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.

Return to the Table of contents.

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, TIPx) are not included in the EEM matrix. 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 Possible values: Atoms (), Residues ()

Analyze tab

• Atom Grouping

Description: Possible values: Atoms (), Residues ()

• Group Property

Description: - Depends on Atom Grouping Possible values: (ResidueName, ChemicalElement, ResidueChargeType), (ResidueName, AtomicComposition, ResidueChargeType) - in tab Analyze

• Plot 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|

• Property Value

Description: same as Plot Value Possible values: same as Plot Value

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