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 pKa values, we can speed up the simulation by setting
ph to the single pH value of the desired output structure.
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