I am performing molecular dynamics simulations on RNA tetra-loops. I have one tetra-loop with the sequence gcUACGgc (5'-3') where the stem residues are the lower case letters and the loop residues are upper case letters. In this tetra-loop the g residue on the 3' end is identified by GROMACS as a RG3 in the rna.rtp file but the c residue on the 5' end is identified by the rna.rtp file as a RC residue. I am wondering why these discrepancies occur. I thought the g,c residues on the 5' end should be identified as RG5 and RC5, the c,g residues on the 3' end should be identified as RG3 and RC3. My assumption is correct for the 3' end but partially correct for the 5' end. I am using the force field amber14sb_OL21.ff. This can be problematic to me since I am running MD simulations of protonated RNA tetra-loops, where I have to edit the rna.rtp file with the additional protons. Please let me know if you have overcome a similar situation or knows a better force field for my situation.