Please see our CHANGELOG at the bottom for the latest updates!
Given the structure of a macromolucule (in a PDB file), MCCE4 can predict the following:
- pKₐ values
- Protonation states
- Electrostatic properties of biomolecules
In this program, protein side chain motions are simulated explicitly while the dielectric effect of solvent and bulk protein material is modeled by continuum electrostatics.
The file MCCE_bin/sudo_install.txt has the necessary information for you or your sys admin to install the packages. To display the file, run this command:
cat ./MCCE_bin/sudo_install.txt
Note: The quick install script will not modify an existing conda environment named 'mc4'. If you want to re-create it, run this command before running the script:
conda env remove -n mc4
- Clone this repo, then cd into it with this command:
git clone https://github.com/GunnerLab/MCCE4-Alpha.git; cd MCCE4-Alpha;
- Run the
quick_install.shscript to download MCCE PBE solver (NGPB) image file and create a conda environment for MCCE4 (this may need several passes if you need to install dependencies such as miniconda and apptainer):
bash ./MCCE_bin/quick_install.sh
- Checks for required
conda; Stops if not found so you can install it (commands provided). - Create a conda environment for MCCE4 named 'mc4' (using 'mc4.yml').
- Checks for required
apptainer; If a system Apptainer installation is not found & an 'unprivilege' version cannot be installed, Apptainer is conda-installed in 'mc4'. - Downloads the generic image for NGPB in MCCE4-Alpha/bin.
- Adds export commands to the PATH variable in ~/.bashrc for:
- 'MCCE4-Alpha/bin' and 'MCCE4-Alpha/MCCE_bin'
- the unprivilege version of Apptainer if installed by the script
If your 'mc4' environment predates 01-08-2026, run these commands to update it:
CLONE=$(dirname $(dirname "$(python3 -c "import os, sys; print(os.path.realpath(sys.argv[1]))" "$(which ms_protonation)")"));
conda env update -n mc4 -f "$CLONE/mc4.yml🚀 Run Your First Job: Quick Start
📖 MCCE4-Alpha Tutorial: Full Documentation
Comprehensive documentation covering:
- Installation
- Guide: Detailed explanations of all settings
- Example Projects
Please also check out the companion repository MCCE4-Tools.
🧰 Explore Now: MCCE4-Tools GitHub
This section will reflect important changes and will provide you with information on how to apply them; For example, if new python packages are added to the environment file (mc4.yml), then the entry pertaining to that change will list the command(s) to update your environment.
-
2026-01-08:
- Updated python dependencies in mc4.yml
- Apply changes: run these commands:
CLONE=$(dirname $(dirname "$(readlink -f "$(which mcce)")")); echo "$CLONE" conda env update -n mc4 -f "$CLONE/mc4.yml -
2025-11-25:
- step1.py: Added error trapping on atom.loadline call
- mfe.py: Updated & moved to MCCE_bin
- Apply changes: cd to your clone, then run
git pull
-
2025-11-11:
- Fixed deleterious typo in bin/pdbs_interfaces.py
- Apply changes: cd to your clone, then run
git pull
-
2025-10-30:
- Updated README: Added CHANGELOG, link to sudo_install.txt
- Added topologies for SO4 and PO4 in param/.
- Updated bin/step3.py with longer timeout value
- Updated MCCE_bin/quick_install.sh
- Apply changes: cd to your clone, then run
git pull
This is a testing version of MCCE4 development. Please let us know about questions, comments or report any issues you encounter here. Thank You and we hope you enjoy using MCCE4!
Learn about MCCE, installation, available tools, and research done with MCCE. (under construction)
Copyright (C) 2024 GunnerLab This software is distributed under the terms the terms of the MIT licence