Hello.

I have some questions on the **env** energy term:

The values in the **EnvPairPotential::env_log_** table should be the **–ln[P]** values defined for the **env** term in **Rohl et al. 2004. Methods Enzymol. 383:66-93 (Table I)**. If the **P's** are sheer probabilities, then the **–ln[P] **values should all be positive or zero. However, looking at the input file from which the **–ln[P]** values are loaded (**database/scoring/score_functions/EnvPairPotential/env_log.txt**), it can be seen that many of them are negative. Why?

Is it because of interpolation? Interpolation is helpful if one wants to minimize **env** energies using derivatives, but derivatives are not defined for this term (the **EnvEnergy** class does not override **OneBodyEnergy::eval_residue_derivatives(){}**). This leads to the second question: Why is it that such an important energy term to centroid mode as the **env** term is left unminimized during derivative-based minimization?

Finally, the code in **EnvEnergy::residue_energy() **indicates that the **env** energy is always multiplied by 2.019, regardless of the amino acid type or neighbor count. What is the meaning of this multiplier?

Thanks,

Andrea.