MCCE Documentation

Table of Contents

1. Installation

1.1. What is in the MCCE program package?

1.2. Installation

2. Quick Start

2.1. Working directory and control file "run.prm"

2.2. Submitting and monitoring mcce job, a simple example

3. Understanding MCCE program

3.1. File flow chart of MCCE program

3.2. Four steps of the mcce program

3.3. Customizing control file - line by line remarks of "run.prm"

3.4 Tricks of using "run.prm"

3.5. Making parameters for a new cofactor

3.6. Running MCCE on a computer cluster

4. Understanding MCCE results

4.1. MCCE Physics

4.2. MCCE program

4.3. Calculating pKa

4.4. Calculating Em

4.5. Proton uptake upon reduction

4.6. The controlling factors of pKa and Em

4.7. Free energy of ionizing a residue at specific pH and Eh

4.8. MCCE tools

5. Trouble Shooting

Appendix: Input and Output files of MCCE

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