Editing ChargeCalculator:FAQ (section)

=Can I combine EEM parameters originating from different sets?=

Suppose you have a biomacromolecule in complex with a drug inhibitor. You may be wondering if it is necessary, or at least possible, to use different EEM parameter sets for the two molecules. From our experience, it is sufficient to employ a parameter set with the attribute ''target=biomolecules'' for the entire complex. Alternatively, you may want to use a certain set suitable for your type of molecule, but which misses EEM parameters for one atom type, and such parameters are available in a different set.

If you really want to combine EEM parameters which originate from different sets, there is a way. In the input file, identify the chemical element column. For all atoms that you would like to treat differently, make some modification to the chemical element. This way, for example, the chemical elements of all ligand atoms can be changed from H, C, N, O, Cl into Hx, Cx, Nx, Ox and Clx. Then upload the molecule. '''ACC''' will report an <span style="color:#DAA520">''unknown chemical element names''</span> warning for the atoms whose chemical elements you have modified. All you need to do now is [[ChargeCalculator:FAQ#How_do_I_add_EEM_parameters_if_they_do_not_exist.3F | create a custom parameter set]] as a copy of one parameter set, with additional ''Element'' tags from a second parameter set.

It is very important to take note of the ''kappa'' parameter. It should be comparable in the two sets you want to merge. If this condition is not satisfied, you might have to alter the values of the new parameters before they can perform effectively with a different set. In general, when trying out such merges it is good to run a few parallel calculations in which you progressively change the value of the parameters in question, and inspect the resulting atomic charges. Try to look for intervals of the parameter space for which the trends in charges remain the same.