I refer to the constraints file instructions provided here:
(1) Does any one know how to input the constraints to Rosetta 3.0 assuming constraints files have been prepared according to the format stated in the above URL?
In particular I'd like to use the "docking_protocol" application provided in Rosetta. However, calling for command line help (eg ./docking_protocol.linuxgccdebug -help) doesn't seem to provide any options that indicate how a constraints file may be specified.
(2)Additionally, I have also tried various flags at command line such as -constraints filename -cst_file filename and so on which have no effect. That is, assuming the "docking_protocol" application accepts constraints -- if it doesn't, which are the other Rosetta 3.0 applications that do accept constraints? Abinitio comes to mind. For reference I am trying to specify atom pair distances as constraints.
(3) The link also advises to update several functions, for eg "add_constraints_from_cmdline()". However, which source code files should these be added into? I'm sorry if these are trivial questions but I'm really quite at a loss.
Any help is appreciated and thank you for your time.