Input Parameters

General Parameters

structure (str)


The input filename in Protein Data Bank or GROMACS formats

ncpus (int)


Number of CPUs to use in the calculations

ionicstr (float)


Ionic strength of the medium

ffinput='GROMOS' (str)
Allowed values


Forcefield of the input structure. GROMOS is also valid for experimentally obtained strucutures

ffID='G54a7' (str)
Allowed values


For the time being, only GROMOS54a7 based charged and radii are allowed. In the future more forcefields will be added.

sites='all' (str)

CLI Syntax: sites_A = all sites_A = 1N, 18, 35, 48, 66, 129C

API Syntax: sites = ‘all’ sites = {‘A’: (‘1N’, ‘18’, ‘35’, ‘48’, ‘66’, ‘129C’)} Titration(parameters, sites=sites)

clean_pdb=True (boolean)

The input structure files are preprocessed with PDB2PQR. To skip this step set clean_pdb to False.

CLI Syntax: yes or no

Poisson-Boltzmann Parameters

epsin (float)


Internal dielectric to be used in the PB calculations.

pbc_dimensions (int)


Allowed values

(0, 2)

Number of dimensions with periodic boundaries. Use 0 for solvated proteins and 2 for lipidic systems.

gsize=81 (int)

DelPhi number of grid points per side of the cubic lattice.

epssol=80.0 (float)

Solvent dielectric to be used in the PB calculations.

relpar=0.75 (float)

DelPhi relaxation parameter in non-linear iteration convergence process.

relfac=0.75 (float)

DelPhi spectral radius.

nonit=0 (float)

DelPhi number of non-linear iterations.

nlit=500 (float)

DelPhi number of linear iterations.

convergence=0.01 (float)

DelPhi convergence threshold for maximum change of potential.

scaleM=4 (float)

DelPhi reciprocal of one grid spacing for the finer grid.

scaleP=1 (float)

DelPhi reciprocal of one grid spacing for the coarse grid used in the focusing step.

slice=0.05 (float)

Only used when pbc_dimensions is 2. Fraction of the exterior of the lipid bilayer to be replicated with periodic boundary conditions.

pbx=False (boolean)

DelPhi periodic boundary conditions for the x edge of the grid

pby=False (boolean)

DelPhi periodic boundary conditions for the y edge of the grid

bndcon=4 (int)
Allowed values

(1, 2, 3, 4)

DelPhi type of boundary condition.

  1. Zero

  2. Dipolar

  3. Focusing

  4. Coulombic

precision='single' (str)
Allowed values

(‘single’, ‘double’)

Precision of the compiled DelPhi version being used.

Monte Carlo Parameters

seed (int)

Seed for the MC random generator

pH='0,14' (str)

pH value of the calculation. It can be a single value or a range.

CLI syntax:

pH = 0, 14

API syntax:

‘pH’: ‘0, 14’

pHstep=0.25 (float)

In case a pH range was provided pH, the pH step of said range is pHstep