Requirements

ACC is a free web service available online since June 2014 at http://ncbr.muni.cz/AtomicChargeCalculator. There is no login requirement for running ACC or accessing the results.

ACC runs on all modern browsers with JavaScript enabled. No further requirements exist for running ACC, or downloading and inspecting the results. For 3D visualization you will need an up to date internet browser with WebGL support.

Check if your browser is WebGL and Javascript compliant.

Limitations

ACC implements the Electronegativity Equalization Method (EEM) for the calculation of atomic charges which respond to changes in the molecular conformation and chemical environment. The limitations of ACC can be intrinsic to EEM, or can be the result of the implementation itself.

EEM related

Conformation dependence maybe not suitable for all applications

and in some conformation relevant for the

Parameter application domain

- missing parameters - we rely on literature for these; it is good to see that new EEM papers are coming out regularly, so there should be no shortage of such; until then, we also provide the user with the opportunity to tune already available parameter sets and add missing parameters according to their judgement, so that they can run the calculations and obtain results which they may interpret accordingly. For instance, if the user produces an EEM model for the estimation of atomic charges compatible with certain force fields (e.g., GLYCAM for sugars which have not yet been included in its parameterization - gather more examples. AMBER???)

Missing parameters

...solved sort of ...

Post-EEM methods

Several derivations of EEM (ABEEM, SFKEEM, SQEEM, etc.) have been published, which mainly aim to improve the ability of the post-EEM model to reproduce certain charge-derived ...dipoles, potentials... ACC currently implements only the classical EEM formalism, adjusted by Yang ... . The reason is that the classical formalism has a straightforward implementation, is ammenable to time and memory optimization techniques, and, most importantly, many EEM parameter sets are available for this formalism.

Implementation related

Structure

In order to produce chemically relevant atomic charges using EEM, it is necessary that the structure of the molecule be complete. No crucial parts should be missing. If parts of the structure are missing, appropriate cappings should be included. All protons should be present according to the relevant protonation state. Since ACC does not currently include functionality for editing the molecular structure, thus you must address these issues prior to uploading the molecule into ACC.

ACC does check valences, and produces a missing H warning if they are not satisfied. Despite the warning though, ACC allows to proceed with the charge calculation step, as it might not always be possible to obtain a perfect structure (e.g., when working with low resolution structures of extremely large complexes). The results from such calculations may not have chemical meaning in their absolute values, but they can be very useful when comparing sets of charges (open vs closed conformation, free vs bound state, etc.).

Total charge

The total molecular charge plays an important role in the quality of the ACC results, as it quantifies the amount of electron density that will be distributed across the molecule during the EEM calculation. The total molecular charge must be in tune with the protonation states. ACC assumes by default that all molecules are neutral, and it is the user's responsibility to mark the charged molecules with their correct total charge.

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