LESSON 2: Performing a HintGrid Molecule Calculation

1. Delete all but one molecule

   If you did multiple Partition calculations in Lesson 1, there are probably several molecule objects currently defined and displayed by InsightII. This lesson is specific to the COCAINE molecule, but any of the molecules suggested in Step 4 of Lesson 1 are applicable. To delete a molecule, pulldown Object and select the Delete command; Execute the Delete Object command for each desired molecule.

2. Setup the Grid parameters

   From the Setup pulldown on the Hint menu bar, select the Grid command. This command defines the three-dimensional grid to be used in the HintGrid calculation.

   In the Grid Setup parameter block, leave the Display_Grid parameter set to on so that the border of the grid is displayed when the command is executed. This aids in visualizing the the volume spanned by the grid.

   The Grid Center parameter should be set to Molecule_Region. Select the Molecule Region parameter box and select COCAINE from the Molecules Value Aid. This defines the center of the grid to be the average of the x, y, z coordinates of the COCAINE molecule.

   Next, select the Border_Space option as the Grid_Size, and type 5.0 as the Border Space. This defines the grid such that there is a 5 Angstrom border between the molecule and the edge of the grid in the direction (x, y, or z) in which the molecule is longest.

   Finally, select Point_Spacing as the Grid Resolution and type 1.0 in the Angstroms/Grid Pt parameter box. This specifies that there will be 1.0 Angstroms between grid points in all (x, y, z) dimensions. One Angstrom is generally sufficient for most Hint studies, although in the interest of speed for some large molecules a larger value may be justified, or for more detailed maps a smaller value may be used. Select Execute to set the Grid parameters.

3. Setup the HintGrid calculational parameters for a Molecule map

   Once again from the Setup pulldown select the Grid_Molecule command. The Grid_Molecule parameter block guides you through the setup of a HintGrid Molecule calculation. From Grid_Types select Hydrophobic/Polar to request a map where positive grid field values represent hydrophobic regions of space, and negative grid field values represent polar (hydrophilic) regions of space. The other option in Grid_Types, Acid/Base, requests a map where Acidic and Polar regions of space are coded with positive grid field values, Basic and Polar regions of space are coded with negative grid field values, and Hydrophobic regions of space are set to zero.

   The CutOff Radius serves to reduce calculation time by not considering atoms farther away than this value from the grid points during the map construction. Enter a value of 6.0 for this parameter. Volume_Averaging produces a smoother map by calculating eight density values for each grid point, and then averaging them. The main disadvantage is loss of calculation speed. Set this parameter to off. The Inside Mol Cutoff 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. Press Execute to set the Grid_Molecule parameters.

4. Setup the Hint Distance Function for a Molecule map

   Next, set the Hint Distance_Function using the Setup Hint_DistFunct parameter block. There are two parts: the Hydropathic Term and the Steric_Term. For a HintGrid Molecule calculation select exp(-nr) for the Hydropathic Term and set the Steric_Term to off. You will use the Steric_Term (van der Waals) in Hint interaction grid calculations. Make sure that the Direction Vectors parameter is set to None (Spherical) for this calculation. See the Theory chapter for a discussion of the Hydropathy distance functions used by Hint.

5. Calculate the HintGrid Molecule map

   Now, from the HintGrid pulldown on the Hint menu bar, select the Molecule command. Parameters in the Molecule HintGrid block initiate the Molecule HintGrid calculation. First make sure that COCAINE is the parameter in the Molecule parameter box. (If it is not, choose it from the associated Value Aid.) Next, choose Interactive as the Execute_Mode parameter. Molecule HintGrid calculations for small molecules require only a few seconds of CPU time to execute, so that the advantage of running these jobs as Background is not evident. Select the HintGrid Object box to pick an Object name for the grid. A default value (COCAINE_HP) will be provided if you enter a carriage return from the keyboard while this box is active. Finally, press Execute to begin the map calculation.

6. Contour and display the map

   The last step is to contour the HintGrid map for display. Go to the Grid pulldown on the Hint menu bar and select the Contour command. This command block allows you to select the desired contour levels and their colors. First select the Grid Name box and pick COCAINE_HP from the associated Value Aid. Next select the Contour Name Root box and enter COC. This will be the root portion of all Contour Objects created from COCAINE_HP. For the Level Specification parameter pick the Single option. This means that each Contour Level must be individually entered and colored. The other option, Range, allows you to select multiple contour levels by designating a minimum, maximum and delta value.

   First contour the Polar portion of the COCAINE_HP HintGrid map. Enter a value of -20.0 for the first Contour Level. Use Display Style of Lines for initial view of maps; the Solid option is recommended for preparation of presentation graphics. Select the Color parameter and pick a red from the Color Palette Value Aid. We suggest red contours to represent Polar hydropathy. The contouring calculation should take only a few seconds, and a red contour surrounding the Polar portion of the cocaine molecule should appear. Next contour the Hydrophobic portion of the map. Enter a value of 5.0 for the Contour Level and pick a shade of green for the Color parameter.

   HINT hydropathic map of cocaine

7. Interpretation of the HintGrid Molecule map

   The contour levels suggested are only guidelines for representation of the relative contributions of Polar and Hydrophobic effects. For balance in visualization it is usually desirable to contour the Polar (-) effect at a level that is 2-5 times that of the Hydrophobic (+) effect. Keep in mind that the most hydrophobic atoms (or Leo fragments) have ai (or fi) values on the order of +1.0, while the most polar atoms (or fragments) can have values of -5.0. Hydrophobicity is a much more subtle effect than the Coulombic type effects encoded by the Polar portion of the HintGrid field.