Member Site › Forums › Rosetta 3 › Rosetta 3 – General › could I add some constrain to the backbone but not completely fix it when relax? › Reply To: could I add some constrain to the backbone but not completely fix it when relax?
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.