View Grid_Molecule Setup Parameter Block

Grid_Types

enumerated choices: {Hydrophobic/Polar|Acid/Base}

The Grid_Types parameter allows the specification of the information to be calculated by the HintGrid command. Alternately, you can calculate a map where the positive grid values represent hydrophobic regions and negative grid values represent polar regions or a map where the polar information has been categorized into acidic regions and polar regions (at the expense of the hydrophobic information which is lost). If all three types of infomation are desired, you will have to run two HINT map calculations. The available Grid Type options are:

Hydrophobic/Polar where positive map values represent hydrophobic regions of space and negative map values represent polar regions of space.

Acid/Base where positive map values represent acidic regions of space and negative map values represent basic regions of space. Note that this option requires the selection of an Acid Base Definition.

AcidBase Definition

enumerated choices: {Coulombic|Bronsted|Lewis}

The AcidBase Definition parameter specifies what model for acids and bases will be used by HINT if Grid_Type is set to Acid/Base. These definitions are static; they are based on the CVFF potential types and are not dynamically reevaluated. Three models are available as options:

Coulombic is a formal charge-based model. Atoms with formal positive charges are considered to be acids and atoms with formal negative charges are considered to be bases.

Bronsted uses the Bronsted-Lowry theory of acids and bases. An acid is a proton donor while a base is a proton acceptor.

Lewis uses the Lewis theory of acids and bases. An acid is an electron pair acceptor and a base is an electron pair donor.

Cut-Off Radius

real number

The Cut-Off Radius parameter represents a method to reduce calculation time for HINT calculations. If the distance between two atoms (for HintTable calculations) or between a grid point and an atom (for HintGrid calculations) exceeds the cutoff-radius that interaction is ignored. Cut-Off Radius values of greater than 6.0 Angstroms appear to have minimal effect on the calculation quality but can save considerable calculation time.

Volume_Averaging

on/off

Turning On the Volume_Averaging parameter produces smoother HINT maps, but at a cost of approximately an eight-fold increase in calculation time. The algorithm surrounds each actual grid point with a box whose corners are at (+/-) 1/3 grid spacing along each cartesian axis. The map is evaluated for each corner of the box and the resulting values averaged to yield the map value at the original grid point.

Van der Waals Limit

real number

The Van der Waals Limit parameter allows limited user control of the HINT Van der Waals radii set. The Van der Waals Limit is a multiplicative factor (default = 1.00) that adjusts the predefined radii set. A value of less than 1 would allow more "bump" between atoms, while a value greater than one would allow less.

Inside Mol Cutoff

on/off

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

Lo Limit

real number

The Lo 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 Cutoff is set to On.

Hi Limit

real number

The Hi 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 Cutoff is set to On.