I'd like to ask few questions related to ddg_monomer application:
1) When I set number of iterations to 50 (-ddg::iterations 50), the average energy in ddg_predictions.out file does not correspond to the arithmetic mean of the individual runs in the full output file. When I set number of iterations to 20 (other settings is the same) everything is OK.
2) Calculation of double-point mutants produces different energies depending on the order of the mutations (A1B, C2D has different energy from C2D, A1B - up to 1 kcal/mol). How does this application functions? How should I run calculation on multiple-point mutants?
If you set the number of iterations to greater than 20, the ddg_monomer application averages only the lowest 20 scores. (There's no way of changing this number, short of editing the code and recompiling.)
The best I can tell, multiple mutations shouldn't be affected by the order. That said, remember that the ddG protocol, like most Rosetta protocols, is stochastic, so there being a small difference between a two runs that should be the same is not too surprising. I'd only be concerned if the difference was systematic across multiple runs. (And that's multiple runs with different random number seeds - don't use the constant_seed flag.)