Reply To: could I add some constrain to the backbone but not completely fix it when relax?

[Anonymous]

The difference between the native and start options is whether the constraints are based on the starting pose for the trajectory, or a user-supplied native pose.

It is possible to set up your own constraints manually; I believe the abrelax code is compatible with constraints. There is a file in the manual describing how to write your own constraint file to constrain the backbone atoms as you want. http://www.rosettacommons.org/manuals/archive/rosetta3.1_user_guide/file_constraints.html

There’s no clean way to translate kcal/mol/area into rosetta energy units – you’ll just have to try different coefficients in the functional form for your constraint until you get the strength you want. I suggest making a graph of the function you choose and setting it so that it adds 5 energy units or more in the zone you want to be forbidden. In fullatom mode, a few REU/residue is expected for a well folded protein, so 5 should be plenty. I don’t know what you’d need in centroid mode.