View Zap Electrostatic Structure Report Dialog Box

Zap Electrostatic Structure Report Dialog Box

Atoms...

pushbutton

This push button calls up an "Atom Select" dialog box wherein the molecules, substructures, and atoms for the operation can be chosen. In most cases choosing "All" atoms is the appropriate option.

Surface Basis

radios: {Molecular|Accessible}

Choose how you want the surface to be represented, either as the Molecular (van der Waal) or (Solvent) Accessible surface.

No. Surface Thresholds

radios: {2|3|4|5|6|7|8}

This selection controls the number of thresholds or divisions the surface potential will be parsed into.

Minimum Threshold

field

Minimum threshold is the lowest threshold; intermediate thresholds will be evenly apportioned between the minimum and maximum values.

Maximum Threshold

field

Maximum threshold is the highest threshold; intermediate thresholds will be evenly apportioned between the minimum and maximum values.

Min Patch Threshold

field

Patches of surface potential below this value will be recorded and tabulated in the report.

Max Patch Threshold

field

Patches of surface potential above this value will be recorded and tabulated in the report.

Calculation Resolution

radios: {Coarse|Fine}

All Zap results are calculated on a grid, even if the resulting grid itself is not needed. This option controls the grid spacing and grid margin indirectly. The higher the Calculation Resolution, the more resource (time and memory) the grid calculation will require. For most purposes Coarse is effective.

Dielectric Constants: Inside

field

This is the dielectric constant assumed for grid points Inside the surface of the molecule. Typically this is 2-5.

Dielectric Constants: Outside

field

This is the dielectric constant assumed for grid points Outside the surface of the molecule, i.e., in solvent. Typically this is 80 for water.

More Zap Details...

pushbutton

The less commonly adjusted zap calculation parameters are accessed through the Zap Details dialog, which is activated by this button.

Report File

field

Filename for the structure report output.

Job Name

field

Enter a Job Name for the calculation if this is to be a SYBYL Netbatch background job.

Batch

check box

Turn this check box on if you wish the calculation to be a background (Netbatch) job. Zap calculations can take from a few seconds to several minutes depending on the size of the molecule and the type of calculation.