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

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

Discussion (0)