How to install AutoDock Vina on Ubuntu

How to Install AutoDock Vina on Ubuntu 20.04

Before starting the installation process, first, we’ll have to update and upgrade our ubuntu apt packages and system. You can do that by typing the following commands in the terminal –

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sudo apt-get update
sudo apt-get upgrade

It will take a little bit of time for it to finish depending upon your internet speed. After the update and upgrade finishes, you can now start the installation process of AutoDock Vina.

Download MGLTools and AutoDock -

The first step will be to download MGLTools and AutoDock in our ubuntu. To download these packages you can either download them directly from their websites or you can use the terminal to download the packages. 

First lets see how we can download MGLTools and AutoDock Vina using the terminal. Before typing the download command make sure you have wget installed on your ubuntu. If wget is not installed on your system then you can install it by using this command –

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Download using Terminal -

sudo apt-get install wget

After installing wget,  download MGLTools. First, create a new directory on your desktop with the name “newdirectory” by using this command –

mkdir -p newdirectory

We’ll download the packages in this new directory. After creating the new directory we’ll change our working directory from the current one to the new one that we created 

cd newdirectory

After that, by using the wget command we’ll download the latest version of MGLTools.

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wget http://mgltools.scripps.edu/downloads/tars/releases/REL1.5.6/mgltools_x86_64Linux2_1.5.6.tar.gz

Alternative download link for MGLTools – https://ccsb.scripps.edu/mgltools/downloads/

(OPTIONAL) If your system is not 64bit and is 32bit then use this command instead of the above one – 

wget http://mgltools.scripps.edu/downloads/downloads/tars/releases/REL1.5.6/mgltools_i86Linux2_1.5.6.tar.gz

After downloading MGLTools, download AutoDock Vina using the command

wget http://vina.scripps.edu/download/autodock_vina_1_1_2_linux_x86.tgz

After this, we’ll need to download the AutoDocksuite so that we can run AutoDock4 analysis.

Here’s the command to download AutoDocksuite.

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sudo wget http://autodock.scripps.edu/downloads/autodock-registration/tars/dist426/autodocksuite-4.2.6-x86_64Linux2.tar

Okay, so all the required packages are now downloaded to our directory. Now before we start the installation we’ll need to download a library.

Sometimes you might get an imaging C module error which you can fix by downloading and installing a library.

sudo apt-get install libjpeg62:i386

Download using Web Browser -

To download MGLTools using Web Browser first go to this link here – http://mgltools.scripps.edu/downloads 

NOTE: This website can sometimes be down so, try this alternative link.

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Here select the version you want, 64-bit version or the 32-bit version. The 64-bit version name will be “mgltools_x86_64Linux2_1.5.6.tar.gz”.

Now to download AutoDock Vina and AutoDock suite using Web Browser we will go to these links here –

AutoDock Vina – http://vina.scripps.edu/download/autodock_vina_1_1_2_linux_x86.tgz

After downloading these file, create a new directory called “newdirectory” and move these files inside that directory. 

After that follow the steps below to complete the installation.

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Install MGLTools and AutoDock Vina -

Okay, so now that we have downloaded all the files required for the installation let’s continue to the next step. 

First, we’ll install MGLTools. To install MGLTools first we’ll unzip the tar file. Use this command to do that – 

tar xvzf mgltools_x86_64Linux2_1.5.6.tar.gz

After the tar file unzips, there will be a new folder named “mgltools_x86_64Linux2_1.5.6 ‘‘ inside the “newdirectory folder.

Now change your working directory from “newdirectory” to “mgltools_x86_64Linux2_1.5.6” using this command – 

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cd mgltools_x86_64Linux2_1.5.6

Once you are inside this directory run the install.sh file to install MGLTools.

./install.sh

After typing this command the installation of MGLTools will start. If there’s a “Commercial Usage” popup appearing on your screen then click on the OK button.

commercial usage popup-2

Once the installation has finished we can continue to the next step which is to install AutoDock Vina.

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Change your working directory back to “newdirectory” using the command –

cd ..

Now you’ll need to unzip the AutoDock tar file. Use this command to unzip the tar file –

tar xvzf autodock_vina_1_1_2_linux_x86.tgz

That’s it, the Installation of MGLTools and AutoDock Vina has been completed. Now we’ll need to create an alias in our bash file.

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Edit the Bashrc File -

We’ll have to create an alias now for AutoDock vina and pymol viewer. To do that we’ll have to edit the Bashrc file.

First, you will have to change your working directory from newdirectory to the root directory.

cd ..

After that, type the command given below in the terminal. This will open the Bashrc file in the default text editor of ubuntu.

sudo gedit ~/.bashrc

Here, inside the Bashrc file go to the bottom of the file. Now below the last line enter these lines.

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alias adt='sudo /home/username/newdirectory/mgltools_x86_64Linux2_1.5.6/bin/adt'
alias pmv='sudo /home/username/newdirectory/mgltools_x86_64Linux2_1.5.6/bin/pmv'

Now the file path here after sudo will be different for everyone. It depends upon where you installed MGLTools.

In place of username type your own username. Other things will be same if you followed my steps.

After that, on the top left, click on the Save button and then click on the red x button to close the editor.

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Now we’ll type the final command that will finish the installation process of AutoDock Vina.

source ~/.bashrc

And, that’s it, AutoDock Vina is now installed successfully on your ubuntu system. You can open AutoDock Vina by typing “adt” in the terminal. And to open the pymol viewer we’ll type pmv in the terminal.

running autodock vina using adt command

If you are facing any problem while installing AutoDock Vina, then you can contact me on Instagram or you can comment below. Thank you.

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Frequently Asked Questions -

Can I install AutoDock Vina without Root permissions?

Yes, you can install AutoDock vina without having root permissions. Download the packages using your web browser and then install it.

Update: To edit the bashrc file, you can do that without using sudo at the back like “gedit ~/.bashrc”.

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