If you have come directly from Lesson 1, you may have copies of DHFR in both M1 and M3. Delete molecular regions M3 and M4.

From the eslc pulldown on the SYBYL menubar, select Zap followed by ZapMaps and Molecule Potential.... This command sets up and executes calculation of a molecular electrostatic potential map with the aid of the Zap Map Molecule dialog box. First choose the Atoms..., which will also identify the molecular area (all atoms in M1).

Next, define the three dimensional extents of the map region by pressing the Region Definition... button to call the Region Definition dialog box. For this type of calculation, pick the Molecule Extents radio button from the Region menu. Choose Molecule... to be M1 (Dihydrofolate_reductase). Margin represents a border space to be placed around the region box defined by the molecule to allow adequate field decay. A value of 5.00 is normally used. Grid Resolution is the spacing between grid points in Angstroms; use a value of 1.00. Press OK to initiate the Region Definition calculation.

The Dielectric Constants of 2.00 (Inside) and 80.00 (Outside) are fine. Press the More Zap Details.. to uncover the Zap Details dialog. Set the Units to kcal/mol. Leave everything else the same and Press OK. Set the Map File name to be dhfr_zap.cnt. (Setting the GRASP Output checkbox to on will write a .phi file that can be read by GRASP. Don't do this unless you have the GRASP program and want to examine this map.)

The Inside Mol Cut Off allows you to set a constant value for any grid point that is within the molecular van der Waals surface. Set this parameter to off. Now that everything is set for this map calculation, press OK to initiate it. (This calculation is quite fast; there is no advantage to running it in batch.)

The last step is to contour the Potential Map for display. Note than when the calculation finished a histogram of the contour field was printed to the Sybyl text window. You can use that as a guide to selection of the appropriate contour levels, or you can use the features of the Map Contour dialog box automatically called at the completion of the Zap Map calculation. This dialog box allows you to select the desired contour levels, their colors, and styles. The Contour File text field should be filled with dhfr_zap.cnt, the Map File name chosen in the Zap Map Molecule dialog box. First choose the Display Area as D1 and a Style appropriate for your display device (Lines and Dots will always work, but Opaque and Transparent require higher than minimum level graphics devices).

We will select two level/color combinations. First press the -50% button and choose Contour of Red. The -50% button chooses the negative contour level to be 50% of the minimum value in the map. Now press the Accept button to define the first contour set. Next contour the positive portion of the potential map. Press the +50% button and choose another color (Purple?) that contrasts with Red, press Accept. The Number of Defined Levels should now be 2. Select the Done button to contour the Potential Map. The contouring calculation should take only a few seconds; red contour surfaces surrounding the negative potential portions of dihydrofolate reductase and purple contour surfaces surrounding the positive potential portions of the enzyme should appear.

The contour levels suggested are only guidelines for representation of the relative contributions of positve and negative potential. It is usually desirable to plot both at the same contour value. There are a variety of features in this map, but one interesting area to explore is the region of the bound methotrexate (MTX) which should be in molecular area M2. For ease of viewing turn the M1 display off with the control in the CheckBox icon. If you zoom in to MTX you will see that there is a nice red contour surface perfectly placed for interaction with the N1 and NA2 nitrogens of MTX. (N1 has a formal positive charge.) Also interesting to note is the purple patch just off the O1-CT-O2 carboxylate.

Zap potential map of dihydrofolate reductase in region of methotrexate