View Zap Map Molecule Dialog Box

Zap Map Molecule 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.

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.

Region Definition...
pushbutton
Select this button to define the spatial extents of the map region. The Region Definition dialog box appears when this button is selected.

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

Inside Mol Cut Off
check box
The Inside Mol Cut Off parameter specifies whether grid points inside the Van der Waals radius of any atom are to be set to predefined constant values.

Low Limit
field
The Low Limit parameter is the constant that will be assigned to negative-valued grid points inside the Van der Waals radius of any atom if Inside Mol Cut Off is set to On.

High Limit
field
The High Limit parameter is the constant that will be assigned to positive-valued grid points inside the Van der Waals radius of any atom if Inside Mol Cut Off is set to On.

Map File
field
Enter the desired filename for the map. In order for the map to be properly recognized by SYBYL for contouring, use .cnt as the filename extension.

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 are generally completed in less than one minute, so it should only be necessary to submit them to batch under unusual circumstances.

GRASP Output/Filename
check box and field
This option will require Zap to write a GRASP-compatible grid file in addition to the Sybyl (.cnt) file.