Editing ChargeCalculator:FAQ (section)

=After uploading my molecule, I got a warning about "unknown chemical element names". How will 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. For example, in .pdb files, '''ACC''' looks for the chemical element in the column after occupancy and temperature factor (positions 77-78).

'''ACC''' holds a predefined list of chemical elements from the periodic table of chemical elements. If '''ACC''' does not recognize the chemical element for an atom at the expected position in the input file, it will not include this atom in the atomic charge calculation because it cannot assign an atom type, and therefore EEM parameters. 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 with unknown chemical elements will be "NaN". If none of the chemical elements are recognized (e.g., the file format guidelines are not respected, or the input file comes from a modeling program which uses the element column to store its own atom types), you will get an error for the entire calculation. Finally, if the input file comes from a modeling program which uses the element column to store its own atom types, and these atom types overlap with known chemical elements, it is possible that '''ACC''' includes the atoms in the calculation, but it assigns wrong atom types. For example, if "Ca" appears in the element column, '''ACC''' will interpret it as calcium even if it was originally meant as C-alpha.

You can circumvent these issues and make sure these atoms are included in the calculation correctly either by fixing the input file, or using a custom EEM parameter set. The first solution is to adjust the element column in the input file so that it really displays chemical elements. Additionally, make sure the input file format follows the formal guidelines. The second solution is to use an EEM parameter set in which you include EEM parameters for the atoms with unknown chemical elements. By doing so you actually define new atom types and corresponding EEM parameters. For example, say your input file contains hydrogen atoms identified in the element column as "H1" and "Ho", depending on their binding partner. '''ACC''' will report them as <span style="color:#DAA520">''unknown chemical element names'' warnings</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 hydrogen (all text enclosed in the ''Element'' tags) twice more into this new parameter set. Then change the ''Element name'' tag in one case to "H1", and in the other to "Ho". Save the new set with a unique name and select it from the list. When you start your computation, the atoms with the previously unknown element names "H1" and "Ho" will now be included in the calculation, and treated by EEM parameters suitable for hydrogen.