Connect with us

MD Simulation

Installing CHARMM on Ubuntu

Published

on

CHARMM installation on Ubuntu

CHARMM (Chemistry at Harvard Molecular Mechanics) is a molecular simulation program that can be used for simulation of macromolecules, complexes, and many-particle systems [1]. In this article, we will install the nonprofit/academic version of CHARMM on Ubuntu.

Downloading CHARMM

The nonprofit/academic version of CHARMM can be downloaded from here. After successful registration, download the tar file of CHARMM.

Installing CHARMM

Updating the system

Let’s update and upgrade first. Open a terminal (Ctrl+Alt+T) and type the following commands:

$ sudo apt-get update

$ sudo apt-get upgrade

Installing CMake

To install CHARMM, it is required to have CMake installed on your system.

$ sudo apt-get install -y cmake

Installing CHARMM package

Change to the directory where you have downloaded the tar file. Let’s say in ‘Downloads

$ cd Downloads/

$ tar xvzf charmm.tar.gz

$ cd charmm/

$ ./configure

Now, change to the directory cmake present in the charmm directory.

$ cd build/cmake/

$ make

$ sudo make install

It will take a few minutes to install. That finishes the CHARMM installation on Ubuntu.


References

  1. Brooks, B. R., Brooks III, C. L., Mackerell Jr, A. D., Nilsson, L., Petrella, R. J., Roux, B., … & Caflisch, A. (2009). CHARMM: the biomolecular simulation program. Journal of computational chemistry30(10), 1545-1614.

Tariq is founder of Bioinformatics Review and CEO at IQL Technologies. His areas of expertise include algorithm design, phylogenetics, MicroArray, Plant Systematics, and genome data analysis. If you have questions, reach out to him via his homepage.

MD Simulation

How to install GROMACS on Apple M1 (MacOS)?

Published

on

Installing GROMACS on Apple M1 (MacOS)

We have provided a few articles on GROMACS installation on Ubuntu. In this article, we are going to install GROMACS [1] on Mac OS. (more…)

Continue Reading

MD Simulation

How to take snapshots of structure at specific times in GROMACS?

Published

on

How to take snapshots of structure at specific times in GROMACS?

It is important to see the behavior of protein during an MD simulation. This can be achieved by taking snapshots in the form of PDB format. In this article, we have provided a few commands that you can use to take snapshots of a complete system or protein during MD simulation. (more…)

Continue Reading

MD Simulation

GROMACS: Uses & Applications

Published

on

GROMACS: Uses & Applications

GROMACS stands for GROningen MAchine for Chemical Simulations [1]. It is a very popular and one of the most widely used open-source bioinformatics software. It is generally used for molecular dynamics simulation of macromolecules. In this article, we will explain its uses and applications in bioinformatics studies. (more…)

Continue Reading

LATEST ISSUE

ADVERT