I am unable to do an energy minimizations because that option is grayed out.
Chem3D needs to see a math co-processor (FPU) in order to run MM2 energy minimizations. If this option is grayed out, your computer either does not have a math co-processor installed or you are using Chem3D 3.1.3 or earlier on a PowerMac. A PowerMac does have a math co-processor, but not one that is recognized by Chem3D version 3.1.3 or earlier, since 3.1.3 or earlier is not native.
For PowerMac users, the solution is to upgrade to the latest version of Chem3D Pro, which is PowerMac native. For 68K Mac users who do not have a math co-processor, the solution is to to install a floating point unit emulator like SoftwareFPU which is available as shareware from John Neil & Associates. PowerMac users who do not wish to upgrade their non-native Chem3D software can also use this FPU emulator. Please note that the software FPU emulator will allow you to run MM2 minimizations, but they will be extremely slow.