Hi,
I need to use rosetta for proteins for side-chain sampling keeping the backbone fixed.
I tried using the fixed-backbone-design module by specifying the residues with the fixed backbone, but the method does the side-chain sampling using some preferred discrete rotamers.
Is there some way I can do the thorough sampling of side chains using MC optimizations (which could be more compute intensive) and not using the discrete rotamers?
Thanks,
Pooja
you may want to try using the mcmin_trials option.
Additionally you can expand the rotamer set using the -ex options
for example
-ex1 7
adds rotamers with chi1 angles sampled in six quarter standard deviation steps
see the README for a little more description.