Input Parameters¶

General Parameters¶

structure (str)

Optional: No

The input filename in Protein Data Bank or GROMACS formats

ncpus (int)

Optional: No

Number of CPUs to use in the calculations

ionicstr (float)

Optional: No

Ionic strength of the medium

ffinput='GROMOS' (str)

Allowed values: (‘GROMOS’, ‘AMBER’, ‘CHARMM’)

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

ffID='G54a7' (str)

Allowed values: (‘G54A7’)

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)

Optional: No

Internal dielectric to be used in the PB calculations.

pbc_dimensions (int)

Optional: No
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.

Zero
Dipolar
Focusing
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