I switched from rosetta2.3 to rosetta3.1 recently and I found that flags are changed in the new edition. I used to do prepacking before docking in rosetta2.3, should I do the same thing in rosetta3.1? Also, I used to do both perturbative docking and ensemble docking using rosetta2.3, could I do the same kind of thing using rosetta3.0?
Anyone knows the answers? Please share with me and I really appreciate that. Thanks a lot.