Hi Priyasha,
If the modification is not meant to unwind the helix, I would recommend
trying to use modXNA to parameterize your modification.
The parameters are built on top of the OL3 RNA force field, and we have
found that modifications parameterized using it maintain helical structure.
There are some tutorials at the modxna.chpc.utah.edu link, as well as a
LiveComMs tutorial.
https://pubs.acs.org/doi/10.1021/acs.jctc.4c01164
https://modxna.chpc.utah.edu/
Good luck!
-Christina
On Thu, Jun 18, 2026 at 3:32 AM Priyasha Majee via AMBER <amber.ambermd.org>
wrote:
>
>
> Hello All,
>
> I am trying to simulate a 10-mer RNA duplex with a modification
> incorporated at the middle of the sequence. The modification is a base
> modification. I have generated the force-field parameters of this
> modification using the prepgen method in antechamber. The frcmod files
> were obtained successfully. There were no missing parameters. After
> generating these files, i incorporated the modification into the
> RNA-duplex using tleap. I followed 19 stages of minimization, 4 steps of
> NVT heating and 22 stages of NPT equilibration with lowering restraints.
> Everything looks fine till equilibration. But, the RNA duplex unwinds
> after i perform a 200 ns of production. The structure gets completely
> distorted and the base pairs break. Can someone help me understand
> what's going on here and how to correct it? I am suspecting a problem in
> force-field parametrization, if there is any. I tried modifying the
> simulation protocol many times. But i think the protocol is not the
> issue here. Please help.
>
> Thanks and regards,
>
> Priyasha
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>
--
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Christina Bergonzo
Research Chemist
Material Data Division, MML, NIST
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Received on Thu Jun 18 2026 - 05:30:03 PDT
