Does anyone know whether the packing option “packing::explicit_h2o” and “packing::solvate” work out in Rosetta3.1?
This paper “A ‘Solvated Rotamer’ Approach to Modeling Water-Mediated Hydrogen Bonds at Protein–Protein Interfaces” said that Rosetta could recover water-mediated h-bond using a rotamer library called Solvated Rotamer. How to use it, add “explicit_h2o” or “solvate” flag ? But I read the code of Rosetta3.1 and couldn’t find the source code implemented these two option.
That paper was not done with the Rosetta3 package (it’s too old; it was done with Rosetta2). I know that there are bits and pieces of solvated rotamer code scattered about but I’m not aware of any publications or demonstrations of it.