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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...
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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...
Download and Install MCCE
Download and Install MCCE MCCE runs on Linux and Mac OSX natively. On Windows, you will need a ...
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
Calculate pKas of Lysozyme (MCCE steps 1 - 4)
Background Lysozyme is a small enzyme that dissolves bacterial cell walls thus kills bacteria. I...
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 ...
MCCE Data Analysis
MCCE data analysis tools fitpka.py Fit the titration curve of an ionizable residue. Syntax: f...
MCCE Program Run and Debug
Commands and Tools getpdb Command line tool to download pdb file from PDB Author: Yanjun W...
MCCE Parameter Preparation
Multi-Conformation Continuum Electrostatics - MCCE
MCCE is a biophysics simulation program developed at Gunner Lab at City College of New York. MCC...