Hello.
Sorry if it is repeated. I have seen some posts talking about MMFF94 forcefield and how partialcharges are assigned in avogadro, but any of them gives a complete answer.
I have 2 related questions:

Which partial charges uses Avogadro for calculations, and can we add custom partial charges?
As I read here ( Partial Charges ), Avogadro by default calculates GasteigerMarsili sigma charges. But, if I have my partial charges already calculated with other code, how can I make Avogadro to use that partialcharges? I have a .xyz file with the partialcharges as last column after the coordinates. If I open this file with jmol it shows my calculated partial charges correctly as labels. But if use Avogadro, the partial charges shown in labels are not my calculated partial charges, but the default ones; How can I tell it to show my own charges?. Connected to this question, is Avogadro using that partial charges when partial charges are required for other calculations (Dipole moment, Force fields…)? 
When I do an optimisation or a conformer search using MMFF94 in Avogadro, how it handles atom types and partial charges?
Do I need to use an input structure file format (like .mol2) implicitly stating the atom types, or will Avogadro interpret them? If, for example, I provide a structure in .xyz format with only the coordinates for each atom, and any information about atom type or connectivity, and I perform a MMFF94 optimization; Are atoms automatically classified as different atom types as required for a correct calculation using MMFF94? If so, how can I know which is the assignment for each atom I am using in such optimization? I tried to save the structure in .mol2, but I am not sure if that are the assignments used for the MMFF94 calculation.
As I understood from here ( https://sourceforge.net/p/avogadro/mailman/message/30379973/ ), the MMFF94 uses partialcharges. Are this partialcharges calculated by MMFF94 or do we need to provide them? If you need to provide them, is it using the Avogadro’s defualt GasteigerMarsili sigma charges? Can we provide other partial charges calculated by other codes (as for example as last column in a .xyz file)?
Thank you very much.
Yours Faithfully.
Yuman SAYEDAHMAD