I am performing Rosetta Ligand docking for a ligand, let 's say A . The ligand A is in contact with both water and water vapor. I have two main quesions and I would really appreciate your help in this regard:
1. Do I need to explicity consider water in my docking as a separate ligand with the ligand A? Or is the implicit solvation in scoring function sufficient?
2. The parameter file generated for the ligand by molfile_to_params.py determines the net charge zero. I think this ligand might be hydrolyzable in the presence of water. So, its net charge might not be zero. Is it correct to use the generated parameter file by Rosetta in my simulation or I need to modify the partial charges? Any suggestions /papers in this regard would be appreciated.