Complete Parameters File Template

parameters.dat

# Mandatory
structure = 4lzt.pdb    # Input structure file name
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)
ncpus = -1              # Number of processes (-1 for maximum allowed)
sites = all             # Titrate all available sites

# Output
output = pKas.txt                       # pKa values output file
titration_output = titration.txt        # Titration curves output file
titration_curve = titration_curve.txt   # Full titration curve (whole system charge) output file
isoelectric_point = yes                 # Calculate isoelectric point
save_pdb = pb_input.pdb                 # save PB input 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")


# Force Field
# f_crg = /home/user/database.crg     # DelPhi charges database file path
# f_siz = /home/user/database.siz     # DelPhi radii database file path
# path to search for .st files -> $ffs_dir/$ffID/$/sts
# ffs_dir = /home/user/database # default value is an internal folder
# ffID = G54A7 # built-in options: G54A7, CHARMM36m
# sts = sts


# Preprocessing
ffinput = GROMOS          # Input structure nomenclature scheme ("GROMOS", "AMBER", "CHARMM")
clean_pdb = True          # Clean the input structure
pdb2pqr_h_opt = True      # Allow pdb2pqr to optimize the hydrogen positions
remove_hs = True          # Remove hydrogens in the input structure
keep_ions = False         # Keep NA+ and CL- ions in the structure
ser_thr_titration = True  # Titrate SER and THR residues


# Poisson-Boltzmann
gsize = 81           # number of grid nodes
scaleP = 1           # inverse grid size of big grid
scaleM = 4           # inverse grid size of small grid
bndcon = 3           # DelPhi type of boundary condition for the big grid. 3 for Coulombic
convergence = 0.01   # PB convergence criterion
nlit = 500           # Number of linear iterations
nonit = 0            # Number of non-linear iterations
relfac = 0.75        # DelPhi spectral radius
relpar = 0.75        # DelPhi relaxation parameter in non-linear iteration convergence process.
epssol = 80.0        # Solvent dielectric constant value

# Monte Carlo
pH = 0,14        # pH range: pH minimum, pH maximum OR single pH value
pHstep = 0.25    # pH range step
seed = 1234567   # random number generator seed number
mcsteps = 200000 # number of production monte carlo steps
eqsteps = 1000   # number of equilibration monte carlo steps