A simple MCCE example of pH titration

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 with these four steps:

Step 1: Make PDB file into MCCE PDB

This step proofreads the structure file and cuts terminal residues and complex cofactors into smaller ones if necessary.

$ step1.py 1DPX.pdb

Step 2: Create side chain conformers

This step makes alternative side chain locations and ionization states.

$ step2.py

Step 3: Calculate energy table

This step calculates conformer self energy and pairwise interaction table.

$ step3.py

Step 4: Simulate a titration with Monte Carlo sampling

This step simulates a titration and writes out the conformation and ionization states of each side chain at various conditions.

$ step4.py

 

Notes

Command help "-h"

Run in background

Jupyter notebook

Here is a Jupiter note book template: mcce.ipynb


Revision #3
Created 9 March 2023 18:22:24 by Junjun Mao
Updated 18 April 2025 17:31:11 by Jared