Backbone and C-alpha atoms equivalent in RNA and DNA

User discussions
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GROMACS version: 2023.3
GROMACS modification: No
In the calculations of RMSD and RMSF for proteins backbone atoms and C-alpha atoms, respectively, are generally used. What index groups should be created for RMSD and RMSF calculations for nucleic acids?
Is it correct to use for RNA the index group containing O1P, O2P, O5’, C5’, C4’, O4’, C3’, O3’, O2’, C2’, and C1’ as the equivalent of backbone group in proteins?
What atoms in RNA/DNA could be selected as the equivalent of proteins’ C-alpha atoms?

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Still looking for solution of this question and would be grateful for help.

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Using the backbone atoms for RMSD would likely be the closest analogy (maybe using P instead of O1P/O2P since fluctuations in the oxygens sticking out probably aren’t as important).

I don’t think there’s any one atom that would be perfectly equivalent to the C-alpha atom, so you might want to try looking through different choices to see which best fits your goal (maybe choose P if you want to avoid fluctuations from the sugar ring, or C1’ if you want to include fluctuations closer to the base, or even the center-of-mass of the atoms involved in the backbone)