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MCCE is a biophysics simulation program developed at Gunner Lab at City College of New York. MCCE combines continuum electrostatics and molecular mechanics. In this program, the protein side chain motions are simulated explicitly while the dielectric effect o...

A MCCE run is a 4-step procedure Step 1 is file formatting, step 2 is rotamer making, step 3 calculates energy look-up table,  step 4 is Monte Carlo sampling of conformers at each pH or Eh. MCCE program can run any steps providing the prerequisit...

MCCE data analysis tools fitpka.py Fit the titration curve of an ionizable residue. Syntax: fitpka.py [-h] RES [RES ...] Fit a titration of charged residues positional arguments:  RES         Charged residue names to plot, as in sum_crg.out or pK.out op...

Commands and Tools getpdb Command line tool to download pdb file from PDB Author: Yanjun Wang Syntax: getpdb pdbID [file] This program gets a pdb file from Protein Data Bank, and saves to a file with its PDB name or a user named file. Example: getp...

Download and Install MCCE MCCE runs on Linux and Mac OSX natively. On Windows, you will need a Linux environment. It could be a virtual box instance, Cygwin, or Linux subsystem that is included in Windows. Here is a short guide of installing Windows Subsyste...

How to install WSL (Windows Subsystem Linux) and MCCE dev tools WSL WSL Installation The official WSL installation instruction can be found on MIcrosoft website. https://learn.microsoft.com/en-us/windows/wsl/install The following is the my WSL installati...

MCCE Development Through Github Part 1. One-time set up On your workstation / coding computers, set up the git environment. Identity: $ git config --global user.name "<Your Name>" $ git config --global user.email <your email> Save credential for 6 hour...

Run MCCE Prepare a working directory: $ mkdir test_lysozyme $ cd test_lysozyme Get a pdb file $ getpdb 1dpx You now have a pdb file 1DPX.pdb in the working directory. The simplest way to run mcce is do these four steps: Step 1 convert PDB file into MCC...

Calculate pKas of Lysozyme Background Lysozyme is a small enzyme that dissolves bacterial cell walls thus kills bacteria. It was discovered as the first antibiotic to inhibit bacteria growth in food, before penicillin. Crystal structure of hen egg white l...

Why do we need "hot" spots? In some cases, we are insterested in what's going on in some particular sites rather than the whole structure. MCCE provides a mechanism to define these spots and sample more rotamers subsequently. These sites are called "hot" spot...

If a residue or a cofactor has rotatable single bond, the user needs to define the rotation rule so that MCCE can make rotamers accordingly. In MCCE, the rotation is for heavy (non H) atoms only, and H atoms have their own position optimization rules. Let'...

Microstate Analysis Library Reference Import library Suppose the ms_analysis.py is in the current working directory or the Python site-packages directory. from ms_analysis import * Global constants Once the library is loaded, two global constants (at te...

GROMACS Server Official Documentation: https://manual.gromacs.org/current/user-guide/index.html Gromacs Server and Environment: Gromacs is pre-installed on a Levich server and user accounts are initilized to include Gromacs path. In case you wan...

Example 1: Lysozyme In this example, we are going to use hen egg white lysozyme (PDB ID 1AKI) to run a MD simulation. Prepare structure and topology files Create a working directory: mkdir lysozyme cd lysozyme Download a pdb file from Protein Data ...

Example 2: Building Biphasic Systems Studay system The original tutorial was to make a heterogeneous biphasic system composed of hydrophobic (cyclohexane) and hydrophilic (water) layers.  Here we are going to use benzene to replace cyclohexane as a demost...