AMBER Archive (2009)

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

From: Sasha Buzko (
Date: Thu Apr 23 2009 - 12:55:58 CDT

Hi Bill,
I haven't and will do it today, following the recommendations of the
list members.



Bill Ross wrote:
>> 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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