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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

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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
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1. Avogadro2

Installation 

sudo apt-get install -y avogadro
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How to run Avogadro2 

avogadro2
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2. PyMOL

Installation 

sudo apt-get install -y pymol
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How to run pymol 

pymol
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3. Gromacs

Installation 

sudo apt-get install -y gromacs
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How to run Gromacs 

gmx
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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
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How to run VMD 

vmd
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5. AutoDock Vina

Installation 

sudo apt-get install -y autodock-vina
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How to run AutoDock Vina 

vina
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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
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How to run Python Molecule Viewer (PMV) 

pmv
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How to run AutoDockTools (ADT) 

adt
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How to run Vision 

vision
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7. Open Babel Command Line Program

Installation 

sudo apt-get install -y openbabel
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How to run openbabel 

obabel
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8. Open Babel Graphical User Interface (GUI)

Installation 

sudo apt-get install -y openbabel-gui
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How to run openbabel gui 

obgui
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