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    Thanks for your reply!

    1. I have several disulfide bonds, so I was trying to preserve them with the -fix_disulf disulf.txt and -norepack_disulf options. As recommended, I tried:

    “rosetta -design -s acdt.pdb -fixbb -ex1 -ex2 -ex2aro_only -ndruns 100 -resfile reslist.res -try_both_his_tautomers”

    All of the scores in the pdb files are around -236 to -230, and the mutants are different, but I guess I am just confused on how to tell which of these mutants are significantly better, if any are.

    2. By removing -use_bw and using soft_rep, I’ve found that I can get better scores, but they are still not much better than the wild type protein. On that note, how do you score the wild type protein typically? I took the crystal structure and ran design with NATRO in the res file, but I did that several times and get different scores between -236 and -233, which implies that Rosetta is manipulating the structure somehow. And should “score” be the metric by which I compare mutants to the wild type?

    3. On the acceptance, if I look at, say acdt_0001.pdb, after the coordinates, I get:

    ntrials: 1

    %accepted: 0.00

    rms_to_start: 2.49374551E-07

    score: -235.91

    In every generated pdb file, ntrials=1 and %accepted is always 0.00, but the mutants are not the same. When I try to place -ntrials 1000 (for instance) in the rosetta command line, the output is the same (i.e. ntrials=1, %accepted=0.00).

    Again, thank you very much for your help with RosettaDesign! Cheers, Gregg