Recently Updated Pages
How does changing MCCE's parameters change accuracy? (under construction)
MCCE offers a wide range of customizable parameter that influence the accuracy of its pKa predict...
Calculate pKas of Lysozyme (MCCE steps 1 - 4)
Welcome to MCCE Tutorial This tutorial will show you how to set up, run and interpret the result...
Sampling more rotamers at "hot" spots
Why do we need "hot" spots? In some cases, we are insterested in what's going on in some particu...
Download and Install MCCE
Download and Install MCCE MCCE runs on Linux and Mac OSX natively. On Windows, you will need a ...
Gehan and MCCE Microstates
Koreena and Proton Loading Sites
Jose Ortiz-Soto and Photosystem II
Test page (video)
MCCE Tools
List of miscellaneous tools MCCE offers for your research and convenience. Most of these tools su...
A simple MCCE example of pH titration
Run MCCE Prepare a working directory: $ mkdir test_lysozyme $ cd test_lysozyme Get a pdb file...
MCCE Mechanism
An MCCE run is a 4-step procedure Step 1: Modify PDB (file formatting) Step 2: Conformer/Rota...
Tautomeric Charge Microstates
All MCCE tools relevant to microstate analysis will start with "ms", like 'ms_top2pdbs" and "ms_h...
What is a microstate?
Microstates are
How to install WSL (Windows Subsystem Linux)
How to install WSL (Windows Subsystem Linux) and MCCE dev tools WSL WSL Installation The off...
Example 2: Biphasic Systems
Example 2: Building Biphasic Systems Studay system The original tutorial was to make a hetero...
Gromacs Server
GROMACS Server Official Documentation: https://manual.gromacs.org/current/user-guide/index.ht...
Example 1: Lysozyme
Example 1: Lysozyme In this example, we are going to use hen egg white lysozyme (PDB ID 1AKI) to...
Microstate Analysis Library Reference
Microstate Analysis Library Reference Import library Suppose the ms_analysis.py is in the cur...
How to contribute code to MCCE
MCCE Development Through Github Part 1. One-time set up On your workstation / coding computers,...
How to add rotamer making rules to parameter file?
If a residue or a cofactor has rotatable single bond, the user needs to define the rotation rule ...