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

From: Bill Ross <ross.cgl.ucsf.edu>
Date: Thu, 23 Apr 2009 18:53:40 +0100

> 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

_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed May 20 2009 - 12:24:22 PDT
Custom Search