8.3.1 PBE SETUP Command
PBE SETUP repeat(pbe-setup-options) atom-selection
pbe-setup-options ::= [WATEr real]
[SMOOTH repeat(smooth-option) END]
interior-options ::= repeat([INTErior real exposure-opts atom-selection END])
exposure-opts ::= [ABSQ real] [EXPOsure real] [RESAve]
charge-options ::= [UNIForm ]
boundary-options ::= BOUNdary [ADEBye ]
charge-edit-options ::= repeat([CHARge edit-type real atom-selection END])
edit-type ::= [SCALe]
averaging-option ::= [HARMonic ]
smooth-options ::= [OFFGrid offgrid-option]
type-option ::= [VOLUME]
weight-option ::= [CONStant]
offgrid-option ::= [SOLVent]
The PBE SETUP command creates the
pbe_info data structure,
see PBE Data Structures, which stores the grids upon which the
electrostatic potential is computed. The command has a large number of
options and an atom-selection, see Atom Selection. The atom
selection allows the user to select any portion of the system for the
calculation. For example, if one is interested in the calculation of the
binding energy of a complex, the atom selection can be used to select
each component and then all the atoms for separate electrostatic
calculations. The options are described in the following table.
- Specifies the dielectric constant of the solvent in units of the vacuum dielectric.
Thus, the vacuum dielectric would be 1, and the dielectric constant of water is
around 78. The default is 78.
- The INTERIOR option is used to specify the dielectric constant of
the interior of the atom selection in the INTERIOR option. Any
number of these options can be specified, and thus, it is possible to
specify different dielectric constants for different parts of the
system. It is possible to adjust the dielectric constant of exposed
atoms to that of the solvent1. If
the either option, ABSQ or EXPOSURE, is specified, then the
exposure adjustment calculation will be done. Any atom whose exposure
and charge meet the criteria will have the dielectric constant set to
the solvent value as specified by the SOLVENT keyword. N.B. This
option is highly experimentally and has not been proven useful in any
meaning of the keywords is given as follows:
- The magnitude of the charge of the atom must be greater than or equal to this
option in order for surface charge adjustment to be performed.
- The relative molecular surface exposure of the atom for the adjustment
is specified by this parameter. If the relative molecular surface exposure
is less than EXPOSURE - 0.1, then the dielectric constant will be
left alone. If the relative molecular surface exposure
is greater than EXPOSURE + 0.1, then the dielectric constant will be
set to the solvent value. Otherwise, it will be scaled harmonically between
the interior value and solvent value.
- The average relative molecular surface is calculated for all the atoms within
a residue, and the exposure test above and the scaling is applied for
The charging options, UNIFORM and TRILINEAR, along with
the options SUBDIVISIONS and SPILL, control how
the charge grid is set. With the TRILINEAR option, the charge of
each atom is divided among the eight nearest points to the atom center.
With the UNIFORM option, the charge of each
atom is divided evenly among all the points within the van der Waals
radii of the atom, except in the case where the number of such points
is less than eight. In that case, trilinear interpolation is used.
The option, NWARN, controls how many warning of this conversion are
The uniform charging option can be further improved using the SUBDIVISIONS
and SPILL options. One problem with the use of grid based methods
to represent molecular structure is the quantization of space. The same problem
has arisen in the development of computer graphics using raster devices, and
using the techniques of anti-aliasing, CONGEN can smooth the charge distribution
of atoms. When the SUBDIVISIONS option is used, the space around each atom
is subdivided into
virtual cubes, and the charge distribution is calculated over these
virtual cubes, and then added onto the real cubes in the grid. If the SPILL
option is turned on (recommended!), then charge can spill onto cubes outside
the van der Waals radius of each atom. If SPILL is not specified, then the
charge will not extend beyond the van der Waals radius.
- The NWARN option specifies the maximum number of warning messages
to be issued if an atom is too small for the uniform charging scheme
to charge eight points. The default is 5.
The boundary-options are used to specify how the potential is set
for the boundary of the grid. The ZERO option specifies that the
boundary potential should be zero. The ADEBYE option specifies
that the atomic Debye method should be used, see Introduction to Poisson-Boltzmann Electrostatics. This option is very slow.
The SDEBYE options specifies
that the system Debye method should be used. The keyword, PREVIOUS,
is not implemented.
The IONSTR parameter is used to set the ionic strength. The units
are in molarity. The default value is 0.0.
The GRID option sets the physical spacing between grid points.
This is a critical parameter in the calculation of electrostatics using
the Poisson-Boltzmann equation. The smaller the grid, the better the
accuracy, but computation time scales as the grid size to the 4th power.
The default value is 1.25 Angstroms.
- The TEMPERATURE option is used to set the temperature for calculating
the Debye-Huckel parameter,
The default value is 300 K.
- The radius of water in Angstroms is set using the WATER option.
The radius of water is added to the van der Waals radii of all atoms
and the dielectric constant of the midpoints of grid lines within
this combined radius is set to the interior dielectric value for
Use of the WATER option causes the program to use the solvent
surface to define the interior.
