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Jose Ortiz-Soto and Photosystem II
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 predictions. Some major options include varying the internal dielectric constants, numerical Poisson-Boltzmann solvers, Van der Waal functions, conformer sampling level, ...
MCCE Documentation
MCCE Documentation What is MCCE? Multi-Conformation Continuum Electrostatics - MCCE MCCE Mechanism MCCE Success Stories Proton Loading Sites in Complex I MCCE Hydrogen Bond Characterization Photosystem II Analysis Quick Star...
How to make a new topology file?
How to make a new topology file? Topology file defines a molecule, including the atom connectivity, atom charge and radius, how conformers are made etc. General format of ftpl file The format of free format tpl file is simple. It is simply a key value pair ...
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 as explain why these residues have those pKas. Continuum Electrostatic interpretation of pKa Free energy and pKa An amino acid and conjugate base in equilibrium:...
Calculate Em of heme in Cytochrome
Calculate Em of heme in Cytochrome Background Cytochrome c is a small protein that transports electrons in mitochondria to facilitate the synthesis of ATP. Its redox potential plays an important role in its function. The regulation of the Cytochrome C redox ...
Compute hydrogen bond network
Compute hydrogen bond network Hydrogen bond network obtained from MCCE is the hydrogen bonds existing in protein in Boltzmann distribution. The network helps reveal proton transclocation pathways, water pathways involving in the protein. The relative publicat...
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MCCE Output Files
As part of the standard four steps, MCCE produces a number of files associated with the initial protein output. These are best understood to be members of six categories: Input: The given PDB file. Often, MCCE programs will symbolically link the name "prot.pd...
Custom MCCE Runs and submit_shell
Default MCCE runs (run_mcce4) By default, each step of MCCE has certain parameters set to it. For example, step 3 defaults to the Gunner Lab's in-house Poisson-Boltzmann solver, NGPB, though Delphi and ZAP are available to those with the respective OpenEye li...
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 containing ".pdb" files, and runs MCCE with identical settings on each protein file. p_batch -h usage: p_batch [-h] [-custom script_path] input_path p_batch accepts...