is there a preferred way to enforce an hydrogen bond ?

Member Site Forums Rosetta 3 Rosetta 3 – General is there a preferred way to enforce an hydrogen bond ?

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    • #1536

        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

      • #8507

          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?

        • #8523

            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.

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