# Adding Bond Connection 2'-5' RNA

**URL:** <https://gromacs.bioexcel.eu/t/adding-bond-connection-2-5-rna/13781>\
**Category:** User discussions\
**Tags:** forcefield, simulation-setup\
**Created:** [October 21, 2026, 4:17am UTC](https://gromacs.bioexcel.eu/t/adding-bond-connection-2-5-rna/13781 "2026-10-21T04:17:40Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![mandarkulkarni](https://avatars.discourse-cdn.com/v4/letter/m/58956e/32.png) [@mandarkulkarni](https://gromacs.bioexcel.eu/u/mandarkulkarni)\
**Post date:** [October 21, 2026, 4:17am UTC](https://gromacs.bioexcel.eu/t/adding-bond-connection-2-5-rna/13781/1 "2026-10-21T04:17:40Z")

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GROMACS version: 2026.3  
GROMACS modification: Yes / PLUMED

Hello,

I’m working on a 2’-5’ RNA linkage. I’ve added the relevant RTP and HDB entries, and the force field looks fine.

The problem is defining the` O2'(i)–P(i+1)` bond in the `[bonds]` section (analogous to `-O3' P`).

The next residue varies across the models I’m simulating, so I currently fix the connection with a Python script after generating `topol.top`.

I could use `O2' +P`, but that would conflict with the `-O3' P` entry in residue i+1. Does `O2' +P` override `-O3' P` by default?

Is there a standard GROMACS way to define the O2’(i)–P(i+1) bond?

Thanks,  
Mandar