https://hpc.mediawiki.hull.ac.uk/index.php?action=history&feed=atom&title=Applications%2FAutodockVina 2026-04-29T15:40:14Z Revision history for this page on the wiki MediaWiki 1.31.16 https://hpc.mediawiki.hull.ac.uk/index.php?title=Applications/AutodockVina&diff=41877&oldid=prev 2025-07-21T16:07:57Z

<p>Created page with &quot;==Application Details== * Versions: 1.1.2 (old) and &#039;&#039;&#039;1.2.7&#039;&#039;&#039; (current) * Module names: autodock/vina/1.1.2 and &#039;&#039;&#039;autodock/vina/1.2.7&#039;&#039;&#039; ==Autodock Vina== AutoDock Vina...&quot;</p> <p><b>New page</b></p><div>==Application Details==<br /> * Versions: 1.1.2 (old) and '''1.2.7''' (current)<br /> * Module names: autodock/vina/1.1.2 and '''autodock/vina/1.2.7'''<br /> <br /> ==Autodock Vina==<br /> <br /> AutoDock Vina is an open-source program for doing molecular docking. It was originally designed and implemented by Dr. Oleg Trott in the Molecular Graphics Lab (now CCSB) at The Scripps Research Institute [https://vina.scripps.edu/ https://vina.scripps.edu/]<br /> <br /> <br /> ==Use on HPC==<br /> <br /> ===Job Submission Script===<br /> Example Job Submission Script:<br /> &lt;pre style=&quot;background-color: #E5E4E2; color: black; font-family: monospace, sans-serif;&quot;&gt;<br /> #!/bin/bash<br /> #SBATCH --job-name=vina_test<br /> #SBATCH --output=vina_%j.out<br /> #SBATCH --error=vina_%j.err<br /> #SBATCH --time=00:30:00<br /> #SBATCH --ntasks=1<br /> #SBATCH --cpus-per-task=4<br /> #SBATCH --mem=4G<br /> <br /> module load autodock/vina/1.2.7<br /> <br /> vina --config data/receptor_config.txt --ligand data/ligand.pdbqt --out receptor-ligand.pdbqt<br /> &lt;/pre&gt;<br /> <br /> =====Interactive=====<br /> &lt;pre style=&quot;background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;&quot;&gt;<br /> [username@viperlogin ~]$ interactive<br /> [username@viperlogin ~]$ interactive<br /> salloc: Pending job allocation 268597<br /> salloc: job 268597 queued and waiting for resources<br /> salloc: job 268597 has been allocated resources<br /> salloc: Granted job allocation 268597<br /> salloc: Waiting for resource configuration<br /> salloc: Nodes c109 are ready for job<br /> Job ID 268597 connecting to c109, please wait...<br /> [username@c109 ~]$ module add autodock/vina/1.2.7<br /> [username@c109 ~]$ vina --help<br /> AutoDock Vina v1.2.7<br /> <br /> Input:<br /> --receptor arg rigid part of the receptor (PDBQT)<br /> --flex arg flexible side chains, if any (PDBQT)<br /> --ligand arg ligand (PDBQT)<br /> --batch arg batch directory or ligands (PDBQT)<br /> --scoring arg (=vina) scoring function (ad4, vina or vinardo)<br /> &lt;etc&gt;<br /> &lt;/pre&gt;<br /> <br /> ===Visualisation===<br /> Autodock Vina also contains [[https://ccsb.scripps.edu/mgltools/ MGLTools]] for visualisation. To access these, please start a Visualisation node session on Viper OnDemand via [[https://viperood.hpc.hull.ac.uk/pun/sys/dashboard/batch_connect/sys/Visu-VNC-gnome https://viperood.hpc.hull.ac.uk/pun/sys/dashboard/batch_connect/sys/Visu-VNC-gnome]] (see [https://hpc.mediawiki.hull.ac.uk/General/OOD Viper Open On Demand] for more details). Once in a session:<br /> <br /> &lt;pre style=&quot;background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;&quot;&gt;<br /> [username@visu01 ~]$ module add autodock/vina/1.2.7<br /> [username@visu01 ~]$ vglrun pmv<br /> &lt;/pre&gt;<br /> <br /> This enables you to run pmv, adt, vision and pythonsh<br /> <br /> ==Further Information==<br /> <br /> {{Licensepagenav}}</div>

Chris.collins