Reply To: docking using rosetta3.1 and rosetta2.3 leads to very different results

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February 4, 2010 at 2:46 pm #4331
Anonymous

    The flags are set differently in the two command lines, the 3.1 command line that best replicates the 2.3 command line you provided is is:

    -ex1 -ex2aro -nstruct 5000 -fake_native -randomize1 -randomize2 -unboundrot

    dock_rtmin is not currently supported in 3.1; docking_local_refine will lead to significantly different sampling as the entire low-res stage will be skipped.

    Also check to see if the ‘slight’ funnel in 2.3 is reproducible in 2.3 and not the result of stochastic noise.

    We are currently in the process of benchmarking the 3.1 docking performance with the 2.3 docking performance, and will make the results public when we have them.