I have finished the fragmentation step using CS-Rosetta (with file aa_t000.xx03xx.v_3 and aa_t000.xx09xx.v_3). Now I want to generate protein structures from them and meanwhile apply NOE distance constraints. I have tried to only build 1 structural model. The resulting pdb structure does not satisfy the NOE constraint. I have the following questions:
(1) what is the appropriate way to check the NOE distance constraints have been applied? In other words, is my expectation (the NOE constraint should be there even though only one model has been generated) right?
(2) what else is needed to be done in addition to have the –cst cst flag in order to apply the constraint for Rosetta 2.3.1?
• For example, will the option “-abrelax” just ignore the constraint introduced by “-cst”
(3) how could I achieve my goal in Rosetta 3.1? what is the current status of Rosetta 3.1 for the above mentioned task.
Any inputs and comments would be highly appreciated.