Materials Studio 4.0 on Linux

I don't know if my question is appropriate for this forum (maybe too basic), but I have been having some problems with energy calculations in Discover in Materials Studio 4.0.
I am able to successfully complete jobs (molecular dynamics simulations, single energy point calcs., etc.) if I use the structures that are in the Materials Studio libraries, or my initial crystal file has a .mol suffix and was modified in Gaussian.
However, if I import a crystal file (a .pdb or .ent file, for instance) my job fails.
Also, if I go to Mercury (which is my usual viewer) and save a .pdb file in a .mol format, the Materials Studio viewer isn't even able to load the file.
Has anybody had this happen to them?
Thanks.

-Ryan