My problems as follows:
1）I repacked protein side-chains by the application of "relax.linuxgccrelease -score:dun08 -database .../... -in:file:s .../.... -nstruct". Does the default action as above call FixbbSimAnnealer FixbbSimAnnealer：：run()？
2)If the first point is right, how can I refine the protein structure had been repacked its side-chains ? The definition of refinement is not to replace existing side-chains, but to optimize the side-chains dihedral angles near the rotamer value. I read some papers achieve this function by using a conjugate gradient's method. How can I get the similar function by using Rosetta3.4?
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