Reply To: RosettaDesign parameters

[Anonymous]

> 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.

You can simply read the “score” value in the output file. The lower is the better.
score: -352.65
env: -109.25 env_weight: 0
pair: -41.67 pair_weight: 0
vdw: 3.50 vdw_weight: 0

> 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?
If you use “NATRO” on every residue in the resfile, the scores should be the same. You can also use “-design -fixbb –natrot ” in the command line without resfile to score native structure.

> 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).
%accepted is not very important here. It should be the monte_carlo counters/diagnostic. I do not know why it is always 0