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How to Install AmberTools

AmberTools is a part of the molecular dynamics simulation package "Amber." It provides various useful tools for molecular simulation, including molecular modeling, assigning Amber force fields, running simple MD simulations, and analyzing trajectories.

This article explains how to install AmberTools on Matlantis.

There are two ways to install AmberTools: (1) building from the source code, and (2) installing via conda, the Python package management system. Building from source can be challenging because there are many dependencies and Matlantis environment does not allow apt get install; thus, you would have to build all of those dependencies yourself. Therefore, this article will focus on the alternative method: installing via the Python package manager, conda.

[Disclaimer] We assume no responsibility for any issues, system damage, or other problems that may occur in your environment as a result of executing the procedures described in this article. Please acknowledge this in advance and proceed at your own risk.

 

(1) Installing Miniconda

Using the package management system conda is the easiest and most reliable way to install AmberTools. Here, we will use the lightweight version, Miniconda

Installing Miniconda

Download the Miniconda installer and run it from the Matlantis terminal. Depending on your Python version, you will download one of the following:

Please check the Official Miniconda website for other versions.

Once you have placed the installer on Matlantis, simply run it from the terminal:

$ bash Miniconda3-py313_26.1.1-1-Linux-x86_64.sh

After the installation is complete, close the terminal once and reopen it to apply the settings. Then, check if it was installed correctly by running the conda --version command.

 

(2) Installing AmberTools

Step 1: Creating and activating a virtual environment 
First, create a virtual environment named AmberTools. You only need to perform this step once.

# Create the virtual environment
$ conda create --name AmberTools

Next, activate the virtual environment you just created.

# Activate the virtual environemnt
$ conda activate AmberTools

Step 2: Installing AmberTools

nstall AmberTools within the activated virtual environment.

# install ambertools
$ conda install conda-forge::ambertools

To confirm that the installation was completed successfully, let's display the help menus for some typical commands included in AmberTools.

# Disply help for tleap
$ tleap -h

# Display the version of cpptraj
$ cpptraj --version

If the above commands run without errors and display the help messages or version information, the installation is a success.

When you are finished working or when you are not using AmberTools, you can deactivate the virtual environment using the following command:

$ conda deactivate

When you want to use it again, simply run conda activate AmberTools.

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