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Fixed bb design with hydrogen bond constraint

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Fixed bb design with hydrogen bond constraint


I want to know how can I define hydrogen bond constraint while doing a fixed bb design for my mutants. I rosetta to select only those residues from resfile that conform to the hydrogen bond constraint ??


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Mon, 2012-04-30 22:56

You should try defining your hydrogen bonds as AtomPairConstraints ( and passing in a constraint weight/file with the flags

-constraints:cst_fa_weight or -constraints:cst_weight
-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.

Tue, 2012-05-01 08:08

Thank you for the advice. I will try it and report back to you...

Tue, 2012-05-01 16:58


I have made the -constraints:cst_fa_file but what has to be done for -constraints:cst_fa ..

Tue, 2012-05-01 18:04

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.

Tue, 2012-05-01 18:08

Yes, you were right . The constraints does not work for fixbb design. So what has to be done next ??

Tue, 2012-05-01 20:53

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:

Wed, 2012-05-02 07:04