pK_a Calculation

In this example we are estimating the pK_a values for all titrable sites of a hen egg-white lysozyme.

The structure may be downloaded from the Protein Data Bank:

wget https://files.rcsb.org/download/4lzt.pdb

PypKa features a API and a CLI. Both interfaces provide the same amount of features.

API

from pypka import Titration

params = {
 'structure'     : '4lzt.pdb', # Input structure file name
 'ncpus'         : -1,         # Number of processes (-1 for maximum allowed)
 'epsin'         : 15,         # Dielectric constant of the protein
 'ionicstr'      : 0.1,        # Ionic strength of the medium (M)
 'pbc_dimensions': 0           # PB periodic boundary conditions (0 for solvated proteins and 2 for lipidic systems)
}

tit = Titration(params)

pH = 7.0
for site in tit:
    state = site.getProtState(pH)[0]
    print(site.res_name, site.res_number, site.pK, state)

You may also try it out on a online notebook.

CLI

The same calculation can be done via CLI by resorting to a input parameter file.

parameters.dat

structure       = 4lzt.pdb      # Input structure file name
ncpus           = -1            # Number of processes (-1 for maximum allowed)
epsin           = 15            # Dielectric constant of the protein
ionicstr        = 0.1           # Ionic strength of the medium (M)
pbc_dimensions  = 0             # PB periodic boundary conditions (0 for solvated proteins and 2 for lipidic systems)
sites           = all           # Titrate all available sites
output          = pKas.out      # pKa values output file

To run the simulation execute the following command:

python3 -m pypka parameters.dat