Reply To: ‘-norepack_disulf’ flag NOT work in Ligand-protein docking ?

Member Site › Forums › Rosetta 3 › Rosetta 3 – General › ‘-norepack_disulf’ flag NOT work in Ligand-protein docking ? › Reply To: ‘-norepack_disulf’ flag NOT work in Ligand-protein docking ?

January 12, 2011 at 10:34 pm #4824
Anonymous

    I think the NATRO command should work. I think that you need to specify the chain ID though, like this:
    6 A NATRO

    would keep the native residue in residue 6, chain A. When you use the NATRO command the repacking system completely ignores it. A side effect is that the residues you specify as NATRO will not be included in energy calculations during packing. This is kind of a bug, but in practice this does not usually have a major effect on the system.

    What smlewis originally said about the fix_disulf option is correct, it is not implemented in the ligand docking application and will therefore have no effect at all.