Using a MD structure

In this example we are calculating the pKa values for all titrable residues using a molecular dynamics generated structure. The argument ffinput needs to be set to the appropriate nomenclature scheme.

structure       = amber.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
ffinput         = AMBER         # Input structure nomenclature scheme ("AMBER", "CHARMM", "GROMOS")

To run the simulation execute the following command:

python3 -m pypka parameters.dat