Hi,
I want to know whether there is any effect for the explicit water-water interaction energy in polypeptide structure prediction. In literature survey, just it is mention as solvation energy. I performed my calculations with the elimination of explicit water-water interaction energy. Is it advisable?


Ramya

Most likely not.
Read the literature to see what others have done to solve similar problems as the one you are working on.

I'd expect (explicit) water to have an important influence on the conformational preference of peptides.