DEV Community

Cover image for How to install Gromacs, PyMOL, AutoDock Vina, VMD, MGLTools, Avogadro2, Open Babel in Ubuntu 20.04
Abdullah Al Nahid
Abdullah Al Nahid

Posted on

How to install Gromacs, PyMOL, AutoDock Vina, VMD, MGLTools, Avogadro2, Open Babel in Ubuntu 20.04

#linux #bash #bioinformatics

One of the most time-consuming and frustrating aspects of computational tasks has always been properly installing software and getting it up and running in no time. In the case of bioinformatics tools, this is notoriously difficult in some cases, particularly in Linux-based operating systems such as Ubuntu, where one-click installer files, unlike Windows, are not an option. Although much of the popular software in the bioinformatics world is easy to install in Ubuntu if one is familiar with the ecosystem, a beginner will certainly have a difficult time circling the internet trying to find a proper installation method, at least, that’s what I had to go through when I first started out.

Here in this article, I compiled out the installation methods of some of the most commonly used bioinformatics and simulation tools, as well as how to run these tools after installing them on an Ubuntu 20.04 machine. Feel free to let me know which software should be added next.

Before running any of the commands below, run this command once: 

sudo apt-get -y update
Enter fullscreen mode Exit fullscreen mode

1. Avogadro2

Installation 

sudo apt-get install -y avogadro
Enter fullscreen mode Exit fullscreen mode

How to run Avogadro2 

avogadro2
Enter fullscreen mode Exit fullscreen mode

2. PyMOL

Installation 

sudo apt-get install -y pymol
Enter fullscreen mode Exit fullscreen mode

How to run pymol 

pymol
Enter fullscreen mode Exit fullscreen mode

3. Gromacs

Installation 

sudo apt-get install -y gromacs
Enter fullscreen mode Exit fullscreen mode

How to run Gromacs 

gmx
Enter fullscreen mode Exit fullscreen mode

4. VMD

Installation 

cd ~

curl -k https://www.ks.uiuc.edu/Research/vmd/vmd-1.9.3/files/final/vmd-1.9.3.bin.LINUXAMD64-CUDA8-OptiX4-OSPRay111p1.opengl.tar.gz --output vmd.tar.gz

mkdir -p vmd

tar -xvzf vmd.tar.gz -C vmd --strip-components=1

cd vmd

./configure

cd src

sudo make install
Enter fullscreen mode Exit fullscreen mode

How to run VMD 

vmd
Enter fullscreen mode Exit fullscreen mode

5. AutoDock Vina

Installation 

sudo apt-get install -y autodock-vina
Enter fullscreen mode Exit fullscreen mode

How to run AutoDock Vina 

vina
Enter fullscreen mode Exit fullscreen mode

6. MGLTools

Installation 

cd ~

curl -k https://ccsb.scripps.edu/download/532/ --output mgltools.tar.gz

mkdir -p mgltools

tar -xvzf mgltools.tar.gz -C mgltools --strip-components=1

cd mgltools

bash install.sh

source ./initMGLtools.sh
Enter fullscreen mode Exit fullscreen mode

How to run Python Molecule Viewer (PMV) 

pmv
Enter fullscreen mode Exit fullscreen mode

How to run AutoDockTools (ADT) 

adt
Enter fullscreen mode Exit fullscreen mode

How to run Vision 

vision
Enter fullscreen mode Exit fullscreen mode

7. Open Babel Command Line Program

Installation 

sudo apt-get install -y openbabel
Enter fullscreen mode Exit fullscreen mode

How to run openbabel 

obabel
Enter fullscreen mode Exit fullscreen mode

8. Open Babel Graphical User Interface (GUI)

Installation 

sudo apt-get install -y openbabel-gui
Enter fullscreen mode Exit fullscreen mode

How to run openbabel gui 

obgui
Enter fullscreen mode Exit fullscreen mode

Top comments (0)

Read next

iamthebuilder profile image

Can't Access Files in XAMPP "public" Folder on Linux? Fix Permissions with chmod

The Builder -

sk_rajibul_9ce58a68c43bb5 profile image

Simplifying Test Execution with pytest.main()

SK RAJIBUL -

rodri-oliveira-dev profile image

El Arte de Programar: No se Enseña Programación, Sino a Programar

Rodrigo de Oliveira -

sk_rajibul_9ce58a68c43bb5 profile image

Leveraging Python's Built-In Decorator for Improved Performance

SK RAJIBUL -