> Perhaps Avogadro generates a file with a specific atoms parameter that it
> uses to optimize with MMFF94.
Avogadro determines the MMFF94 atom types internally (i.e., in memory) and does
not write it to a file.
If you want to define atom types, such as for MMFF94, you should look at the
Open Babel "Tinker" file format:
http://openbabel.org/docs/current/FileFormats/Tinker_XYZ_format.html
Hope that helps,
-Geoff
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