The ionizer doesn’t seem to recognize some kinds of structures, especially some fused rings. What can I do about it?

The ionizer is intended as a simple practical tool for generating ionized forms from some commonly encountered functional groups. The default patterns for these groups provided in the ionizer.ini file may not cover those groups in all circumstances. For instance, for patterns meant to cover aromatic groups some resonance structures involving fused rings may not match. This had been noted to occur if the resonance structure has bond orders that contradict those given in the pattern in the ionizer.ini file.

If you encounter such problems, you may add more patterns to the ionizer.ini file to cover such cases. However, we recommend that you use Epik instead, as it is intended to handle such cases properly.

Keywords: LigPrep

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