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How to generate config file for docking using Autodock Tools?

Dr. Muniba Faiza

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How to generate config file for docking using Autodock Tools?

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 [1].

  1. 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.
  2. Click '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’.
  3. Browse for receptor and ligand pdbqt files.
  4. Enter center coordinates from grid file.
  5. Browse for the directory where youwant to save the config file by clicking on 'Browse'tab present after 'Out'option.
  6. Enter the name of the output log file and configuration file.
  7. Click on 'Show options'. Here, you can set the number of modes and exhaustiveness for docking.
  8. After setting every value according to your requirements, click 'Save'. You will find ‘config.txt’ in your directory.

References

  1. 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 chemistry30(16), 2785-2791.

Dr. Muniba is a Bioinformatician based in New Delhi, India. She has completed her PhD in Bioinformatics from South China University of Technology, Guangzhou, China. She has cutting edge knowledge of bioinformatics tools, algorithms, and drug designing. When she is not reading she is found enjoying with the family. Know more about Muniba

Docking

How to install Autodock on Ubuntu (Linux) with CUDA GPU support?

Dr. Muniba Faiza

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How to install Autodock on Ubuntu (Linux) with CUDA GPU support?

Autodock [1] is most widely used for docking. To accelerate the docking process, especially, during virtual screening, Autodock-GPU [2] provides great help. In this article, we are going to install Autodock-GPU on Ubuntu. (more…)

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Docking

Autodock Vina: Uses & Applications

Tariq Abdullah

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Autodock Vina: Uses & Applications

Autodock Vina [1] is one of the most widely used bioinformatics software for computational docking. For beginners and those who are new to the field of bioinformatics, such software may appear confusing without having an initial idea of what this software actually used for. In this article, we have discussed some of the primary uses and applications of Autodock Vina software. (more…)

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Docking

How to perform virtual screening using Pyrx?

Dr. Muniba Faiza

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How to perform virtual screening using Pyrx?

Pyrx is a bioinformatics tool to perform virtual screening [1]. We previously provided an article on performing simple protein-ligand site-specific docking using Pyrx. In this article, we are going to perform virtual screening using Pyrx. (more…)

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