Hi Priyasha,
Yes, it’s probably your modified parameters. Without knowing your modification, it’s hard to know what you did that may be causing problems. How did you treat charges? How did you place your modification (your starting structure)? Do you have steric clashes? When you visualize the simulation from the beginning, through all the relaxation steps, what is happening?
Maria
> On 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jun 18 2026 - 05:00:02 PDT
