Because of limitations in RAPID, the termination criterion should be quite large - say GNORM=5 or more. Also, after a RAPID calculation, a conventional MOZYME calculation should be run, in order to get a more correct heat of formation.
If the following conditions are used, the optimization will run smoother:
1. Use Cartesian coordinates.
2. Before using RAPID, a useful step is to optimize the whole system.
The effort to set up a system with RAPID is well worth while, particularly if only a few (up to 10-20%) of the atoms are flagged.
As an example of the effect of using RAPID, for a decapeptide containing 143 atoms, with the coordinates of the atoms of the last residue being optimized, the times required for 10 cycles of geometry optimization are as follows:
|Using conventional MOPAC||19.4|
|Using MOZYME with RAPID||2.8|