How can i introduce hydrogen bond as constraint?

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    • #1221

        Hi everyone,

        i need you help~

        i am trying to introduce hydrogen bond constraints.

        something like this:

        Let O on residue 1 and N on residue 10 form hydrogen bond.
        Let N on residue 1 and O on residue 20 form hydrogen bond.

        i had tried to place the two hydrogen bond atoms close as distance constraint.

        but mostly the distance constraint is not enough

        so i want to calculate hydrogen bond as a constraint.

        i had tried to use hbonds.HBondSet().

        but i can only display hydrogen bond state uwing hbonds.HBondSet().show()

        and cannot get the information as string or other formats.

        how can i get the hydrogen bond states between two atoms?

        i am welcoming any suggestions!

        thank you in advance.

        Seungpyo Hong

      • #6875

          If you have set distance constraints on the hydrogen bonds you want, but the constraints are not obeyed, there are three possibilities:

          1) the constraint isn’t set right and Rosetta is ignoring it (or its scorefunction weight is zero)
          2) the constraint scorefunction weight (probably atom_pair_constraint) is too small, and Rosetta isn’t obeying it strongly enough
          3) Rosetta thinks the hydrogen bonds cannot form for some conformational reason

          For digging into the hbondset – if you want some output other than the human-readable show() function, look in the C++ at the HBondSet class (src/core/scoring/hbonds/HBondSet.hh) – I don’t know what information you want so I’m hoping what you need may be there. Notice HBondSet is a read-only object – you can’t tell it where the hbonds you want should be, it tells you where the hbonds you already have are.

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