APBS

The APBS tool is an interface for running APBS (Adaptive Poisson-Boltzmann Solver) electrostatics calculations, using either a web service provided by the National Biomedical Computation Resource (NBCR) or a locally installed copy of the program. Users should cite:

Electrostatics of nanosystems: application to microtubules and the ribosome. Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Proc Natl Acad Sci USA. 2001 Aug 28;98(18):10037-41.

The resulting electrostatic potential map will be opened as a new model in Chimera and the Electrostatic Surface Coloring tool for coloring molecular surfaces by potential will appear. Alternatively, the map can be shown as isopotential surfaces; these are not displayed automatically, but can be shown by starting Volume Viewer and clicking the eye icon or by using the volume command.

See also: Coulombic Surface Coloring, DelPhiController

There are several ways to start APBS, a tool in the Surface/Binding Analysis category. It is also implemented as the command apbs.

• Molecule - the structure of interest (choose from pulldown menu of models in Chimera) ** If charges were assigned with PDB2PQR, the model output by that step should be used, not the original model.**
  
  
• DX output file (optional) - name and location of output electrostatic potential map; if not specified, a temporary filename and location will be used.

Focusing will be performed automatically; that is, there will be an initial electrostatics calculation on a larger grid with relatively coarse divisions, followed by another calculation on a smaller grid with finer divisions, for which the boundary conditions are determined from the first run (APBS keyword mg-auto). Default grid sizes (see dime, cglen, and fglen below) are based on the dimensions of the input structure. APBS keywords are shown in parentheses below; see the documentation at the APBS site for further details on specific options.

• Grid dimensions (dime): [nx][ny][nz] - grid points per processor; dimensions in integer grid units along the molecule X, Y, and Z axes; commonly used values are 65, 97, 129, and 161
• Coarse grid lengths (cglen): [xlen][ylen][zlen] - dimensions in Å of the coarse grid along the molecule X, Y, and Z axes; the coarse grid should completely enclose the biomolecule
• Use molecule center for coarse grid center (cgcent) (true/false) - whether to center the coarse grid on the molecule
• Coarse grid center coordinates: [xcent][ycent][zcent] - if not centering on the molecule, coordinates of the center of the coarse grid in the molecule coordinate system
• Fine grid lengths (fglen): [xlen][ylen][zlen] - dimensions in Å of the fine grid along the molecule X, Y, and Z axes; the fine grid should enclose the region of interest in the molecule
• Use molecule center for fine grid center (fgcent) (true/false) - whether to center the fine grid on the molecule
• Fine grid center coordinates: [xcent][ycent][zcent] - if not centering on the molecule, coordinates of the center of the fine grid in the molecule coordinate system
• Boundary condition for coarse grid (bcfl) - how to initialize potential at the boundary of the coarse grid (results from the coarse run are then used to initialize potential at the boundary of the fine grid)
  • zero - boundary potential set to zero; generally not recommended
  • single Debye-Hückel (default) - potential set to values prescribed by a Debye-Hückel model for a single sphere with a point charge, dipole, and quadrupole; the boundary should be sufficiently far from the molecule
  • multiple Debye-Hückel - potential set to values prescribed by a Debye-Hückel model for multiple noninteracting spheres with point charges; works better than the single approximation when the boundary is near the molecule, but can be very slow for large molecules
• Solute dielectric constant (pdie) (default 2.0) - dielectric constant inside the molecule
• Solvent dielectric constant (sdie) (default 78.54) - dielectric constant outside the molecule
• Charge mapping method (chgm) - how atomic partial charges are mapped to grid points
  • trilinear interpolation - linear spline, charges mapped onto nearest-neighbor grid points; resulting potentials are very sensitive to the grid setup
  • cubic B-spline discretization (default) - charges spread out to two layers of grid points (nearest- and next-nearest neighbors); intermediate sensivity to the grid setup
  • quintic B-spline discretization - charges spread out to three layers of grid points; lowest sensivity to the grid setup
• Include mobile ions (ion) (true/false) - whether to include mobile ions in the calculation
• Positive ion charge (e), conc. (M), and radius: [q][c][r] - if including mobile ions, positive ion charge in electron units (the value should be positive), molar concentration, and radius in Å. The total system of mobile ions must be electroneutral; for example, if the positive ion has twice the charge magnitude of the negative ion, its concentration should be half as high.
• Negative ion charge (e), conc. (M), and radius: [q][c][r] - if including mobile ions, negative ion charge in electron units (the value should be negative), molar concentration, and radius in Å
• Poisson-Boltzmann equation:
  • linearized (lpbe) (default)
  • nonlinear (npbe) - more computationally expensive to solve than the linearized equation, but more accurate for highly charged systems such as nucleic acids or phospholipid membranes
  • size-modified (smpbe)
• How to map dielectric values and ion accessibility (srfm)
  • molecular surface - partition space into regions of solute and solvent dielectric by the molecular surface (solvent-excluded surface calculated with the specified solvent radius and density of points), and into regions of ion inaccessibility or accessibility by the VDW surface inflated by the ion radius
  • smoothed molecular surface (default) - as above, except smooth the dielectric and accessibility values to reduce sensitivity to the grid setup
  • cubic-spline surface - use a cubic-spline surface to partition regions of solute dielectric and ion inaccessibility from regions of solvent dielectric and ion accessibility; the spline window width is set to 0.3 Å (APBS keyword swin)
  • 7th-order polynomial - use a seventh-order polynomial to partition regions of solute dielectric and ion inaccessibility from regions of solvent dielectric and ion accessibility
• Surface density (sdens) (default 10.0 points/Ų) - density of points used to calculate a molecular surface for mapping values
• Solvent radius (srad) (default 1.4 Å) - solvent (probe) radius used to calculate a molecular surface for mapping values
• System temperature (temp) (default 298.15 K) - temperature to use in the Poisson-Boltzmann equation
• Include explicit solvent (solvent) (true/false) - whether to include any explicit solvent (typically water molecules) present in the input model

• Opal web service (default)
  • Server - URL of web service implemented using Opal; clicking Reset restores the URL for the service provided by the NBCR
• Local
  • Path - pathname of locally installed executable

OK initiates the calculation and dismisses the dialog, whereas Apply initiates the calculation without dismissing the dialog. The job will be run in the background; clicking the information icon in the Chimera status line will bring up the Task Panel, in which the job can be canceled if desired. Close dismisses the dialog, and Help opens this manual page in a browser window.

The electrostatic potential map will be opened as a new model in Chimera, and the Electrostatic Surface Coloring tool for coloring molecular surfaces by potential will appear. Alternatively, the map can be shown as isopotential surfaces; these are not displayed automatically, but can be shown by starting Volume Viewer and clicking the eye icon or by using the volume command.