ChargeCalculator:Index

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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 - level of theory used to solve Schrödinger's equation - HF, B3LYP, etc.
  • Basis Set - 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.
Possible values: For EEM parameter sets focused on biomolecules, priorities are assigned based on their performance in the external validation stage of their development. For sets focused on organic molecules, priorities are assigned based on year of publication, level of theory of the QM reference data, and the results of a small in-house QM benchmark on paracetamol. Lower values are preferred.
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

The computation method refers to the EEM implementation that will be used during the atomic charge calculation , along with related computation options specific to each 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

The raw data is available in tabular form, and refers to the actual values of atomic charges resulted from the EEM calculation, or read in from the input file. Residue charges are also available if residue annotations are available in the input file. No additional statistics are included here.

Atom Grouping
Description: level of resolution at which the atomic charges will be listed.
Possible values: Atoms, Residues (sum of atomic charges for each residue).

Analyze tab

ACC provides several statistical descriptors for the results at more levels of resolution, in graphical and tabular form.

Atom Grouping
Description: Level of resolution at which the statistics will be calculated.
Possible values: Atoms, Residues.
Group Property
Description: 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: Depend on Atom Grouping. For Atom Grouping = Atoms: ResidueName, ChemicalElement, ResidueChargeType, For Atom Grouping = Residues: ResidueName, AtomicComposition, ResidueChargeType.
Plot Value, Property Value
Description: Controls which statistics will be displayed in the graph.
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|.
Raw Data
Description: Display statistics for a certain set of charges (resulted from a single job, or read from the input file).
Possible values: any set of charges available for that molecule.

Compare tab

ACC allows to compare sets of charges at more levels of resolution, in graphical and tabular form. These sets of charges may have resulted from different jobs, or were read from the input file.

Atom Grouping
Description: Level of resolution at which the charges will be compared.
Possible values: Atoms, Residues.
X Axis, Y Axis
Description: Which two sets of charges will be compared.
Possible values: any sets of charges available for that molecule. X Axis must be different from Y Axis.
Raw Data
Description: Display descriptors for each pairwise comparison between the set of charges on the X Axis and all other sets of charges available for that molecule (resulted from ACC jobs, or read from the input file).
Possible values: The values of the following descriptors are displayed for each pairwise comparison:
  • R², Pearson - squared Pearson's correlation coefficient
  • ρ, Spearman - Spearman's rank correlation coefficient
  • δ², RMSD - root mean square deviation
  • Diff. - sum of absolute differences.

3D Model tab

ACC allows a few basic charge visualization options to aid in interpreting the results of the atomic charge calculation.

Atom Grouping
Description: Level of resolution at which the 3D model will be built and colored.
Possible values: Atoms (build 3D model based on atomic positions, color based on atomic charges), Residues (build 3D model based on positions of residue centroids, color based on residue charges).
Display Charges
Description: which set of charges will be used for coloring the 3D model.
Possible values: any set of charges available for that molecule.
Show Differences
Description: allow to color the 3D model based on differences in charges from individual charge sets. Each atom or residue is colored according to the difference which results as the value in the set chosen at Display Charges, minus the value in the set chosen at Show Differences.
Possible values: any set of charges available for that molecule, and not chosen at Display Charges.
Display Mode
Description: Type of graphical representation used for building the 3D model.
Possible values: Depend on Atom Grouping.

For Atom Grouping = Atoms:

  • Balls and Sticks - render atoms as spheres and bonds as tubes.
  • Surface - surface built as a set of points given by the potential of each atom at that point in space; potential computed as a function of the VDW radius and Probe Radius parameter.
  • Cartoons - render amino acids and nucleotides as cartoons; secondary structure is approximated if not explicit in input file.
  • C-α trace - smooth trace of the molecule backbone based on the position of C-α atoms.
  • VDW spheres - render atoms as spheres with VDW radius.

For Atom Grouping = Residues:

  • Balls and Sticks - render residue centroids as spheres connected in the amino acid sequence by tubes
  • Surface - surface built as a set of points given by the potential of each residue at that point in space; potential computed as a function of the Probe Radius parameter.
Additional display options for each Display Mode
Description: Certain Display Modes allow further tuning of what parts of the model are displayed, and how.
Possible values: Depend on Display Mode.

For Display Mode = Balls and sticks:

  • Charge Scaling - Scales the size of the balls (atoms or residue centroids) according to the absolute value of the corresponding (atomic or residue) charge. Possible values: Yes (default), No.

For Display Mode = Surface:

  • Probe Radius - determines the shape of the surface. Lower values lead to a more VDW-like surface.

For Display Mode = Cartoons or C-α trace:

  • Show HET atoms - render atoms annotated as HETATM (typically ligand or cofactor atoms) as Balls and Sticks. Possible values: Yes (default), No.
  • Show Waters - render atoms annotated as water (residue names HOH, H2O, WAT) as Balls and Sticks. Possible values: Yes, No (default).
Display Quality
Description: Number of tetrahedrons used to display 3D objects. Finer detail is achieved by using a higher number of tetrahedrons.
Possible values: Very Low, Low, Medium (default), High, Very High
Min. Value, Mid. Value, Max. Value
Description: Enable in order to adjust lowest/highest limit and middle point of the charge scale. The default is given by the values in each particular set of charges (or of differences in charges).
Value Gap
Description: Further adjustment to the coloring scheme can be achieved by using fewer discrete values of the color scheme. Charges which are similar (absolute difference smaller than Value Gap) are displayed in the same color. This allows to visually emphasize the difference in charge distribution in different areas of the molecule. Emphasis increases with Value Gap.
Possible values: 0.05-1.