Connect with us

Software

[Tutorial] How to install Autodock Vina on Mac OS?

Published

on

[Tutorial] How to install Autodock Vina on MacOS?

We have provided several articles on Vina [1] installation on Ubuntu including the video tutorials. In this article, we are going to install Autodock Vina on Mac OS.

Installing prerequisites

You have to install a Windows system implementation to run X11-based applications on Mac OS X. You will install Apple X11 for up to Mac OS v10.3 and XQuartz for Mac OS v11 and above. Download Apple X11 from here and XQuartz from here depending on your system’s configuration.

After downloading the dmg file, double-click on it. It will ask for permissions and start verifying the downloaded file and will show a .pkg file. Again, double-click on it and continue with the steps. It will take a few minutes to finish the installation. Further, it will ask you to drag this into the Applications folder, do as it says. You can move the downloaded dmg file to the trash.

Downloading MGLTools for Mac OS

Currently, MGLTools is not working on Mac Catalina. If you are using Catalina, then, unfortunately, you cannot run MGLTools. Try if you can install VirtualBox.

Now, download MGLTools from here. We are going to use a GUI installer for its installation. Download the installer, namely, mgltools-1.5.7-MacOS-X-Install.dmg (GUI installer 91Mb).

Downloading Autodock Vina on Mac OS

Download 64-bit or 32-bit files (depending on your system’s configuration) from here. We are downloading the 64-bit version of Autodock Vina. It is a tar.gz file.

Installing MGLTools on Mac OS

Now, double-click on the dmg file. It will show you an installer after verification. Double-click on that too. If it does not open, then control+click –> click ‘Open’. It will ask for your permission, click on ‘Allow‘. It will open with the help of XQuartz or the Apple X11 launcher. Accept the agreement and let it install. It will take a few minutes to finish.

To check your installation, go to the Applications folder, you will find a mgltools folder that contains Autodock Tools 1.5.7 version. Double-click on it to launch.

Installing Autodock Vina on Mac OS

Double-click the downloaded tar file, it will create a new folder, namely, ‘autodock_vina_1_1_2_mac_catalina_64bit‘. Move inside the folder (by double-clicking on it). You will see a ‘bin’ folder inside that you will find the vina executable file. You will have to provide permissions to it as shown below.

Open a terminal and paste the following commands.

% cd autodock_vina_1_1_2_mac_catalina_64bit/

% cd bin/

% chmod +x vina

Now, let’s add this vina executable to the path so that you can run it easily from the terminal. Follow the commands given below.

% sudo nano /etc/paths

Now add the full path to the vina executable.

% /Users/username/Downloads/autodock_vina_1_1_2_mac_catalina_64bit/bin

Press Control+X, type ‘Y’, and return.

Now, type ‘vina‘ in the terminal, it should display the usage. It means that you have successfully installed vina on your system.


References

  1. Trott, O., & Olson, A. J. (2010). AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of computational chemistry31(2), 455-461.

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

Software

Installing PyVOL plugin in Pymol on Ubuntu (Linux).

Published

on

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…)

Continue Reading

Software

How to execute matlab from terminal in Ubuntu (Linux)?

Published

on

How to execute matlab from terminal in Ubuntu (Linux)?

While trying to install Matlab [1], it generally gives an error stating “matlab: command not found.”. Here, we provide a solution to this error.

(more…)

Continue Reading

Software

How to install Kpax on Ubuntu (Linux)?

Published

on

How to install Kpax on Ubuntu (Linux)?

Kpax is a bioinformatics program to search and align protein structures [1]. It is currently available for Linux platforms only. In this article, we are going to install the latest version of Kpax (5.1.3) on Ubuntu (Linux). (more…)

Continue Reading

LATEST ISSUE

ADVERT