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7.3.4 Comparing with Delphi results

Under identical condition, PBSA is highly consistent with Delphi in term of computed reaction field energies.
In this subsection, we briefly go over the details on how you can obtain comparable energies from both program.
Apparently, you need coordinates, atomic charges, and atomic radii that have exactly the same numerical values
but in both the Amber format and the Delphi format, i.e. the pqr format.

For a Delphi computation with the following input parameters:

salt=0.150
ionrad=2.0
exdi=80.0
indi=1.0
scale=2.0
prbrad=1.5
perfil=50
bndcon=4
linit=1000

a comparable computation in PBSA can be obtained by using the following input file:

Sample PB for delphi comparison
 &cntrl
   ntx=1, imin=1, ipb=1, inp=0
 /
 &pb
   npbverb=0, istrng=150, epsout=80.0, epsin=1.0,
   ivalence=1, iprob=2.0, space=0.5, accept=1e-3,
   dprob=1.5,  radiopt=0, fillratio=2, bcopt=6,
   smoothopt=2, nfocus=1, dbfopt=1, cutnb=0,
   maxitn=10000
 /

The above sample input files are also provided in the current release under
$AMBERHOME/test/pbsa_delphi. Note that the values of exdi, indi, prbrad, and
ionrad in Delphi should be consistent with the values of epsout, epsin, dprob,
and iprob in PBSA, respectively. In Delphi salt=0.150 is set in the unit of M,
while in PBSA istrng=150 is in the unit of mM. In Delphi the grid spacing is set
as the number of grids per \AAngstrom, i.e. scale=2.0, while in PBSA the grid spacing
is set straight as space=0.5 in \AAngstrom. In Delphi the grid dimension is set as
percentage of the solute dimension over the grid dimension, i.e. perfil=50, which
is equivalent to the ratio of solute dimension over grid dimension set as
fillratio = 2 in PBSA. Finally, Delphi sets the boundary condition by bndcnd=4 and
PBSA sets the boundary condition as bcopt=6; both programs mean to use the
Debye-HŸckel limitation behavior for each atomic charged sphere. There are
additional options in PBSA that do not have corresponding counterparts in Delphi.
For example, smoothopt is used to instruct the program to use a specific dielectric
boundary smoothing option, which is equivalent to that used in Delphi when set to 2.
(see Section 7.1.3); arcres is used to set the resolution of numerical dot
representation of the solvent accessible arcs, the default is 1/16 \AAngstrom,
which is similar to the numerical resolution of solvent accessible arc dots used in Delphi.

7.4 PBSA in SANDER

All PBSA functionalities are available in SANDER and all input options are exactly the same as
in the standalone PBSA. Apparent exceptions are ipb and inp: you need to really set ipb/inp to
nonzero in order to invoke PBSA functionalities.

7.5 PBSA in NAB

PBSA functionalities are available in NAB as a part of the standard build.
However the available input options are limited, please refer to the table in
Section 14.1 for the list of available PBSA input options. The structures
and parameters are supplied by NAB's facility. An extra feature for PBSA in
NAB is the availability of electrostatic forces or gradients. We describe special
consideration in its applications in the following section.

7.5.1 Electrostatic Forces/Gradients in PBSA

Force calculation in the finite-difference Poisson-Boltzmann method is
straightforward, though not a trivial issue. It can be shown, by using the
variation of the electrostatic free energy, that the electrostatic force
density consists of three components, viz., the reaction field force,
the dielectric boundary force, and the ionic force.
\begin_inset CommandInset citation
LatexCommand cite
key "Gilson:1993p11929"
\end_inset
Since the ionic force is much smaller in absolute value than the other two
components, we only include the reaction field force and the dielectric
boundary force in this release.

The reaction field force only exists where there are atomic charges, so that
it is straightforward to be mapped onto atoms. In contrast, the dielectric
boundary force exists on the molecular surface where the dielectric constant
changes. The surface force, or pressure, cannot be easily mapped onto atoms.
This is because a force-mapping procedure from the molecular surface to atoms
apparently needs the derivatives of molecular surface with respect to atomic
positions. However such derivatives do not exist for the widely used molecular
surface definition, i.e. the solvent excluded surface (SES). We are actively
developing an analytical molecular surface definition that is consistent with
the widely used SES definition for the numerical PB methods so that this
difficulty will be overcome in future releases.

Temporarily, there is a partial solution in the mapping of dielectric boundary
force as described by Gilson et al
\begin_inset CommandInset citation
LatexCommand cite
key "Gilson:1993p11929"
\end_inset
when the SES definition is used. This is currently adopted in the PBSA module.
Note that the method is rigorously correct only for two overlapping atoms.
On solvent-exposed surface with well-packed and highly charged atoms, such as
nucleic acid backbones, the error in the force-mapping procedure can be very large.
Our tests show that the deviations from the numerical finite-difference forces
can be in the orders of several tenths of kcal/mol-\AAngstrom. In other situations,
the errors are in the orders of several hundredths of kcal/mol-\AAngstrom.

7.5.2 Example
.
.
.
mm_options("ntpr=1, cut=99.0"); // No solute-solute cutoff
mm_options("ipb=1");            // Use PBSA
mm_options("accept=0.000001");  // Convergence criterion
mm_options("sprob=1.6");        // Solvent probe radius for SASA
mm_options("radiopt=1");        // Useatom-type/charge-based radii
mm_options("fillratio=4");      // Coarse/Fine ratio of electrostatic focusing
.
.
.
********************************************************************************
@Article{Gilson:1993p11929,
author = {Gilson, M.K. and Davis, M.E and Luty, B.A. and McCammon, J.A.},
journal = {J Phys Chem},
title = {{Computation of electrostatic forces on solvated molecules using the
Poisson-Boltzmann equation}},
number = {14},
pages = {3591--3600},
volume = {97},
year = {1993}
}