How to install GMXPBSA on Ubuntu (Linux)?

GMXPBSA is a tool to calculate binding free energy [1]. It is compatible with Gromacs version 4.5 and later. In this article, we will install GMXPBSA version 2.1.2 on Ubuntu (Linux).

Contents

Preparing system Installing prerequisites Downloading GMXPBSA Installing GMXPBSA References Further Reading

Preparing system

It is good to update and upgrade your Ubuntu system first. Log into your Ubuntu system and open the terminal by pressing Ctrl+Alt+T altogether. and type the following commands:

$ sudo apt-get update

$ sudo apt-get upgrade

Installing prerequisites

In order to perform binding energy calculations using GMXPBSA (www.gromacs.org), you must have GROMACS and APBS (http://www.poissonboltzmann.org/apbs/) installed on your system. Hopefully, you would have installed GROMACS earlier but if not, read the “Further reading” section for installation tutorials.

Now, let’s install APBS. Paste the following command in your terminal.

$ sudo apt-get install apbs

Downloading GMXPBSA

You can either download yourself from here or use the following command. Let’s change to the directory where we want to download the software. I am downloading in the Downloads directory.

$ cd Downloads/

Paste the following command in the terminal.

$ wget https://github.com/aspitaleri/gmxpbsa/archive/refs/heads/master.zip

Installing GMXPBSA

Let’s extract the downloaded file.

$ unzip gmxpbsa-master.zip

A new directory would be created namely, ‘gmxpbsa-master‘. Move inside the new directory.

You will see some shell scripts in there, for example, gmxpbsa0.sh, gmxpbsa1.sh, and so on. You will use these scripts to run the binding energy calculations. We are not discussing it here. We will explain it in the upcoming articles.

Now, let’s add gmxpbsato the path. Ensure that you are using bash. To check type $ echo $SHELL. It should display /bin/bash. If not then type $ bash in the terminal.

$ export GMXPBSAHOME=/home/username/Downloads/gmxpbsa-master

Provide a complete path to your gmxpbsa directory.

Now, let’s provide permissions to this directory. Return to your Downloads directory and enter the following command in the terminal.

$ chmod +x gmxpbsa-master

Move back inside the gmxpbsa-master directory and try running the shell scripts as shown below.

$ ./gmxpbsa0.sh

It should display an error asking for an input file.

Now, you have successfully installed the GMXPBSA tool on your system.

References

Paissoni, C., Spiliotopoulos, D., Musco, G., & Spitaleri, A. (2015). GMXPBSA 2.1: A GROMACS tool to perform MM/PBSA and computational alanine scanning. Comput. Phys. Commun., 186(Supplement C), 105-107.