ChargeCalculator:Index: Difference between revisions
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*'''Target''' | *'''Target''' | ||
Description: type of molecules that are likely to be well described using a specific set of EEM parameters | 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. | Possible values: organic molecules, drug-like molecules, proteins, etc. | ||
*'''Approach: QM Method, Basis Set, Population Analysis''' | *'''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. | 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. | 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''' | *'''Training Set Size, Data Source''' | ||
Description: | Description: | ||
Possible values: | Possible values: | ||
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*'''Priority''' | *'''Priority''' | ||
Description: Serve to identify a suitable default setup, and give hints about | Description: Serve to identify a suitable default setup, and give hints about | ||
Possible values: 1, 2, 3... Currently curated manually. | Possible values: 1, 2, 3... Currently curated manually. | ||
*'''Atoms''' | *'''Atoms''' | ||
Description: | Description: List of atom types covered by the EEM parameter set. An EEM parameter set generally covers atom types for H,C,N,O, but also halogens, metals, etc, depending on the molecules targetted during the development of the EEM parameters. | ||
Possible values | Possible values: H, C, N, O... | ||
*'''Missing Atoms''' | *'''Missing Atoms''' | ||
Description: | Description: | ||
Possible values: | |||
==Computation Method== | ==Computation Method== | ||
Revision as of 13:05, 19 December 2014
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:
Possible values:
- Id
Description: unique identifier of an EEM parameter set
- Priority
Description: Serve to identify a suitable default setup, and give hints about
Possible values: 1, 2, 3... Currently curated manually.
- Atoms
Description: List of atom types covered by the EEM parameter set. An EEM parameter set generally covers atom types for H,C,N,O, but also halogens, metals, etc, depending on the molecules targetted during the development of the EEM parameters. Possible values: H, C, N, O...
- Missing Atoms
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