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How do I run multiple proteins at once? p_batch and pro_batch
p_batch is a program included in MCCE, under the folder MCCE_bin. It accepts a directory containi...
Custom MCCE Runs and submit_shell
Default MCCE runs (run_mcce4) By default, each step of MCCE has certain parameters set to it. Fo...
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...
MCCE Documentation
MCCE Documentation What is MCCE? Multi-Conformation Continuum Electrostatics - MCCE MC...
MCCE Output Files
As part of the standard four steps, MCCE produces a number of files associated with the initial p...
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...
MCCE Tools
List of miscellaneous tools MCCE offers for your research and convenience. Most of these tools su...
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Gehan and MCCE Microstates
Compute hydrogen bond network
Compute hydrogen bond network Hydrogen bond network obtained from MCCE is the hydrogen bonds exi...
Calculate Em of heme in Cytochrome
Calculate Em of heme in Cytochrome Background Cytochrome c is a small protein that transports e...
How to break down the energy of a residue ionization?
How to break down the energy of a residue ionization? MCCE calculates theoretical pKas as well a...
How to make a new topology file?
How to make a new topology file? Topology file defines a molecule, including the atom connectivi...
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 ...
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 ...
Koreena and Proton Loading Sites
Jose Ortiz-Soto and Photosystem II
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...