AtomicChargeCalculator - ACC

First Time User Guide

DO: calculate, visualize and analyze

WHAT: atomic charges which respond to changes in molecular conformation and chemical environment

WHERE: biomacromolecules and drug-like molecules.

Calculate atomic charges in 3 easy steps

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Upload your protonated molecule in a supported format: pdb, pqr, mol2, mol... Upload multiple molecules as .zip

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Step 1 – Upload molecule(s)

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Once you chose the input file with molecule(s), click Upload.

Step 1 – Upload molecule(s)

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Once you upload your molecule(s), ACC tries to prepare a default setup, so you can start your calculation immediately...

Step 2 – Setup

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Start calculation

using default setup

… or check and adjust

the setup

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A default setup may not be available, or may not be optimal for your calculation. Check and adjust each section of the setup...

Step 2 – Setup

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Check and adjust the

setup

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Check the total molecular charge (default=0)Check the messages (missing H, suboptimal formatting...)

Total molecular

charge

Step 2 – Setup

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EEM is an empirical approach used to calculate atomic charges. Click Show sets to list all EEM parameter sets available in ACC.

EEM parameters

Step 2 – Setup

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Help...Step 2 – Setup

For biomacromolecules, ACC provides time and memory efficient implementations of EEM. Click Add to pick a suitable method.

Efficiency

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Help...Step 3 – Start

Keep the default settings or make your adjustments, then start the calculation 10

… try any of the multiple

interactive guides

... check the tool tips

… consult the Wiki manual

Got lost during setup?

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Download structure files with charges (mol2, pqr...), statistics.Unique URL available for later access

Retrieve results

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URL

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Alternatively, for each molecule you can examine the results directly in your browser...

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URL

Retrieve results

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A job is defined by its unique setup (total molecular charge, set of EEM parameters, computation method), and produces a unique set of charges.

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Examine results for each molecule - Summary

Molecule

Input and computation warnings

Basic info about the computation

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The charges can be inspected at two levels of resolution: - atomic charges - residue charges (sum of atomic charges per residue)

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Examine results for each molecule – Raw Data

Molecule

Unique set of charges, resulted from a job or read in from the input file

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Interesting statistics available for atomic and residue charges

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Examine results for each molecule – Analyze

Molecule

The charge on the Mg ions does

not vary much

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Examine results for each molecule – Compare

Molecule

Comparison between sets of charges resulted from different jobs, or read from the input file 17

3D model built using:- atomic positions, colored by atomic charges or charge differences- residue positions, colored by residue charges or charge differences

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Examine results for each molecule – 3D Model

Molecule

Several visualization options to help interpret the results

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… try any of the multiple interactive guides

... check the tool tips

… consult the Wiki manual

Need help with interpreting the results?

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Try the setup examples, with detailed explanations...

Don't know where to start?

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… or view the setup and results for a few interesting computations...

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Don't know where to start?

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