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 ?
It seems likely to me that it’s just ignoring your resfile. Probably whoever wrote it never thought of having disulfides nearby.
You could try just resetting those residues back to their appropriate conformations after the ligand docking application is finished, then checking their score (score.cc) to make sure they don’t clash too bad.
You could try going through the code looking for spots where packing occurs, and we can stick in code to make it respect the disulfides (I’ll give more details if you want to try this)
You can try waiting for the rebooted version in 3.2; I think it’s been reworked with the RosettaScripts such that it will be more flexible.