CHAPERONg: A Shell repository from abeebyekeen

CHAPERONg: Automated GROMACS-based MD Simulations and Trajectory Analyses

For detailed documentation and tutorials, see the CHAPERONg homepage.

0. Contents

Contents
Prerequisites/Requirements
Installation
Uninstall
Optional Dependencies
Usage
Updating the Code
Citation

1. Prerequisites/Requirements

The only essential requirement of CHAPERONg is, of course, a functional installation of the GROMACS software run on Linux (Ubuntu) or Windows (via WSL). You can download and install a version by visiting the GROMACS documentation page, or you could find the latest version of GROMACS here.

CHAPERONg has been tested with GROMACS versions 2020.x, 2021.x, and 2022.x, but should generally work with GROMACS 5.x versions and later.

2. Installation

In the instructions that follow, replace "xxx" with "main" or "v0.1" as you have it in the downloaded package

Step 1: Copy the CHAPERONg package to your preferred installation directory.

Step 2: Extract the package with:

tar xzvf CHAPERONg-xxx.tar.gz

or with:

unzip CHAPERONg-xxx.zip

Step 3: Enter the extracted CHAPERONg folder:

cd CHAPERONg-xxx

Step 4: Run the install script:

chmod +x install_CHAPERONg.sh && ./install_CHAPERONg.sh

Enter y or yes when prompted for permission. During installation, CHAPERONg will append the installation path to your $PATH via the ~/.bashrc file. After installation, you should see a completion message.

3. Uninstall

At any time, you can uninstall CHAPERONg by simply, and CAREFULLY, deleting the relevant lines that have been added your ~/.bashrc file.

4. Optional Dependencies

CHAPERONg will run the entire GROMACS simulation pipelines without additional dependencies installed. However, some other dependencies are required to run some specific analyses. The more of these additional tools you install, the more you are able to maximize the usage and functionalities of CHAPERONg.

Existing dependencies do not need to be re-installed, i.e., you do not need to re-install any active packages.

There are two options by which you can install the dependencies:

installation in conda environment (recommended), or
global (system-wide) installation.

4.1. Installing dependencies with conda (recommended)

Installation in conda environment is recommended for most of the dependencies.

Step 1: Change to your base anaconda (default) environment:

conda activate base

Step 2: Run the conda environment setup script conda_env_setup.sh while in the CHAPERONg folder:

chmod +x conda_env_setup.sh && ./conda_env_setup.sh

This step requires an internet connection and could take a while to complete depending on the stength of your connection. So, relax and give it time.

In case of errors, see the installation page of the CHAPERONg documentation for guides on troubleshooting.

You should see a message indicating that the chaperong environment has been set up successfully.

You can confirm the newly created environment with:

conda env list

You should see chaperong listed among your conda environments.

You can then change into the chaperong environment with:

conda activate chaperong

If, after setting up the conda environment as described above, some python modules/libraries are, for some reasons, not accessible, you can further run the commands described in the system-wide option 1 below.

4.2. Installing dependencies system-wide

4.2.1. Option 1: Batch installation

Step 1: Install all of the dependencies at once:

sudo apt install grace pymol libpng-dev libjpeg-dev ghostscript-x imagemagick-6.q16 ffmpeg

Step 2: Install/update python libraries as well as a few other packages:

pip3 install numpy==1.23.4 scipy matplotlib pandas networkx==2.3

If networkx==2.3 fails, install networkx==2.5 instead

If you don't have pip installed, you can first install it with:

sudo apt install python3-pip

And then, run the command:

pip3 install numpy==1.23.4 scipy matplotlib pandas networkx==2.3

4.2.2. Option 2: One-by-one installation

See the relevant section of the CHAPERONg documentation and installation page.

5. Usage

The basic usage of CHAPERONg is:

run_CHAPERONg.sh -i inputStructure_filename [more options]

For more details, see the CHAPERONg documentation and tutorials

6. Updating the Code

With the updates of CHAPERONg pushed since Nov. 5 2023, it is now possible to automatically update CHAPERONg for users who installed CHAPERONg from this date onwards. To update the code, simply navigate to the CHAPERONg installation directory:

cd $CHAPERONg_PATH

Run the install_CHAPERONg.sh script in the installation directory:

./install_CHAPERONg.sh

CHAPERONg will detect the existing installation, and you will be prompted to confirm if you would like to proceed with an update of the code.

7. Citation

If you use this code in your work, kindly cite it as:

Yekeen A. A., Durojaye O. A., Idris M. O., Muritala H. F., and Arise R. O. (2023). CHAPERONg: A tool for automated GROMACS-based molecular dynamics simulations and trajectory analyses, Computational and Structural Biotechnology Journal 21: 4849-4858. DOI: https://doi.org/10.1016/j.csbj.2023.09.024

For BibTeX, you can insert the following:

@article {yekeenCSBJ2023chaperong,
	author = {Abeeb Abiodun Yekeen and Olanrewaju Ayodeji Durojaye and Mukhtar Oluwaseun Idris and Hamdalat Folake Muritala and Rotimi Olusanya Arise},
	title = {{CHAPERONg}: A tool for automated {GROMACS}-based molecular dynamics simulations and trajectory analyses},
	journal = {{Computational and Structural Biotechnology Journal}},
	volume = {21},
	pages = {4849-4858},
	year = {2023},
	issn = {2001-0370},
	doi = {https://doi.org/10.1016/j.csbj.2023.09.024},
	publisher = {Elsevier},
	url = {https://www.sciencedirect.com/science/article/pii/S2001037023003367}
}

abeebyekeen/CHAPERONg