AutoDock Vina Example

AutoDock Vina is generally used to model molecular docking and for virtual screening; a process important for drug discovery and other molecular analysis. AutoDock Vina is an improved version with superior local search routine and makes use of multicore/multi-CPU computer setups.

With its simple workflow, Rescale’s ScaleX platform can be used to run complicated molecular docking sequences using AutoDock Vina in batch mode.

autodock vina 1
Import Job Setup
Get Job Results
Simulation CodeAutoDock Vina 4.2.5.1
Analysis TypeMolecular Docking & Virtual Screening
DescriptionThis is a molecular docking job using Vina 4.2.5.1. It first prepares the .pdb files and turns them into .pdbqt files required by Vina using the AutoDock utilities. It then runs AutoDock Vina using the conf.txt file.
Suggested HardwareTitanium / 4 cores
Command 
pythonsh $AUTODOCKUTILS/prepare_receptor4.py -r protein.pdb;
pythonsh $AUTODOCKUTILS/prepare_ligand4.py -l ligand.pdb;
vina --config conf.txt
Estimated Run Time3 minutes