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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Received on Thu Jun 18 2026 - 01:00:02 PDT
