ChargeCalculator:Index

This index contains a list of keywords involved in setting up calculations in ACC, and interpreting the results of these calculations. A brief explanation is provided for each keyword.

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Setup keywords

EEM parameter set

A set of EEM parameters, or EEM parameter set, represents a collection of EEM parameters that has been developed for a certain group of target molecules, using a certain kind of reference data and a certain kind of fitting procedure.

• Author, Publication, Journal, Year

Description: citation identification for that particular set of EEM parameters

• Target

Description: type of molecules that are likely to be well described using a specific set of EEM parameters

Possible values: organic molecules, drug-like molecules, proteins, etc.

• Approach: QM Method, Basis Set, Population Analysis

Description: The nature of the reference data used during the development of the parameters. Reference data generally comes from high level Quantum Mechanical (QM) calculations. The applicability domain of an EEM parameter set is closely related to the applicability domain of the reference QM data used during the development.

Possible values: QM Method refers to the level of theory used to solve Schrödinger's equation - HF, B3LYP, etc.; Basis Set refers to the set of basis functions used to solve Schrödinger's equation - 6-31G*, STO-3G, etc.; Population Analysis defines how the reference data (most commonly atomic charges) were obtained after solving Schrödinger's equation - MPA (Mulliken population analysis), NPA (Natural population analysis), MK (Merz-Kollman scheme for fitting to electrostatic potentials), etc.

• Training Set Size, Data Source

Description: Number and type of molecules used to produce reference data during the development of the EEM parameters.

• Id

Description: unique identifier of an EEM parameter set

• Priority

Description: Very basic grading system. Serves mainly to identify a suitable default setup. Currently curated manually.

• Atoms

Description: List of atom types covered by the EEM parameter set. Depends on the type of molecules used to produce reference data during the development of the EEM parameters.

Possible values: H, C, N, O, Cl, etc.

• Missing Atoms

Description: List of atom types present in the input file and not covered by the EEM parameter set. These atoms will not be included in the atomic charge calculation using this EEM parameter set. To include all atoms, use an EEM parameter set with no Missing Atoms. Alternatively, Add a new EEM parameter set where all necessary EEM parameters are provided.

Computation Method

• Ignore Waters

Description: do not include water molecules in the atomic charge calculation. Specifically, all atoms annotated with a residue name typically associated with water (HOH, WAT, H2O) are not included in the EEM matrix. Other residue names sometimes associated with water, such as SOL and TIP, are not considered here because the Protein Data Bank contains instances of such residues which are chemical components different from water. Thus, if you wish to ignore water which is annotated in your file as SOL or TIPx, you will need to remove these records before submitting to ACC. Possible values: False (default), True.

• Precision

Description: Number of bits (64 or 32) used to represent charges. Possible values: Double (64-bit numbers, default), Single (32-bit numbers).

• Cutoff Radius

Description: Parameter of the EEM Cutoff and EEM Cutoff Cover methods. Controls the number of atoms included in each reduced EEM matrix, based on their distance (in ångströms) from a pivot atom. Accuracy and computation time increase with Cutoff Radius. Possible values: up to 17. Recommended 8-15.

Results keywords

Raw Data tab

• Atom Grouping

Description: Controls the level of resolution at which the atomic charges will be listed.

Possible values: Atoms, Residues (sum of atomic charges for each residue).

Analyze tab

• Atom Grouping

Description: Controls the level of resolution at which the statistics will be calculated.

Possible values: Atoms, Residues.

• Group Property

Description: Controls the type of property based on which the statistics will be calculated. ResidueName gives statistics for all atoms/residues with a certain residue name appropriately annotated in the input file. ChemicalElement gives statistics for all atoms of a certain chemical element. ResidueChargeType gives statistics for all atoms/residues with a residue name recognized by ACC to be of a certain type (polar/nonpolar, positively/negatively charged). AtomicComposition gives statistics for all residues with a certain atomic composition (number of atoms of different chemical elements).

Possible values: Depends on Atom Grouping. For Atom Grouping = Atoms: ResidueName, ChemicalElement, ResidueChargeType, For Atom Grouping = Residues: ResidueName, AtomicComposition, ResidueChargeType.

• Plot Value, Property Value

Description:

Possible values: MinimumCharge = Min, MaximumCharge = Max, Average Charge = Avg, Average Absolute Charge = |Avg|, Median Charge, Median Absolute Charge, Standard Charge Deviation = σ, Standard Abs. Charge Deviation = |σ|

Compare tab

R² = Pearson, ρ = Spearman, δ² = RMSD, Diff. = sum of absolute differences?

3D Model tab

• Display Charges
• Show Differences
• Display Mode

- Depends on Atom Grouping: Atoms (Balls and Sticks, Surface, Cartoons, C-α trace, VDW spheres), Residues (Balls and Sticks, Surface)

Charge Scaling - Depends on Display Mode