Member Site Forums Rosetta 3 Rosetta 3 – General ddG from backrub

  • This topic has 3 replies, 2 voices, and was last updated 14 years ago by Anonymous.
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    • #679
      Anonymous

        How do you get the ddG from a mutation doing the backrub simulation? I.e. if you have two pdb structures (the original and the mutant, which is the result of the backrub simulation), what script or commands do you use to get the ddG based on the two structures.

      • #4639
        Anonymous

          I’ve forwarded this along to a relevant developer.

          • #4643
            Anonymous

              Thanks smlewis. If I don’t hear from them, how can I contact them? Thanks again.

              > I’ve forwarded this along to a relevant developer.

          • #4644
            Anonymous

              This is all I got back:

              “I haven’t made any effort myself to transform the scores from backrub runs into approximate ddGs. What I have done is described in the JMB backrub paper, namely run 10 different 10,000 step simulations at a kT of 0.6 for both the wild type and mutant. I then take the lowest score.

              Obviously that’s a pretty simplistic protocol that far undersamples.”

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