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: option menu: {Off|Lennard-Jones 6-9|Lennard-Jones 6-12}; 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 Lennard-Jones 6-12 Steric Term for Map and HintTable interaction calculations, but set it off for Molecule and Complement Map calculations. The Lennard-Jones 6-9 function is a bit less harsh, but serves the same purpose as Lennard-Jones 6-12.
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.