HintTable 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.

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.

Table Extents: Output Radius

real number

The Table Extents parameters are used to filter the quantity of data written to the HintTable file. Without filtering the HintTable can become exceedingly large. For instance, a interaction calculation between two subunits of a protein, each possessing 10^3 atoms would yield 10^6 data records in an unfiltered HintTable. Interactions between atoms that are farther apart than the Output Radius parameter are not written to the file.

Table Extents: Output Value

real number

Interactions between atoms that have a HINT interaction score of less than the Output Value parameter are not written to the HintTable File.

Table Extents: Output Resolution

enumerated choices: {Low|High}

This parameter controls the resolution (reported significant figures) of Table output data.

Low reports all b_ij data to ±1 score units.

High reports all b_ij data to ±0.00001 score units.

Proton Suppress

on/off

The Proton Suppress parameter specifies whether hydrogens are to be represented explicitly in the HintTable (Off) or incorporated into their associated heavy atom (On). In most experimental studies involving proteins, only the heavy atoms are known precisely and hydrogen atom positions are modeled. Regardless of Proton Suppress all interactions involving hydrogens are individually made; the difference is only how this data is tabulated. One consequence of Proton Suppress is the definition of hydrogen bonds. If Proton Suppress is On, hydrogen bonds are characterized by a heavy atom-heavy atom distance. If Proton Suppress is Off, hydrogen bonds are characterized by hydrogen-heavy atom distances.

H-Bnd Distance X-H

real number

This parameter, H-Bnd Distance X-H describes the distance below which a polar hydrogen/hydrogen bond acceptor interaction is classified as a Hydrogen Bond. Above this value the interaction is classified as Acid/Base.

H-Bnd Distance X-Y

real number

This parameter, H-Bnd Distance X-Y describes the distance below which a hydrogen bond donor/hydrogen bond acceptor interaction is classified as a Hydrogen Bond. Above this value the interaction is classified as Acid/Base.