Oluwaseyi,
Thank you for the response!
So I did some researching and found out that those files are PTC source code files, so they mean nothing to use because we don't have the source code.
Also, it seems that mda files and mma files are equivalent, and mdb and mmp files. See How to view Mechanica Structure mesh.. WF2 . Moreover,
(1) I made a part
(2) meshed the part and saved the mesh elsewhere
(3) Simulated the part without using the mesh in step 2.
(4) copied the mdb file to the part folder and changed the extension to mmp.
(5) AutoGEM detected and loaded that new mmp file successfully as a mesh.
Also, I still am not sure why my model was failing in the time analysis, but I created a much simpler model (replacing many of my components with beam and mass idealizations), which, although not ideal, enabled it to run. Even with the simplification, the analysis file sizes were MASSIVE. With the unsimplified model, they would be even more massive.