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| Introduction |
Calculation Setup |
Visualizing Electrostatic Potentials |
Preparing an APBS calculation involves three steps:
A PQR file provides the molecular information (coordinates, charges, and radii). Most modeling packages can convert PDB files into PQR files with the representative force field radii and charges. The PDB2PQR portal, http://agave.wustl.edu/pdb2pqr/ is a convenient tool that provides CHARMM, AMBER or PARSE parameters, optimizes hydrogen bonding networks, and generates a sample APBS input file.
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.
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The detailed format of the input file is discussed in the APBS manual (http://agave.wustl.edu/apbs/doc/html/user-guide/index.html). |
Table 1. Basic APBS input parameters
| Parameter description | APBS variable names | Common values |
|---|---|---|
| Grid dimensions | dime | 65, 97, 127, 161
Note that these follow C*2 nlev+1 +1 where C is a constant and nlev, the number of grids used, is 4 |
| 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. It is important to insure overall system neutrality |
| 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. |
We will see an example input file in the next section, Visualizing Electrostatic Potentials
Assuming that the input script is named apbs_run1.in, then an APBS run can be performed by typing:
apbs apbs-run1.in > apbs-run1.out |
Note it is generally nice to pipe the output to a file for future use especially if one is calculating energies as we will do in the second and third examples.
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