View Distance Function Dialog Box

Distance Function Dialog Box

Hydropathic Term: option menu: {Off|exp(-nr)|(1/r**n)|exp(-nr)**m}; The Hydropathic Term of the Distance Function controls the mathematical form of the distance dependence for hydropathic interactions. (See Theory Chapter for more information.) Off disables the hydropathic term; exp(-nr) uses an exponential decay function to represent the distance dependence of hydropathy through space; (1/r**n) uses an inverse power function to represent the distance dependence of hydropathy through space; and exp(-nr)**m is a more complex function. The values of n and m are set in separate parameters.
n: field; The n parameter is the integer number in the (1/r**n) or exp(-nr) hydropathic term of the HINT distance function.
m: field; The m parameter is the integer number in the exp(-nr)**m hydropathic term of the HINT distance function.
Steric Term: check box; The Steric_Term of the Distance_Function is an adaptation of the Lennard-Jones function. For the most part it represents a penalty function to prevent the too-close approach of interacting atoms. In general, use the Steric_Term for Map and HintTable interaction calculations, but don't use it for Molecule and Complement Map calculations.
Steric/Hydro Scaler: field; The Steric/Hydro Scaler is an empirical parameter designed to balance the two terms (Steric and Hydropathic) of the HINT Distance_Function. Experience has shown that a value of 50.0 for this parameter gives a HINT atom-atom interaction score that is about 2/3 hydropathic and 1/3 steric for an acid-base interaction at Van der Waals contact distance. The primary purpose, however, of the HINT Steric_Term is to flag invalid contact distances between interacting atoms.
Directionality Vectors:: option menu: {None (Spherical)|Bond Axes (Geometric)|Hybridized Pi/Lone Pairs}; The Directionality Vectors parameter(s) provide a mechanism to more specifically direct hydropathy along either Bond Axis or Lone Pair vectors. This is especially important for polar/H-Bond interactions where directionality of interactions is expected to be important. Hydrophobic interactions are less likely to be directional.; Bond Axes (Geometric) directs the hydropathy along the axis of the bond (or average of bonds) to the selected atom.; Hybridized Pi/Lone Pairs directs the hydropathy along vectors coinciding with the placement of lone pairs and pi orbitals on the selected atom. The magnitude of these vectors are weighted for the occupancy (electrons) of the lone pair or pi orbital.
Vector Focus:: field; The Vector Focus parameter allows control over the focus of the directionality vectors, larger Vector Focus parameters cause a tighter focus of the probability function controlling interactions.
HINT Dielectric Screening: check box; Choosing this option indicates you wish to use a HINT Dielectric Screen map as part of the Distance Function definition. This map is created with the HINT Dielectric Screening dialog box which controls the long-range and short-range functions that may be applied to HINT intermolecular and intramolecular interactions. The long-range HINT dielectric correction takes into account the effects of the extra-local environment on the ability of species (particularly polar ones) to interact. The short-range HINT dielectric correction takes into account local effects such as blocked interaction pathways, etc.
Dielectric Screen File: field and push button; Select the SYBYL (.cnt) file that encodes the Dielectric Screen data. Press the push button to obtain a file list filtered to include only .cnt.