Molecule Partition Parameter Block

Molecule_Spec

identifier

The Molecule_Spec parameter identifies a molecule or portion of molecule. Each molecule object within InsightII has a name. The name is assigned when the molecule is read in with Get Molecule or when a Sketch object is converted to a 3D molecule. Select the collection of atoms or molecule that you wish to "partition".

Partition Method

enumerated choices: {Calculate|Dictionary}

HINT offers two methods of partitioning the molecule on this option menu: "Calculate" or "Dictionary". The Calculate method uses the molecule's potential types (CVFF) and bond connections as input data to the partition algorithm. This technique is most appropriate for small organic molecules such as ligands, substrates or drugs. The Dictionary method relies on a predefined set of predefined data for regularly occurring substructures or monomers such as amino acid residues and nucleic acid bases. In this case the input data is the atom names and substructure names/types.

Partition_File

on/off

The Partition File check designates whether or not you want to write a file of the molecule partition data as it is calculated. The default is Off.

Partition File

long text

The Partition File parameter is the name of the disk file to be written of molecule partition data if Partition_File is set to On. Any valid unix file name may be used, but the HINT convention is for the extension to be .par.

Hydrogen_Treatment

enumerated choices: {Retain_All|Polar_Only|United_Atom}

This menu describes how the Partitioning will treat hydrogens; there are three options: "United_Atom" (using an approach the treats all hydrogens implicitly as part of their parent heavy atom), "Polar_Only" (using an approach that treats (only) polar hydrogens explicitly), and "Retain_All". Note that the selection of this parameter has implications in following interaction calculations. For example, hydrogen bonding will be incorrectly modeled by HINT if the United_Atom option is chosen. In general the Polar_Only option is best for most applications. The Retain_All option appears to "dilute" the hydrophobic density, but treats aromatic hydrogens as potential hydrogen bond donors.

Solvent_Condition

enumerated choices: {Inferred|Neutral|Acid|Base}

This option menu is active only if the "Dictionary" method is chosen. The menu lists four options: "Inferred", "Neutral", "Base", "Acid". The latter three represent the pH conditions under which the molecule is to be partitioned. Inferred represents a special case where each substructure (e.g., residue) will be partitioned based on its hydrogen count. For example, if one aspartic acid in a protein is believed to be protonated while other acidic and basic residues are to remain at neutral pH, using the Inferred Solvent Condition is the appropriate approach. Note that all essential hydrogens must be present in the entire model, not just in the "special" residues.

Polar_Proximity

enumerated choices: {Off|Via_Bonds|Through_Space}

This option menu is only active if the "Calculate" method is chosen. When two or more polar groups are in "in proximity" within a molecule, their effects are cumulatively diminished -- this is termed the polar proximity effect and is dealt with by the Leo method of LogP estimation and by HINT as corrective factors to the hydrophobic atom constants. HINT offers three options for Polar Proximity: "Off", "Via_Bond", and "Through_Space". The Via_Bond method is most compatible with the Leo system, and is the option recommended. Through_Space may be appropriate for some larger molecules that have significant intramolecular non-covalent interactions between polar groups. It uses a through-space distance function to estimate the polar proximity effect.

Thru_Space_Function

enumerated choices: {I exp(-Jr)|I/r**J}

Choose the functional form for Through_Space Polar Proximity. Two options are provided: a exponential and a power function. Each has two parameters that can be used to generate a wide range of functional behavior.

I

real number

I is a parameter used to tailor the functional behavior of Through_Space Polar Proximity.

J

real number

J is a parameter used to tailor the functional behavior of Through_Space Polar Proximity.