Fast methods of atomic charge calculation: parameterization of EEM for applicability to metal containing proteins
C. M. Ionescu, R. Svobodová Vařeková, J. Vaněk, J. Koča
National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 61137 Brno, Czech Republic
Atomic charges, although not physical observables, are used to explain many molecular properties and are needed in many molecular packages. The quantum chemical approach to calculating various types of atomic charges can be very precise, but extremely time demanding; in any case, its applicability to biomolecules is restricted by the size of the systems. One of the already available alternative solutions is the Electronegativity Equalization Method (EEM), which allows for the fast calculation of partial atomic charges with remarkable precision , provided that the proper parameters have been previously determined.
Previous studies in this respect have made great progress since the original development of EEM by improving the formalism , increasing the number of covered atom types , testing the amenability of various atomic charge schemes , implementing the EEM formalism in modeling software  etc. However, none of them has dealt with system sizes of more than 200 atoms, a number which is hardly relevant at a biomolecular level.
We have obtained EEM parameters for the elements commonly found in proteins (C, H, N, O, S) and the Ca ion that may appear as a ligand, for systems whose size is around 1000 atoms. All these systems are parts of very large proteins, and therefore the parameters we have obtained should be able to predict partial atomic charges on full-sized real proteins to a good approximation. We present the complete process of generating these EEM parameters.
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