The default value is 0.0. Our current view is that
this parameter should be left at 0.0 because ion solvation energies
are calculated more accurately that way.
- The thickness of the ion exclusion layer (Stern layer) is
set to the STERN option. Within this distance of any atom,
it is assumed that ion screening does not take place, and the Debye-Huckel
parameter is set to zero. The default value is 2.0 Angstroms.
- If the MARGIN option is non-negative, this option has no effect.
when the CENTER option is specified, the center of grid is placed at
the geometric center of the system. Otherwise, the center of grid is placed at the
- The XDIM option sets the number of grid points in the X direction.
- The YDIM option sets the number of grid points in the Y direction.
- The ZDIM option sets the number of grid points in the Z direction.
- The MARGIN option sets the number of empty grid points surrounding
the molecule. If set to a non-negative number, then CONGEN determines a rectangular
box that will surround the molecule including the van der Waals radius, plus two
grid spacings if the SPILL option is on. Then, the dimensions of the box will
be increased in order to center this box within the grid with MARGIN grid points
around all sides. When the MARGIN option is non-negative, the CENTER
option has no effect.
- The MINRADIUS keyword allows the user to specify the minimum radius for
any atom placed on the grid. This keyword is important for potentials, such
as AMBER94, see AMBER94PARM, which have several atoms with zero or
small radius. Because the electrostatic self energy of a sphere is inversely
proportional to the radius, such small atoms cause convergence problems.
Therefore, one can set the minimum radius using the above option.
- The REUSE option specifies that the current PBE SETUP command
should update rather than initialize the
pbe_info data structure. For the
keyword options described here, the default values are taken from the current
values rather than the values described in this documentation. The OLDGRID
option is similar, except it maintains only the grid, but not the values
are important for doing binding energy calculations. In order to cancel errors
due to grid positioning, it is essential to first calculate the energy of
the complex, and then, using the OLDGRID option, calculate the energies
of the components by selecting the atoms of the components, but leaving the
atoms and grids in the same spatial positions.
When this option is used, you should not specify any grid dimensions or
the MARGIN option. If you do, and they are different than the
actual values, then the REUSE or OLDGRID option will be turned off.
- This option specifies that the interior of the molecule is defined by
the molecular surface as computed by the GEPOL algorithm, see Atom Properties, for more information about GEPOL. The dielectric constant
of points covered by the molecular surface but not atomic spheres is
determined by the following scheme: GEPOL generates additional spheres
which define the molecular surface. Each of these spheres derives from
one or two previous spheres or atoms. The dielectric constant of each
sphere is set to the average of its “parents”, where the average is
determined by the EPSAVE keyword. Then, points covered by each of
these spheres is averaged into the dielectric grid.
- Whenever dielectric constants are combined, the EPSAVE controls
how the averaging is performed.
The averaging can either be
ARITHMETIC (the "standard" mean) or HARMONIC (the reciprocal
of the mean of the reciprocals). This option applies to averaging dielectric
constants when atoms overlap in the grid, for dielectric smoothing, and
for generating the dielectric constant for spheres generated by the molecular
- The charge-edit-options allows the user to modify the charges used
for a calculation. Charges for the atoms in the atom-selection can
be changed in one of three ways. The SET option specifies the
charge explicitly. The SCALE option specifies a multiplicative
scale factor to be applied to the current charges of the selected
atoms. The SHIFT option specifies an additive term to be added to
the current charges of the selected atoms.
The SMOOTH command “smooths” the dielectric grids. After the
dielectric grids have been assigned internal and external values
“smoothing” averages each point with the other points in its
neighborhood to produce a dielectric grid with less abrupt changes in
value. One hope of the process is to reduce the position dependence of
the PBE electrostatic calculations. Its success in this endeavor is
still a topic of research.
Several types of smoothing are supported. The smoothing TYPE can
either be NONE, VOLUME, or GRID. Of course, no
smoothing is done when NONE (the default) is specified. For
VOLUME based smoothing the dielectric is averaged over a fixed
volume in real space defined by the RADIUS keyword. For
GRID based smoothing the dielectric is averaged over a set number
of points specified by the POINTS keyword (9 and 15 point
averaging are currently supported). In both case all three dielectric
grids are averaged togeher. In 9-point averaging each point is averaged
with the eight grid points from the other two grids which surround this
point in space. In 15-point averaging the six nearest neighbors from
the same grid are also included. (Note that volume smoothing with a
radius just smaller (larger) than the grid spacing is equivalent to
9-point (15-point) averaging.)
Which ever TYPE is selected,
The type of averaging is determined by the EPSAVE keyword above.
The WEIGHTING can
either be CONSTANT (all points in average counted equally), or
GAUSSIAN weighted (points are weighted by
where r is the distance from the central point in units of the grid dimension
and alpha is
specified by the ALPHA keyword).
For points at the edge of the grid the averaging extends to points
beyond the grid. Using the OFFGRID keyword,
these offgrid points can either be assumed to be
SOLVENT or equal to the value at the nearest EDGE of the
grid. (Note that the SOLVENT assumption will run faster.)