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MGL Tools & Autodock Vina installation: Frequently Asked Questions and Answers

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I have been receiving several e-mails from researchers and students alike regarding the installation of MGL Tools and Autodock Vina on Ubuntu. Most questions are similar in nature, so I thought of answering them once and for all. In this article, I have collected some frequently asked questions and provided the link to their answers present in our question-answer section of Bioinformatics Review.

Question: Error in running autodock vina adt mgltools on Linux.

Question: Error while trying to open Autodock tools.

Question: Problem in launching Autodock tools from the terminal.

Question: Problem in moving Autogrid and Autodock.

Question: How should I use “pmv” or “adt”?

Question: Error in running Autodock Vina from the terminal.

Question: Unable to run Autodock using “adt” alias.

Question: Error while installing mgltools.

If these are not the questions you are looking for, then feel free to ask in our ‘Bioinformatics Discussion‘ section or write to [email protected].

Tariq is founder of Bioinformatics Review and CEO at IQL Technologies. His areas of expertise include algorithm design, phylogenetics, MicroArray, Plant Systematics, and genome data analysis. If you have questions, reach out to him via his homepage.

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How to calculate binding pocket volume using PyVol plugin in PyMol?

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How to calculate binding pocket volume using PyVol plugin in PyMol?

Previously, we provided a tutorial for PyVol plugin [1] installation. In this article, we will calculate the binding pocket volume of protein using the same plugin in PyMol [2]. (more…)

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How to generate electron density map using Pymol?

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How to generate electron density map using Pymol?

Electron density maps are available for most of the protein structures in PDB. Therefore, in this article, we are using PDB to generate electron density maps in Pymol.

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Installing PyVOL plugin in Pymol on Ubuntu (Linux).

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Installing PyVOL plugin in Pymol on Ubuntu (Linux).

PyVOL [1] is an excellent plugin of Pymol [2] for pocket visualization of proteins. In this article, we will install the PyVOL plugin in Pymol on Ubuntu. (more…)

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