I want to use a two-step design procedure in which a fixed backbone design is combined with a backbone relaxation.
The two steps are supposed to be repeated alternately as long as they bring improvement in the energy.
(something like this http://www.ncbi.nlm.nih.gov/pubmed/22632833)
Which fixbb design parameters are the most important? I use -packing:ex1, -packing:ex2. But perhaps there is something else I should consider?
Next, I want to relax the resulting designed structure. However, I want to avoid big changes in the backbone. Which parameters can I use to make the relaxation less 'aggressive'? Will be -relax:fast enough? Does the relax protocol supoprt symmetry?
The relaxation step is supposed to allow for small backbone movements that resolve potential steric clashes (sophisticated alternative for -score:weights soft_rep_design).
Such a relaxed structure will be an input for another round of fixbb design. The question is whether to use the relaxed backbone or the full structure (bb+sequence) for design? In the latter case, how to tell fixbb design to optimize the input sequence instead of starting from a random one? Do I need to perform an idealization step at some point?
Finally, when the procedure should be stopped? I consider to take RMSD to the initial backbone structure (should not be too big) together with the change in the energy.
I would appreciate your comments and hints, especially on the technical aspects.