From the File pulldown on the SYBYL menubar select the Read... command. Select the file hiv1.pdb and choose No when asked to Center the Molecule.

The HIV1 molecule needs to have the proper end-groups. HINT uses special atom names for C- and N- terminus residues so that the proper HINT parameters are assigned during the molecule partition. First color and label the residues we will be modifying. Use View on the SYBYL menubar to select Color and Atoms.... From the Atom Expression dialog box pick the Substructures... button. Select PRO1, PHE99, PRO101, and PHE199 from the list. Press OK for each dialog; choose RED from the Color option list. Now, use View on the menubar to to select Label and Atom Name...; pick the same Substructures... from the Atom Expression dialog box. Manipulate the display until one of the two highlighted areas are in the center of the display. Pulldown Build/Edit to Modify; select Atom...; and pick NAME from the displayed Option menu. An Atom Expression dialog box is now available. We will pick the atoms to be modified directly from the screen. A summary of the changes is in the table below. Basically pick each of the listed atoms and end by pressing OK on the Atom Expression dialog box. Choose the QUERY mode for generating names and change each name as it is presented in the IDENTIFIER (Atom name) dialog.

HINT Names for End Group Atoms

Substructure	Old Name	New Name
PRO1	N	NI
	H1	H
	H2	HNCAP
	CA	CAI
PHE99	C	CT
	O	OX2
PRO101	N	NI
	H1	H
	H2	HNCAP
	CA	CAI
PHE199	C	CT
	O	OX2

Go to the eslc pulldown on the SYBYL menubar and select Hint, Partition, and Molecule... to display the Partition Molecule dialog box. Select the Atoms... as All in Molecular Area M1. For proteins or other macromolecules consisting of well-defined monomers, more reproducible HINT results are obtained when the Partition Method is set to Dictionary. Hydrogen Treatment dictates how HINT will calculate parameters for the defined hydrogens in the current molecule. Choose Essential now.

In the Solvent Condition parameter box there are four options for partitioning the macromolecule. Acidic, Neutral, and Basic represent the most benign and generalized definition of these solvent conditions. This gives you an opportunity to rapidly explore the effect of pH on the hydropathy of a macromolecule. The fourth option, Inferred, calculates the protonation state for each monomer based on the number and connectivity of the hydrogens actually present in the macromolecule. (Note that this is not compatible with Hydrogen Treatment set to United.) For this lesson select the Neutral Solvent Condition. Finally, press the OK button to perform the Molecule Partition calculation for HIV1. The reported LogP for HIV1 (neutral solvent condition) is -9.00.

Pulldown eslc from the SYBYL menubar to Hint, HintMap, and Molecule... to invoke the Map Molecule dialog box. First, select the Molecule... button and pick M1 (HIV1). 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 (HIV1). 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, but use 4.00 here to make the calculation go somewhat faster. Grid Resolution is the spacing between grid points in Angstroms; use a value of 1.25. Press OK to initiate the Region Definition calculation.

Back again in the Map Molecule dialog box, select Hydrophobic/Polar as the Grid Type 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. Next, set the HINT Distance Function..., which calls up the Distance Function dialog box. There are two parts: the Hydropathic Term and the Steric Term. For a Molecule HintMap calculation select exp(-nr) for the Hydropathic Term and set the Steric Term to off. Press OK to return to the Map Molecule dialog box.

Enter a value of 6.0 for the Cut Off Radius. Set the Volume Averaging parameter to off; and set the Inside Mol Cutoff parameter to off. Enter hiv1_hp.cnt as the Map File name. As this calculation may take ca. one-half hour, set the Batch check box to on. Press OK to begin the calculation. Depending on how NetBatch is configured on your system, you will get prompted to set the hostname, etc. for the run.

Repeat the map calculation to create a parallel Acid/Base map for HIV1. Return to the Map Molecule dialog box and set all parameters as above, except: 1) Grid Type = Acid/Base; 2) Choose Lewis as the Acid Base Definition to use the Lewis model for acids and bases; 3) Map File name = hiv1_ab.cnt; and 4) Job Name = HintMolMap2.

When both map calculations are complete you may contour the HintMaps for display. Choose Contour... from eslc, Hint, HintMap. Since these two maps were run as NetBatch jobs, in order to contour them we will have to specify their filenames explicitly. In the Map Contour dialog box press the ... button next to the Contour File field to call a Read File dialog box that has been filtered to list only SYBYL .cnt files. First select hiv1_hp.cnt to contour the Hydrophobic map. Choose D1 as the Display Area and select a Style appropriate for your computer. Enter 10 for the Contour Value and pick Green for the Contour Color parameter. Press Accept followed by Done to contour the Hydrophobic map. Invoke the Map Contour dialog box a second time to contour the polar (acid and base) map. Select hiv1_ab.cnt as the Contour File either by typing directly in the text field or by using the Read File dialog box (...). Select Display Area D2. Contour this map with -20.0 (red) and 50.0 (blue). The net display of the two contoured maps shows hydrophobic regions and differentiates between two types of Polar regions (Acid-like and Base-like) based on Lewis definitions of acids and bases.

HINT hydropathic map of HIV-1 Protease