> 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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Received on Wed May 20 2009 - 12:24:22 PDT
