The protein-RNA hydrogen bond numbers display more variation. In the Ago2 system, the nonpolarizable force fields display about the same number of hydrogen bonds as the crystal structure, and the AMOEBA and O3P water simulations display less. In Cas12j system, ff14SB+OL3 and OPLS4 display more hydrogen bonds, ff19SB+OL3 and AMOEBA agree with crystal structure and O3P water simulations display less. In RIG-I simulations, the non-polarizable force fields agree with the crystal structure about the number of hydrogen bonds and the polarizable water model and AMOEBA display less hydrogen bonds.