AMBER Archive (2009)

Subject: Re: [AMBER] Problem with RNA hairpin unwinding in explicit water

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Thu Apr 23 2009 - 12:53:40 CDT

> I'm trying to simulate a hairpin structure of RNA using an NMR structure
> as a starting point (1MFY in PDB). However, the RNA unwinds from a
> helical structure into a linear base-paired one. This happens within
> several ns of simulation.
>
> I'm using Amber9 with rna.ff99. The initial structure is solvated in
> TIP3P water box, and the input files are given below.
> If you have any suggestions or experience simulating structured RNA, any
> help will be very much appreciated.

Did you add ions?

Bill

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