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 do these four steps:
Step 1 convert PDB file into MCCE PDB
This step proof reads the structure file and cuts terminal residues and complex cofactors into smaller ones if necessary.
$ step1.py 1DPX.pdb
Step 2 make side chain conformers
This step makes alternative side chain locations and ionization states.
$ step2.py
Step 3 make 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"
- For more detailed command usages, use "-h" switch in each command above.
Run in background
- Some steps take hours to finish, so it is recommended to run at the background. For example:
step3.py > run.log &
Jupyter notebook
Here is a Jupiter note book template: mcce.ipynb