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MCCE4-Alpha Quick Start Tutorial

🎉 Congratulations on successfully installing MCCE4-Alpha!

Now that MCCE4-Alpha is up and running, the next question is: what can we use it for?

Perform pKₐ and Em calculations
Calculate protonation states via boltzmann-weighted Monte Carlo microstate sampling
Determine which protonation microstates dominate under physiological conditions
Explore electrostatic coupling and pH/redox sensitivity in biomolecular systems

Setup a dedicated directory for the sample workflows:

The best way to build confidence in addressing these tasks is to run a set of well-defined excercises.

mkdir mcce_workflows
cd mcce_workflows

➡️ Let’s start the first excercise Exercise #1: Sanity check using `p_info`.

The excercises in this section are designed to help you understand MCCE’s behavior on controlled systems, gain intuition for interpreting its output and verify that your installation is working properly. Each of these excercises designed to be self-contained and reproducible.

Organization

Each excercise highlists highlighting a specific physical, chemical, or numerical aspect of the MCCE workflow as a standalone page and includes:

A clear physical or biochemical motivation
Input structure details (PDB source, modifications, waters)
MCCE parameter settings used
Expected qualitative or quantitative behavior
Notes on convergence, artifacts, or known limitations

Available Excercises

Excercise #1: Sanity check using p_info A fast verification test to confirm MCCE can parse the input structure, load topology/parameter files, and generate the expected bookkeeping outputs (e.g., residue/protein info summaries).
Excercise #2: pKₐ example (pH titration + pKₐ fitting)
A standard pH-titration workflow to compute pKₐ values for ionizable residues and validate protonation behavior across a pH range.
Excercise #3: Eₘ example (redox titration over a defined Eₕ range)
A redox titration workflow to compute Eₘ values for redox-active groups by scanning over an electrochemical potential window.
Recommended Eₘ scan range: -300 mV to +300 mV (typical starting window; widen if transitions occur near the endpoints).
Excercise #4: Charge microstate analysis on 4LZT at pH7
A single-pH run on 4LZT designed for microstate sampling and coupling analysis (not pKₐ fitting).
This is the go-to test for studying charge microstate populations, residue coupling, and protonation correlations at a fixed pH.
Excercise #5: Obtaining H-bonding pairs and H-bonding microstates data
The microstate file at a given pH/Eh is processed for H-bonding microstates. The two main outputs are csv files that:
- list the H-bonding microstates along with their count and occupancy (states file)
- list the effective count and occupancy of each H-bonding pairs (pairs file) The pairs file can then be used for H-bond network analysis.

This test suite is under active development and will expand as new physical scenarios, methodological features, and validation benchmarks are explored.