ChargeCalculator:UserManual

AtomicChargeCalculator, or ACC offers an efficient, user-friendly, interactive and platform independent environment for the calculation, visualization and analysis of conformationally dependent, quantum mechanics quality atomic charges in both biomacromolecules and drug-like molecules. ACC computes atomic charges using the Electronegativity Equalization Method, a powerful empirical approach which can provide conformationally dependent, quantum mechanics atomic charges with minimal computational resources.

Below you can find the ACC user manual, which contains all the information you need in order to make efficient use of ACC. Additional support is provided on the ACC web pages. When you first access the ACC page, you will find basic information in the Quick Help tab, and useful examples in the Samples tab. Follow the green ? buttons to access the embedded interactive guides that assist you in setting up your calculations and interpreting the results. Many tool tips are available when hovering over various elements of the interface.

We hope you make good use of AtomicChargeCalculator.

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Terminology

1. Structural elements
   1. Atom
   2. Molecule
   3. Residue
2. Charges
   1. Atomic charge
   2. Residue charge
   3. Molecular charge
3. Work flow
   1. EEM parameters
   2. EEM parameter sets
   3. Computation method
   4. Computation parameters

Principles

1. Main steps
2. Types of results
3. Types of analyses

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Job submission

1. Upload_molecules
2. Pick EEM parameter sets
3. Pick computation methods

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Interpretation of results

1. Synopsis page
2. Specifics page
   1. Summary
   2. Raw data
   3. Analyze
   4. Compare
   5. 3D model

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