syntaxhighlight lang="bash">
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">
<syntaxhighlight lang="bash">
bash /mnt/fac/CX900007_DS1/soft/super_dock3r.sh
bash /mnt/fac/CX900007_DS1/soft/super_dock3r.sh
</syntaxhighlight>
</syntaxhighlight>

Latest revision as of 21:25, 21 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_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

Run this from your working directory, which must contain your dockfiles and a subdirectory named 'sdi' holding your SDI file: 

bash /mnt/fac/CX900007_DS1/soft/super_dock3r.sh
Retrieved from "http://wiki.docking.org/index.php?title=Building_and_Docking_on_CoreHPC&oldid=17544"