Building and Docking on CoreHPC: Difference between revisions

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# DOCK 3.8 — 3D Ligand Building & Docking
== 3D Ligand Building ==
 
Workflow for building 3D ligands from a SMILES file and running docking on CoreHPC (SLURM).
 
---
 
## 1. 3D Ligand Building


Source the DOCK environment:
Source the DOCK environment:


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


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


```bash
<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 5HT2C_actives.smi
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
```
</syntaxhighlight>


Launch the array job:
Launch the array job:


```bash
<syntaxhighlight lang="bash">
sbatch building_array_job.sh
sbatch building_array_job.sh
```
</syntaxhighlight>


Collect the built bundles into an SDI file:
Collect the built bundles into an SDI file:


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


## 2. Docking
== Docking ==


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


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