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.
“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.”