Install MCCE

This source code is based on MCCE 2.3. I removed the library dependencies so all you need is a gfortran and gcc compiler.

To download:

mcce2.7: mcce source code.

getpdb: an updated command line tool to download pdb file from Protein Data Bank

preprocess.py: a script to pre-process PDB file to make it friendly to MCCE

mfe.py: a command line tool to analyze ionization free energy. documentation

To install

• 1. tar -zxvf mcce.tar.gz

  2. cd mcce

  3. make clean

  4. make

On Mac OS X, an explicit memory free for tree is not supported. You may have to change this subroutine in file lib/db.c

/* release database memory */ void free_param() {    tdestroy(param_root, free);    return; }

to

/* release database memory */ void free_param() {    return; }

A set of sample run.prm files are under top mcce directory.

To install through conda

You can install mcce through conda 

conda install -c https://conda.anaconda.org/salahsalah mcce   

Test run mcce program

Assume mcce was compiled under /home/jmao/mcce2.7, mcce and delphi executables are now located under /home/jmao/mcce2.7/bin directory. Your installation location may differ.

• 1. Download getpdb and save it under /home/jmao/mcce2.7/bin

  2. chmod +x /home/jmao/mcce2.7/bin/getpdb

  3. Append mcce bin to $PATH

  4. export PATH=$PATH:$HOME/mcce2.7/bin

  5. Prepare a working directory with pdb file.

  6. cd mkdir 4pti cd 4pti getpdb 4pti

  7. preprocess.py 4PTI.pdb > prot.pdb

  8. copy run.prm.quick to "run.prm

  9. cp /home/jmao/mcce2.7/run.prm.quick run.prm

  10. Edit run.prm to point pdb file, parameter directory, and delphi to the correct path

1. Change these lines as

   1. prot.pdb                                                    (INPDB) t        step 1: pre-run, pdb-> mcce pdb                    (DO_PREMCCE) t        step 2: make rotatmers                             (DO_ROTAMERS) t        step 3: do energy calculations                     (DO_ENERGY) t        step 4: monte carlo sampling                       (DO_MONTE) 8.0      Protein dielectric constant for DelPhi             (EPSILON_PROT) /home/jmao/mcce2.7/extra.tpl                                (EXTRA) /home/jmao/mcce2.7/name.txt MCCE renaming rule.             (RENAME_RULES) /home/jmao/mcce2.7                                          (MCCE_HOME) /home/jmao/mcce2.7/bin/delphi DelPhi executable             (DELPHI_EXE)

   2. Run mcce

   3. mcce > run.log &

   4. Check log file for progress

   5. cat run.log