What are the differences between Minimize Structural Error and Minimize Energy?
A structural minimization uses an error function that takes into account all of the atoms in the model. The error function consists of four terms: a bond length error term, a bond angle error term, a planar atom flattening term, and a double bond rotation term. The variables for Minimize Structural Error consist of the Cartesian coordinates of all the atoms of the structure. The Minimize Energy command, minimizes the energy of the molecule based on the MM2 Force Field. It performs a local minimization only. Therefore, the results of minimization may vary depending on the starting conformation in a model.