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 setclean_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 ispHstep