Like the Chimera APBS tool, the apbs command runs APBS (Adaptive Poisson-Boltzmann Solver) electrostatics calculations.
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** Requires installing APBS locally **
As of 4/30/2020, the APBS web service from the National Biomedical Computation Resource (NBCR) has been discontinued. The apbs command will no longer work unless you install APBS (available from GitHub) on your own computer and use the backend local and location options of the command. Alternatively, the APBS web service at server.poissonboltzmann.org can be run separately (not using Chimera) and the resulting electrostatic potential map (.dx file) opened in Chimera. |
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.A structure should be prepared for APBS calculations by reconstructing missing heavy atoms, adding hydrogens, and assigning atomic charges and radii. These tasks can be done with pdb2pqr alone or in combination with parts of Dock Prep. Atomic charges can be assigned with addcharge or pdb2pqr, although the latter may be preferred because it includes force fields developed specifically for Poisson-Boltzmann calculations. By default, any explicit solvent (typically water) will be omitted from the APBS calculation.
If more than one molecule model is present, the molecule option should be used to specify which to act upon. ** If charges were assigned with pdb2pqr, the model output by that step should be used, not the original model.**
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.
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, scolor, DelPhiController
Option keywords for apbs can be truncated to unique strings and their case does not matter. A vertical bar “|” designates mutually exclusive options, and default values are indicated with bold. Synonyms for true: True, 1. Synonyms for false: False, 0.
Several keywords are the same as for running APBS directly; see the documentation at the APBS site for details on specific options.
molecule atom-spec
Limit the calculation to the specified model (the molecule model containing the specified atoms). Only one model should be specified. If atom-spec includes any spaces, it must be enclosed in single or double quote marks. ** If charges were assigned with pdb2pqr, the model output by that step should be used, not the original model.**
solvent true | false
Whether to include any explicit solvent (typically water molecules) present in the input model.
output file
Pathname (name and location) of the output electrostatic potential map (*.dx type). If not specified, a temporary name and location will be used.
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.
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.
cgcent true | false
Whether to center the coarse grid on the molecule.
_cgcentcoord xcent,ycent,zcent
If not centering on the molecule, coordinates of the center of the coarse grid in the molecule coordinate system.
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.
fgcent true | false
Whether to center the fine grid on the molecule.
_fgcentcoord xcent,ycent,zcent
If not centering on the molecule, coordinates of the center of the fine grid in the molecule coordinate system.
bcfl condition
How to initialize potential at the boundary of the coarse grid, where condition can be: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
- sdh (default) - single Debye-Hückel; 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
- mdh - 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
pdie dielectric1
Solute dielectric constant (default 2.0).
sdie dielectric2
Solvent dielectric constant (default 78.54).
chgm method
How to map atomic partial charges onto grid points, where method can be:
- spl0 - trilinear interpolation (linear splines), charges mapped onto nearest-neighbor grid points; resulting potentials are very sensitive to the grid setup
- spl2 (default) - cubic B-spline discretization, charges spread out to two layers of grid points (nearest- and next-nearest neighbors); intermediate sensivity to the grid setup
- spl4 - quintic B-spline discretization, charges spread out to three layers of grid points; lowest sensivity to the grid setup
ion true | false
Whether to include mobile ions in the calculation.
_posion charge,conc,radius
If including mobile ions, the 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.
_negion charge,conc,radius
If including mobile ions, the negative ion charge in electron units (the value should be negative), molar concentration, and radius in Å.
_equation lpbe | npbe | smpbe
Which form of the Poisson-Boltzmann equation to use:
- lbpe (default) - linearized
- npbe - nonlinear (full); more computationally expensive to solve than the linearized equation, but more accurate for highly charged systems such as nucleic acids or phospholipid membranes
- smpbe - size-modified
srfm model
How to map dielectric values and ion accessibility, where model can be:
- mol - 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
- smol (default) - as above, except smooth the dielectric and accessibility values to reduce sensitivity to the grid setup
- spl2 - 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).
- spl4 - use a seventh-order polynomial to partition regions of solute dielectric and ion inaccessibility from regions of solvent dielectric and ion accessibility
sdens density
Density of points used to calculate a molecular surface for mapping values (default 10.0 points/Å2).
srad radius
Solvent (probe) radius used to calculate a molecular surface for mapping values (default 1.4 Å).
temp T
Temperature to use in the Poisson-Boltzmann equation (default 298.15 K).
backend opal | local
Whether to use an Opal web service (default) or a locally installed executable.
location opal-URL | local-path
Depending on the backend setting, the URL of the web service (default is the URL for the service provided by the NBCR) or the pathname of the local executable. Since the NBCR web service has been retired, users need to download APBS and use both the backend local and location options.
wait true | false
Whether to wait for the calculation to finish before starting to execute any subsequent commands.