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 Subsystem Linux (to be done):

Prerequisites

Compilers: C, gfortran

MCCE comes with two parts:

MCCE main code in c/c++
Poisson Boltzmann equation solver delphi in c/fortran

It is recommended to use the compilers under conda. Conda provides compilers and other programming tools under user space. If you don't have conda, you can follow instruction here https://docs.conda.io/en/latest/miniconda.html to install miniconda.

To install c and gfortran compilers:

Create mcce environment

conda create -n mcce
conda activate mcce

Install compilers

conda install -c conda-forge gcc gfortran

Now roll back gfortran to 9.5.0 (delphi requires an old compiler)

conda install -c conda-forge gfortran=9.5.0

Python and modules

We need Python3 and optionally these modules: numpy, scipy, matplotlib, pygraphviz, pandas, xlrd, and openpyxl

Install Miniconda Python3: https://docs.conda.io/en/latest/miniconda.html
After installing Miniconda, install these optional modules for data analysis:

conda install numpy scipy matplotlib pygraphviz pandas xlrd openpyxl

Download from github¶

Under a terminal window, run:

git clone https://github.com/GunnerLab/Stable-MCCE.git

Compile the code¶

The above command creates a directory named Stable-MCCE, enter the directory and compile:

$ cd Stable-MCCE
$ make clean
$ make

Configure environment:

Find the path of Stable-MCCE installation directory:

(base) jmao@pc:~/projects/Stable-MCCE$ pwd
/home/jmao/projects/Stable-MCCE

In my case the installation directory is /home/jmao/projects/Stable-MCCE/

Add the executable to your path:

export PATH=/home/jmao/projects/Stable-MCCE/bin:$PATH

Remember to replace the installation directory /home/jmao/projects/Stable-MCCE/ with your own installation path.

Also put this line at the end of .bashrc file under your home directory so that the environment is properly set every time you open a terminal window.

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

If this step quits and complain about unrecognized residues, please refere to the section of making new paramter files.

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