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How to Install AmberTools

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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]
This procedure involves installing Conda and managing virtual environments. Since unexpected system conflicts or package dependencies may affect your existing Matlantis environment, please proceed with care and at your own discretion.

 

 

(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

Please use conda in accordance with conda's Terms of Service.
https://www.anaconda.com/legal/terms/terms-of-service

 

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.

Please refer to the official documentation for information on configuring conda.
https://docs.conda.io/projects/conda/en/latest/user-guide/configuration/index.html

 

 

(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

Install 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.

# Display 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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