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