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