GROMACS version:gromacs-2025.1
GROMACS modification: No
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I am currently trying to perform MD simulations on a pronated RNA tetra-loop in gas phase using GROMACS. I have noticed that rna.rtp file of Charmm27 ff have not described the terminals clearly. For an example Amber ff has different sections for RG5(5’), RG and RG3 (3’). Charmm27 doesn’t have different sections like that (it only has RG, RU, RA and RC sections) and it makes it impossible to describe the terminal atoms in the PDB file. Did anyone else come across the same problem? Please let me know.