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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
1. Avogadro2
Installation
sudo apt-get install -y avogadro
How to run Avogadro2
avogadro2
2. PyMOL
Installation
sudo apt-get install -y pymol
How to run pymol
pymol
3. Gromacs
Installation
sudo apt-get install -y gromacs
How to run Gromacs
gmx
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
How to run VMD
vmd
5. AutoDock Vina
Installation
sudo apt-get install -y autodock-vina
How to run AutoDock Vina
vina
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
How to run Python Molecule Viewer (PMV)
pmv
How to run AutoDockTools (ADT)
adt
How to run Vision
vision
7. Open Babel Command Line Program
Installation
sudo apt-get install -y openbabel
How to run openbabel
obabel
8. Open Babel Graphical User Interface (GUI)
Installation
sudo apt-get install -y openbabel-gui
How to run openbabel gui
obgui
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