http://wiki.docking.org/index.php?action=history&feed=atom&title=Building_and_Docking_on_Cluster_7 2026-09-22T20:42:24Z Revision history for this page on the wiki MediaWiki 1.39.1 http://wiki.docking.org/index.php?title=Building_and_Docking_on_Cluster_7&diff=17520&oldid=prev 2026-09-15T21:56:33Z

<p></p> <table style="background-color: #fff; color: #202122;" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 21:56, 15 September 2026</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l10">Line 10:</td> <td colspan="2" class="diff-lineno">Line 10:</td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;syntaxhighlight lang=&quot;bash&quot;&gt;</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;syntaxhighlight lang=&quot;bash&quot;&gt;</div></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>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/<del style="font-weight: bold; text-decoration: none;">building_pipeline_oss</del>.sif [smiles].smi</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>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/<ins style="font-weight: bold; text-decoration: none;">building_pipeline</ins>.sif [smiles].smi</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;/syntaxhighlight&gt;</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;/syntaxhighlight&gt;</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr> <!-- diff cache key wikidb:diff::1.12:old-17519:rev-17520 --> </table>

Kholland http://wiki.docking.org/index.php?title=Building_and_Docking_on_Cluster_7&diff=17519&oldid=prev 2026-09-15T21:56:10Z

<p>Created page with &quot;== 3D Ligand Building == Source the DOCK environment: &lt;syntaxhighlight lang=&quot;bash&quot;&gt; source /nfs/software/dock/versions/dock385/env.sh &lt;/syntaxhighlight&gt; Submit the building pipeline (Apptainer container, SLURM scheduler): &lt;syntaxhighlight lang=&quot;bash&quot;&gt; 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_INSTA...&quot;</p> <p><b>New page</b></p><div>== 3D Ligand Building ==<br /> <br /> Source the DOCK environment:<br /> <br /> &lt;syntaxhighlight lang=&quot;bash&quot;&gt;<br /> source /nfs/software/dock/versions/dock385/env.sh<br /> &lt;/syntaxhighlight&gt;<br /> <br /> Submit the building pipeline (Apptainer container, SLURM scheduler):<br /> <br /> &lt;syntaxhighlight lang=&quot;bash&quot;&gt;<br /> 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<br /> &lt;/syntaxhighlight&gt;<br /> <br /> Launch the array job:<br /> <br /> &lt;syntaxhighlight lang=&quot;bash&quot;&gt;<br /> sbatch building_array_job.sh<br /> &lt;/syntaxhighlight&gt;<br /> <br /> Collect the built bundles into an SDI file:<br /> <br /> &lt;syntaxhighlight lang=&quot;bash&quot;&gt;<br /> find /path/to/building/output -maxdepth 2 -name &quot;bundle.db2.tgz&quot; &gt; [sdi_file_name].sdi<br /> &lt;/syntaxhighlight&gt;<br /> <br /> == Docking ==<br /> <br /> From a directory containing your dockfiles and the SDI file, set the environment variables:<br /> <br /> &lt;syntaxhighlight lang=&quot;bash&quot;&gt;<br /> export MOLECULES_DIR_TO_BIND=[outermost folder containing the molecules to dock]<br /> export DOCKFILES=[path to your dockfiles]<br /> export INPUT_FOLDER=[the folder containing your .sdi file(s)]<br /> export OUTPUT_FOLDER=[where you want the output]<br /> &lt;/syntaxhighlight&gt;<br /> <br /> Then run the docking script:<br /> <br /> &lt;syntaxhighlight lang=&quot;bash&quot;&gt;<br /> bash /nfs/software/dock/versions/dock385/super_dock3r.sh<br /> &lt;/syntaxhighlight&gt;</div>

Kholland