A configuration file is one of the required files for docking using Autodock Vina. In this article, we are going to generate a config file using Autodock Tools GUI .
- Open ADT on by typing ‘
$ adt‘ in a terminal on Ubuntu and by launching ADT GUI either by double clicking on shortcut or by searching for it on Windows.
'Docking'from next to the top menu, then go to
'Output' --> 'Vina Config(config.txt)...'. It will show a new window entitled ‘Vina Output Parameters’.
- Browse for receptor and ligand pdbqt files.
- Enter center coordinates from grid file.
- Browse for the directory where youwant to save the config file by clicking on
'Browse'tab present after
- Enter the name of the output log file and configuration file.
- Click on
'Show options'. Here, you can set the number of modes and exhaustiveness for docking.
- After setting every value according to your requirements, click
'Save'. You will find ‘config.txt’ in your directory.
- Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., & Olson, A. J. (2009). AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. Journal of computational chemistry, 30(16), 2785-2791.
What values are considered as good or bad in computational docking?
How to sort binding affinities based on a cutoff using vs_analysis.py script?
Previously, we have provided a Python script (vs_analysis.py) to analyze the virtual screening (VS) results of Autodock Vina. Now, we have updated this script to sort binding affinities based on user inputted cutoff value. (more…)
Virtual Screening using Autodock Vina: Frequently Asked Questions & Answers for Starters
Virtual Screening (VS) is one of the important techniques in bioinformatics. It can be easily performed using Autodock Vina. We have provided detailed articles on this topic. In this article, we are trying to answer some FAQs for beginners. (more…)