MD Structure Preparation

In this example we are preparing a structure for molecular dynamics by assigning the most likely protonation state to all titrable sites.

In order to output this structure we need to add the argument structure_output. Since we aren’t interested in calculating pK_a values, we can speed up the simulation by setting ph to the single pH value of the desired output structure.

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
structure_output = out.pdb, 7, amber  # Output structure with the most likely protonation state at a given pH value
# filename, pH value, force field ("gromos_cph", "amber")
pH = 7                          # pH range

To run the simulation execute the following command:

python3 -m pypka parameters.dat