How can i introduce hydrogen bond as constraint?

[vatsanraman]

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.
etc.

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.

Sincerely,
Seungpyo Hong

[Anonymous]

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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