Found as Zap under "eslc". There are two Zap license levels, called
Zap (basic) and ZapHV (high voltage, which is a superset
of the basic version). Each has its own specific set of enabled
commands. The (basic) Zap command set allows you to calculate
Atom Potentials & Energies (from atomic charges), 3D Potential Energy Maps,
and calculate molecular solvation energy. The ZapHV license
enables additional tools to calculate 3D solvation energy maps,
ligand binding energies, residue pKa predictions and
a variety of surface and volume electrostatic descriptors. These
commands are arrayed in a variety of Zap submenus which will be
described in turn in this chapter. In addition there is a
ZapQSAR submenu that contains some useful utilities for applying Zap
to the SYBYL Molecular Spreadsheet.
This submenu activates a single command, to calculate and display
in the Sybyl graphics window the Atomic Potentials & Energies. Note that
this permanently replaces the atomic charges for the molecule, so it
would be prudent to save the molecule to disk prior to executing this
command. These energies are calculated by solution of the Poisson-Boltzmann
equation for the molecule and its dielectric environment. The current
atomic charges are used in the calculation, and the result will
be dependent on the quality of these.
Zap Atom Potentials & Energies Dialog Box
The Zap Atom Potentials & Energies Dialog Box defines the setup of the
calculation for a molecule that is currently displayed in SYBYL.
The sub-dialog Zap Details contains options
that need to be adjusted less commonly.
View Zap Molecule Potentials Dialog Box
The Zap Details Dialog Box assists in defining several less
commonly adjusted Zap setup parameters. These are generally associated
with Dielectric Model selection and the details of Zap convergence.
View Zap Details Dialog Box
This submenu activates three commands: to calculate the solvation energy
(induced solvent charge) for a currently active Sybyl molecule, to calculate
the binding energy for a ligand/target complex, and to produce a report of
electrostatic properties and decriptors for a currently active Sybyl molecule.
It is necessary, as in all Zap calculations, for the molecule to have Valid charges.
The Molecular Solvation Energy Dialog Box defines/sets up the parameters
for the calculation.
View Zap Molecular Solvation Energy Dialog Box
The Electrostatic Binding Energy Dialog Box defines/sets up the parameters
and molecule(s) for the calculation.
View Zap Electrostatic Binding Energy Dialog Box
The Electrostatic Structure Report gives an output text file of a selection
of electrostatically-relevant features. This Dialog Box defines/sets up the parameters
for the calculation.
View Zap Electrostatic Structure Report Dialog Box
The Zap Map Molecule is an electrostatic potential map of the
molecular region. This dialog box aids in setting up the region
for the map and important parameters for the calculation. It is
necessary, as in all Zap calculations, for the molecule to have Valid
charges. At the completion of the calculation, you will be given an
opportunity to contour the map for display within Sybyl.
View Zap Map Molecule Dialog Box
The Zap Map Induced Solvent Charge is an electrostatic potential map of
solvation energy in the molecular region. This dialog box aids in setting up the region
for the map and important parameters for the calculation. It is
necessary, as in all Zap calculations, for the molecule to have Valid
charges. At the completion of the calculation, you will be given an
opportunity to contour the map for display within Sybyl.
View Zap Map Induced Solvent Charge Dialog Box
The Map Difference Dialog Box enables you to calculate the
difference (or sum) of two separate Zap (or other) contour
files. The Difference between two Zap maps for
two related molecules can be used to determine the areas
where there is significant difference in potential, etc.
Note that the validity and interpretability
of a map difference result is enhanced when the two input
maps match closely in terms of region spanned and grid
spacing.
View Map Difference Dialog Box
The Map Contour Dialog Box is a convenience utility for
contouring and displaying SYBYL (.cnt) contour files.
View Map Contour Dialog Box
The Region Definition Dialog Box assists in describing
the region in 3D cartesian space that the map calculation
should span.
View Region Definition Dialog Box
The Zap QSAR submenu contains some utility functions to
aid in the use of Zap with the SYBYL QSAR module.
Most of the Zap QSAR functionality is associated with
the SYBYL Molecular Spreadsheet. This will be discussed
in the next section.
The two options available in the ZapQSAR submenu are
Graph ZapQSAR... and Fill MSS Cells with ZapCoMFA Field.
This command allows you to fill specified MSS cells with a
ZapCoMFA field. You may wish to use this option if you
are attempting to predict activity of a new compound with
a CoMFA model that includes a Zap field.
View Fill MSS Cells with ZapCoMFA Field Dialog Box
The Retrieve ZapQSAR Dialog Box is a convenience
function to facilitate creation (for graphing) of the
CoMFA coefficients*standard deviation contour maps for
PLS runs where a Zap potential field was included.
The dialog box enables selection of the desired field
information and writes the selected CoMFA fields to
scratch disk files. Then these fields are sequentially
contoured.
View Retrieve ZapQSAR Dialog Box
Zap provides added functionality to the molecular
spreadsheet. Three additional column types are defined
by Zap/ZapHV: ZAPSOLVATION,
ZAPDESCRIPTORS and ZAPCOMFA. These are available
through the Spreadsheet "Autofill" button in the list
of column types. Note: Occasionally the ZAPCOMFA
column type is dropped by the Autofill menu. If this
happens, type mss!reset_eslc to the Sybyl> prompt.
The Add Column (ZapSolvation) Dialog Box sets the
parameters for filling the cells in a spreadsheet
column with the solvation energy of each
molecule (row) in the table.
View Add Column (ZapSolvation) Dialog Box
The Add Column (ZapCoMFA) Dialog Box sets the
parameters for filling each cell in a spreadsheet
with a Zap Potential or Energy field. This Dialog Box
contains parameters related to the Zap calculation
for each molecule and parameters related
to the map creation for each molecule (row) in
the table.
View Add Column (ZapCoMFA) Dialog Box
This dialog box is called from the Zap COMFA routine
and is used to set the parameters for defining the
CoMFA region based on the union space spanned by the
entire molecule set. The routine determines the
spatial extents of each molecule and creates a region
that encompasses all molecules.
View Calculate CoMFA Region Automatically Dialog Box
The Define CoMFA Region Dialog Box is used if the
cartesian coordinate set defining the region (Lower
Box Corner, Upper Box Corner) is known, or if a
custom region that includes more than one Box is
needed. This latter case may be a useful option for
some CoMFA experiments where much of the molecular
structures are identical and a "closeup" on the
areas of difference is appropriate.
View Define CoMFA Region Dialog Box
The Add Column (ZapDescriptors) Dialog Box sets the
parameters for filling the cells in a spreadsheet
column with a variety of Zap Electrostatic Structure
Descriptors for each molecule (row) in the table.
View Add Column (ZapDescriptors) Dialog Box