Calculation input
The APBS input file provides the parameters used in Poisson or Poisson-Boltzmann electrostatics calculations. The basic ingredients of an electrostatics calculation are listed in the following table.
 | The detailed format of the input file is discussed in the APBS manual (http://apbs.sourceforge.net/doc). |
Table 1. Basic APBS input parameters
| Parameter description | APBS variable names | Common values |
|---|---|---|
| Grid dimensions | dime | 65, 97, 127, 161 |
| Grid spacing or length | grid or [ fglen | cglen | glen ] | Grid spacings should be 0.5 A or smaller for quantitative calculations; grid lengths should be large enough for the boundary conditions to hold. |
| Grid position | [ gcent | fgcent | cgcent ] | The position of the grid center should coincide with the region of interest of the system; e.g., a binding site, etc. |
| Boundary condition definition | bcfl | The most common setting is sdh which considers only the monopole moment of the system when assigning boundary conditions. The much slower mdh option considers all multipole moments of the protein but assumes non-interacting spheres (thereby only approximately describing the solvation behavior). |
| Dielectric constants | sdie for the solvent and pdie for the biomolecule. | The common dielectric value for water at 300 K is 78.54 (~80). Biomolecular dielectric constants range from 2 (electronic polarization only) to 20 (implicit side chain relaxation) with the specific value dependent on the application. |
| Temperature | temp | The temperature of the calculation; should be chosen consistently with the dielectric coefficients. |
| Ion species and concentrations | ion | Specify the concentrations, charges, and radii of the mobile ion species to be included in the Poisson-Boltzmann calculation. |
| Coefficient (surface) definitions | srfm, srad, swin | These parameters determine the surfaces used to define the dielectric and ion accessiblity coefficients. As described in numerous articles, the results of PBE calculations can be very sensitive to the surface definition. These should be chosen consistently for each calculation -- and the results should be examined for their dependence on the particular surface definition used. |
For the Born ion, we will be running a series of calculations on ions of different radii. However, in order to make a meaningful comparison of the results, these calculations will all be performed with the same parameters! Specifically, we will be using a common input file which is given below and available here.
The major elements of this calculation are:
Read in the molecular data.
Calculate the electrostatic potential and energy in the solvated state.
Calculate the electrostatic potential and energy in the reference (vacuum) state to remove self-energies, etc.
Compute the energy change.
Example 2. Born ion APBS input file
# READ IN MOLECULES
read
mol pqr ion-RADIUS.pqr
end
elec name solv # Electrostatics calculation on the solvated state
mg-manual # Specify the mode for APBS to run
dime 97 97 97 # The grid dimensions
nlev 4 # Multigrid level parameter
grid 0.33 0.33 0.33 # Grid spacing
gcent mol 1 # Center the grid on molecule 1
mol 1 # Perform the calculation on molecule 1
lpbe # Solve the linearized Poisson-Boltzmann
# equation
bcfl mdh # Use all multipole moments when calculating the
# potential
pdie 1.0 # Solute dielectric
sdie 78.54 # Solvent dielectric
chgm spl2 # Spline-based discretization of the delta
# functions
srfm mol # Molecular surface definition
srad 1.4 # Solvent probe radius (for molecular surface)
swin 0.3 # Solvent surface spline window (not used here)
sdens 10.0 # Sphere density of accessibility object
temp 298.15 # Temperature
gamma 0.105 # Apolar energy surface coefficient (not used here)
calcenergy total # Calculate energies
calcforce no # Do not calculate forces
write pot dx potential-RADIUS
# Write out the potential
end
elec name ref # Calculate potential for reference (vacuum) state
mg-manual
dime 97 97 97
nlev 4
grid 0.33 0.33 0.33
gcent mol 1
mol 1
lpbe
bcfl mdh
pdie 1.0 # The solvent and solute dielectric constants are
# equal
sdie 1.0 # The solvent and solute dielectric constants are
# equal
chgm spl2
srfm mol
srad 1.4
swin 0.3
sdens 10.0
temp 298.15
gamma 0.105
calcenergy total
calcforce no
end
# Calculate solvation energy
print energy solv - ref end
quit
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