Editing ChargeCalculator:FAQ (section)

=The calculation ran, but I got the warning "Missing parameters for symbol ... and multiplicity .... Using value for multiplicity ... instead."=

EEM, the empirical approach used by '''ACC''' to calculate atomic charges, operates with atom types based on chemical elements. Furthermore, some EEM parameter sets available in literature employ atom types which depend not only on chemical element (or ''symbol''), but also on the maximum ''bond multiplicity''. This means that in such EEM parameter sets there are, for example, different EEM parameters for carbon atoms with sp&sup3; hybridization, than for carbon atoms with sp&sup2; hybridization. In order to keep a consistent scheme of storing and assigning parameters, '''ACC''' implements by default an EEM parameter scheme which supports ''bond multiplicity'' information via the tag ''Bond'' and its attribute ''Type''. EEM parameter sets which are based solely on chemical elements contain multiple ''Bond'' tags as well, but the parameters associated with different ''bond multiplicities'' (''Type'' attribute) are actually merely copies. 

Because the unified parameter scheme employs bond multiplicity information, '''ACC''' needs to establish the chemical element of each atom, as well as its maximum bond multiplicity, so that it can assign a suitable atom type, and subsequently EEM parameters. When uploading the input file, '''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). 

As soon as the calculation starts, ''ACC''' attempts to obtain bond information. First, it
searches the input file for connectivity information. If this is not present, '''ACC''' attempts to establish the maximum bond multiplicity based on interatomic distances. This algorithm generally has trouble when interatomic distances vary significantly from the expected norms, or when handling coordinated atoms, and it may generate unexpected bond multiplicities for which no EEM parameters are available. To overcome such situations, '''ACC''' falls back to the EEM parameters for the nearest bond multiplicity available.

This fallback also happens when the input molecule contains an atom type with a maximum bond multiplicity which was indeed not covered during the development of the EEM parameters used in a given calculation. For instance, if the reference data used for the development of the particular EEM parameter set you chose did not contain any sp&sup2; nitrogen (''Bond Type''="2"), '''ACC''' will fall back to the EEM parameters for sp&sup3; nitrogen (''Bond Type''="1"). '''ACC''' will produce a warning to inform you of this fact, and in the final results the atom type will still be N:2, as originally detected in the input file. It is up to you to decide if the values of atomic charges for these problematic atoms are acceptable.