When I do a minimization, the results I get are not what I expected.
If you are doing an MM2 minimization, it may be that you need to define missing parameters. If you get any warning or error messages, they might explain which parameters are guessed or missing. You either need to define missing parameters or try a different calculation like MMFF94, MOPAC, Gaussian or GAMESS. Note that some calculations cannot handle certain atom types. See the manual or Help for more details on defining missing atom types.