Reply To: Computing ddg_binding

Member Site › Forums › Rosetta++ › Rosetta++ – General › Computing ddg_binding › Reply To: Computing ddg_binding

October 1, 2008 at 2:59 pm #4017
Anonymous

    There are two very important things you should be aware of while calculating ddG using analyze_interface protocol.

    1) There is no minimization of the side chains at any stage. You can put -min_interface flag and that will do interface minimization while calculating ddG. But that will still keep your Edun = 0.

    2) Edun is a one body energy term and what you see in your OUT file is dEdun( or delta Edun). If you look carefully, you will find that ddG includes only those terms which are two body (meaning both the partners are required). Since
    ddG(binding) = dG(AB) – dG(A) – dG(B)
    any Edun contribution in dG(AB) will be canceled in dG(A) or dG(B).

    Hope that helps.

    —
    Ramesh Jha