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