Thanks smlewis very much.
I’m using rosetta3.1 to dock a peptide to a protein. I found that my protocol could sample the near-native conformation but it’s energy wasn’t the lowest. Score function used in my protocol was standard.wts patched by score12.patch.
I had tried several other score functions but the results were the same. So I think I need to change the weights of score functions to find a good correlation between decoy energy and rmsd. I’ve sent an e-mail to Rosetta-commons two weeks ago but got no reply till now. Could you tell me the protocol to calculate the weights?