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

• Author, Publication, Journal, Year

Description: Citation identification for that particular set of EEM parameters

• Target

Description: Possible values:

• Approach: QM Method, Basis Set, Population Analysis

Description: Possible values:

• Training Set Size, Data Source

Description: Possible values:

• Priority

Description: Possible values

Computation Method

• Ignore Waters

• Precision

Description: Possible values: Double, Single

• Cutoff Radius

Description: Possible values:

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