After running an MM2 minimization, I get irrational results. For example, some atoms get pushed much too far away creating really long bonds.

After running an MM2 minimization, I get irrational results. For example, some atoms get pushed much too far away creating really long bonds.

It could be the that the starting geometry of the model is already too close to a saddle point or local minimum. Try moving an atom to a different location and then restart the minimization.