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:
- Residue pKₐ, cofactor Eₘ and protein PI in protein-solvent systems
- Protonation States and ionization changes in response to protein structural changes
- Location and stoichiometry of proton transfers coupled to electron transfer
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.
Comprehensive documentation covering:
- Installation
- Guide: Detailed explanations of all settings
- Example Projects
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