Thanks a lot for your guide. I just figured it out to use loopmodel to
optimize the loop.
I am going to build up a large number of conformations of the loop by
setting a.loop.ending_model to a large value.
Just another question, will set "a.ending_model" more than 1 help a
little bit, as the total number will be a.ending_model *
a.loop.ending_model?
a.ending_model controls how many models of the entire protein are
generated. It makes sense to increase that from 1, particularly if you
are not sure where your loop termini should be.