Editing ChargeCalculator:FAQ (section)

=Can I get good electrostatic potentials?=

Whether or not atomic charges can generate accurate electrostatic potentials depends on several factors. First, certain ''charge definitions'' (see above) are based on principles which relate atomic charges to electrostatic potentials. Therefore, if you expect to compute potentials based on the atomic charges, you should probably pick an EEM parameter set developed for a suitable ''charge definition'' (MK, CHELPG...). Second, the concept of atomic point charges is inherently limited with respect to describing charge gradients, therefore the resulting potentials in some areas of the 3D space around the molecule will be better described than in some other areas.

Further, one should keep in mind that EEM, the method used by '''ACC''' to calculate atomic charges, is an empirical approach. EEM parameters available in '''ACC''' were mostly fitted to reference data in the form of atomic charges from quantum mechanical (QM) calculations. EEM is an approximation meant to keep as much accuracy as possible (compared to reference data) while maximizing computational efficiency. Therefore, the maximum accuracy to be expected for EEM atomic charges cannot exceed the accuracy of the corresponding QM charges in reproducing electrostatic potentials. 

Finally, note that some papers provide straightforward evaluations of the ability of their EEM parameter sets to reproduce electrostatic potentials from QM calculations. So follow the citation of the EEM parameter set you plan to use, and see if this information is available in the original paper. Note that the current implementation of '''ACC''' provides only the values of atomic charges, and you will have to compute the electrostatic potentials yourself (e.g., on the [http://nbcr-222.ucsd.edu/pdb2pqr_1.8/ pdb2pqr server]). In the future '''ACC''' might support such functionality.