Editing ChargeCalculator:FAQ (section)

=All of the built-in EEM parameter sets report warnings about Missing Atoms. How does it affect my calculation?=

EEM, the empirical approach used by '''ACC''' to calculate atomic charges, operates with atom types based on chemical elements. When uploading the input file, '''ACC''' needs to establish the chemical element of each atom, so that it can assign a suitable atom type, and subsequently EEM parameters. '''ACC''' expects to find the chemical element at a pre-defined position in the input file, which depends on the formal guidelines established for each file format. 

It may happen that '''ACC''' does not recognize the chemical element (see above why), or there are no EEM parameters associated with that chemical element. In this case, the atom in question will not be included in the atomic charge calculation. This means that the calculation will run only on the remaining atoms, and when you view the results the atomic charge value for the atoms for which there were no EEM parameters will be "NaN". If none of the atoms can be assigned suitable EEM parameters, you will get an error for the entire calculation. 

If none of the built-in EEM parameter sets contains parameters for all the atoms in your input molecule, you can circumvent this issue and make sure all atoms are included in the calculation by using a custom EEM parameter set in which you manually include EEM parameters for atoms listed as ''Missing Atoms''. By doing so you actually define new atom types and corresponding EEM parameters. For example, say your input file contains phosphorus. '''ACC''' will report <span style="color:#DAA520">''Missing Atoms''</span>. You may create a new EEM parameter set based on one of the built-in sets already available in '''ACC''' (see below how to do that). Copy/paste the parameter information for one of the atoms already present (all text enclosed in the ''Element'' tags) once more into this new parameter set. It is good to choose some atom that has similar chemical properties to phosphorus - especially electronegativity and hardness (S would probably be the best choice if available). Change the ''Element name'' tag to "P". Inside each ''Bond Type'' tag, you will find the values for parameters ''A'' and ''B''. You may keep these values, or modify them (see below how to do that). Save the new EEM parameter set with a unique name and select it from the list. When you start your computation, the phosphorus atoms will now be included in the calculation, although the EEM parameters might not be optimal.