AutoDock Vina is a free and open source simulation program for molecular modeling and in particular for docking. Molecular docking is a computer simulation of how a ligand might bind to a target. It is widely used for drug discovery and development. This article showcases with a simple example how to run a docking simulation with AutoDock Vina on Qarnot’s cloud computing platform.
The test case uses a AutoDock Vina version 1.1.2.
If you are interested in another version, please send us an email at email@example.com.
Before launching the case, please ensure that the following prerequisites have been met.
This test case is a simple example of using AutoDock Vina on Qarnot cloud with the Python SDK. It showcases the docking of Indinavir, an HIV-1 protease inhibitor, used as an antiretroviral in the treatment of AIDS. The ligand, the target and the configuration file needed to launch the simulation can be downloaded from here. You need to unzip the indinavir-HIV-docking.zip archive to be able to launch the computation on Qarnot cloud.
Launching the case
Copy the following code in a Python script and save it in the same path as the indinavir-HIV-docking folder.
Be sure you have copied your authentication token in the script (instead of <<<MY_SECRET_TOKEN>>>) to be able to launch the task on Qarnot cloud.
Make sure that all input files (2 pdbqt file and 1 config.txt file) are in the same folder named indinavir-HIV-docking. Your working directory should look like this :
config.txt : for readability, some command line options have been placed in a configuration file.
hsg1.pdbqt : crystal structure of human HIV.
ind.pdbqt : preprocessed Indinavir ligand.
autodock.py : Python script to run the computation on Qarnot cloud.
To launch this script, open a terminal in your working directory and execute python3 autodock.py &.
At any given time, you can monitor the status of your task on the Console.
Successful AutoDock Vina execution on Qarnot’s cloud Console
You should now have an output folder in your working directory on your computer and a autodock-out bucket on Qarnot’s coud Console containing the output (results.pdbqt file, see bellow).