This question is regarding the implementation of the Dunbrack rotamer energy term (fa_dun).
Based on my understanding of the implementation in Rosetta 2.3, I noticed that the fa_dun energy is comprised of two components:
1) A backbone-dependent probability of the rotamer : E = -log (p)
2) An "un-normalized" gaussian penalty parametrized using the average chi angles and the standard deviations for the rotamer: E_penalty = -log (gaussian)
My concern is regarding the use of an "un-normalized" gaussian penalty term. My understanding of the Dunbrack rotamer libraries is that the probabilities are for the "entire" rotamer(i.e. over the entire distribution of the chi-angles for a rotamer within the cutoffs that classify an angle as g+, g- or t), not just the rotamer conformation *at* the mean values listed in the rotamer library file. Therefore, I believe that there is a correction term that is missing for the penalty terms that would be comprised of the normalization constants of the gaussian:
E_correction = -log (normalization of the gaussian).
As long as one stays within the same rotamer, the correction term would cancel out between the different side-chain perturbations. However, as one samples different rotamers or samples different amino-acids(for a design calculation), the correction terms would be different since the chi-angle standard deviations are different.
Please let me know if this is a known issue or if I am misunderstanding either the rotamer libraries or their implementation in Rosetta.