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is there a preferred way to enforce an hydrogen bond ?

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is there a preferred way to enforce an hydrogen bond ?

In an ab_initio run with restraints, is there a preferred way to introduce a hydrogen bond ie. in cases where a sheet is known from a series of reliable observations ? Is it acceptable to include an HN-O/N-O restraint or is there a better way that allows the Rosetta engine to handle the details of geometry/distance?

thank you

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Wed, 2013-03-20 13:14

A) forcing sheet in your secondary structure predictions from which fragments are generated is a good idea

B) hydrogen to acceptor distance constraints along the sheet are probably the cleanest thing to use. I wouldn't bother with angle/torsion constraints - Rosetta should pick up the hbond and do that automatically. You can use AmbiguousConstraints if you aren't quite sure of the pairing - is that your case?

C) There is likely to be a much better way to force sheet pairing with some sort of external input file...Rocco, do you know?

Wed, 2013-03-20 15:41

Constraints are definitely the way to do it (after the fragment secondary structure enforcement). After a quick check, I don't see any constraint that is specific for sheet-sheet pairing. Atom pair constraints are probably the way to go.

The remodel protocol (which I believe should be in the 3.5 release) has a bunch of facilities for enforcing certain tertiary structure geometries, but that's set up primarily for protein design where a large number of interactions are being made, rather than ab initio folding with one particular pairing.

Thu, 2013-03-21 11:23