MetalloEnZymE parameterisation program (meze)

Metalloenzyme parameterisation tool for alchemical free energy calculations.

Important

This repository is in active development. The old meze repository can be found at https://github.com/meyresearch/metalloenzyme_rbfe/tree/main.

Installation instructions

1. Prerequisites:

• Make sure you have ambertools (and pmemd if you want to use GPUs) installed. See here for instructions.
• Currently the packages meze depends on require cuda=12.4 if you're on a Linux/Windows machine.
• Ideally, you should have miniforge3 so that you can install meze with mamba. The installation will work with conda as well, but will be significantly slower. See here for installation instructions.

3. Download environment.yml file:

curl -O https://raw.githubusercontent.com/meyresearch/meze/main/environment.yml

3. Create enivronment

mamba env create -f environment.yml
mamba activate meze-env

Updating environment after updates to meze

mamba activate meze-env
pip uninstall -y meze
pip install --no-cache-dir git+https://github.com/meyresearch/meze.git@main

If there are updates to the environment.yml:

First, get the latest environment.yml:

curl -O https://raw.githubusercontent.com/meyresearch/meze/main/environment.yml

Then:

mamba env update -n meze-env -f environment.yml --prune
mamba activate meze-env
pip uninstall -y meze
pip install --no-cache-dir git+https://github.com/meyresearch/meze.git@main

Once you have installed meze, you need to make sure the $AMBERHOME environment variable is set in the conda environment:

conda env config vars set AMBERHOME=/path/to/amber 
conda deactivate && conda activate <env>

You can double-check the environment variable is set:

echo $AMBERHOME

which should return a path to your amber.sh file.

Developing and contributing

See the CONTRIBUTING.md page for detailed instructions on developing and contributing to meze.