Fixed bb design with hydrogen bond constraint

You should try defining your hydrogen bonds as AtomPairConstraints (http://www.rosettacommons.org/manuals/archive/rosetta3.4_user_guide/de/d50/constraint_file.html) and passing in a constraint weight/file with the flags

-constraints:cst_fa_weight or -constraints:cst_weight
and
-constraints:cst_fa_file or -constraints:cst_file

That said, I don’t think fixbb actually accepts constraints. Give this a shot. If it doesn’t work, I’ll see about adding a line of code to fixbb to tell it to use constraints (probably core::scoring::constraints::add_fa_constraints_from_cmdline_to_pose() immediately after the scorefunction is defined). You’ll know if it works because constraint-related scorefunction terms will show up in your output score file.

For -constraints:cst_fa_weight, pass a number weight for your constraint, based on how strong you want it to be. You can plot your constraint with a plotting program to see what scores it will have at what distances….or just give it a weight between 1 and 10 and not worry too much about it.

I looked at fixing the fixbb application, but it turns out the better way to do this is via RosettaScripts. If you write yourself a simple script using ConstraintSetMover followed by PackRotamersMover it ought to work. (I’m not much good with RosettaScripts yet, so I can’t really help specifically). I’m told the “RosettaScripts” section of the manual is the best-documented part of the code and that you’ll have no problem writing yourself the script you’ll need: http://www.rosettacommons.org/manuals/archive/rosetta3.4_user_guide/