Since the cluster does not support graphical interface, all preparations and calculations are done in a text-driven manner.
TUTORIAL 1 Autodock Vina on Linux Cluster with HTCondor
(last updated: April 18, 2017 – recompiled April 2019)
- Autodock Vina on Linux Cluster with HTCondor: (same content, different formats)
- PDBQT exercise files: protein | ligand
- Stefano Forli, Ruth Huey, Michael E Pique, Michel F Sanner, David S Goodsell & Arthur J Olson (2016), “Computational protein–ligand docking and virtual drug screening with the AutoDock suite“ Nature Protocols 11: 905–919, doi:10.1038/nprot.2016.051
- Trott, O.; Olson, A.J. (2010), “AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading”, Journal of Computational Chemistry, 31 (2): 455–461, doi:10.1002/jcc.21334
External video tutorial(s)
AutoDock Vina Tutorial by Sari Sabban
The following 1h long tutorial provides a python script to prepare data without Autodock Tools and offers many useful tools.
The Python script used during the video can be downloaded from github: AutoDock.py
During the video ligands are pulled from the Zinc15 database: