I have a pdb with crystallographic waters which appear to be important for the protein structure, and perhaps function. I am generating mutations using pyrosetta and evaluting their relative scores, and exporting structures to be simulated with MD.
I would therefore prefer to leave the explicit waters and use the TP3.params from database/chemical/residue_type_sets/fa_standard/residue_types/water. The structure does not appear to have any issues or errors, but I have seen this note "Typically, you simply want to remove the water since PyRosetta does not use these for any application and they can cause problems." and want to be sure I don't run into such problems with this hybrid explicit/implicit solvent method (using ref2015 score function)
Thanks in advance for your feedback!