Zap 1.00 Manual: Chapter 6S

Tutorial

In this tutorial you perform several Zap calculations designed to acquaint you with the most commonly used features and calculation strategies of Zap.

In Lesson 1, you calculate and display the atomic potentials of methotrexate, a well-known inhibitor of dihydrofolate reductase. Atomic potential is calculated from atomic charge. In this lesson the Gasteiger-Hückel charge is used, but any method of atomic charge calculation can be used.

The topics covered in Lesson 1 are:

Reading in a enzyme/inhibitor SYBYL .mol2 files.

Setting desired Zap calculation parameters.

Performing the Zap atomic potential calculation.

Lesson 2 illustrates how to calculate and display three-dimensional Zap Potential contour maps for biomacromolecules.

The topics covered in Lesson 2 are:

Setting up parameters for a Zap potential map molecule calculation.

Performing the Zap calculation.

Display and interpretation of the map contours.

Lesson 3 demonstrates using Zap fields in 3D QSAR (CoMFA). The example in this lesson is the calculation of a Zap potential field for a set of dopamine D2 agonists that have very poor correlation (unusable) with the CoMFA electrostatic field, but a potentially useful correlation with the Zap potential field.

The topics covered in Lesson 3 are:

Using Zap to fill a QSAR table column with a electrostatic potential field similar to the standard CoMFA electrostatic and steric fields.

Adjusting Zap field setup parameters to modify a 3D QSAR model.

Analyzing 3D QSAR results with contour maps.

Lesson 4 (for Zap^HV only) demonstrates the calculation of Electrostatic Binding Energy for a complex, which is in this case the DHFR/MTX complex described in lesson 1. This lesson also describes the use of the Zap Electrostatic Structure Report command.

The topics covered in Lesson 4 are:

Setting up and executing an intermolecular Zap calculation.

Calculation of a structure analysis report.