Grid_Interactions Setup Parameter Block

Interaction Select

enumerated choices: {All|Hydrophobic|Polar}

The Interaction Select parameter allows you to choose the types of interactions to be recorded by the calculation. The options are:

All records all interactions in the HintTable or map. Positive values represent favorable binding situations such as hydrophobic-hydrophobic, acid-base, hydrogen bonding, Coulombic, etc. Negative values in the HintTable or map represent unfavorable binding situations such as hydrophobic-polar, repulsive (like charge) Coulombic interactions, etc.

Hydrophobic records only interactions involving hydrophobic atoms in the HintTable or map. Positive values generally represent hydrophobic-hydrophobic interactions and negative values generally represent hydrophobic-polar interactions.

Polar records all interactions that do not involve hydrophobic atoms. Positive values generally represent acid-base and hydrogen bonding and negative values generally represent acid-acid and base-base unfavorable interactions.

IntraMonomer

on/off

The IntraMonomer parameter specifies whether IntraMolecular interactions within the same monomer or substructure are to be recorded by the HintTable or map.

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 map 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.