AMBER Archive (2006)

Subject: Re: AMBER: force fiels for a-rna

From: Carlos Simmerling (
Date: Fri Oct 13 2006 - 17:41:21 CDT

you need to tell us more about your simulations that
distorted the RNA and what kind of distortions you saw.
What water model were you using? How did you do
the equilibration?
Also, have you worked through the DNA tutorial on the
Amber web page?

asli ertekin wrote:

> Hi,
> I am working on a ds-rna structure which exhibits a-type double helix
> conformation. I have been using ff99 force field parameters but in
> every scenerio i tried the double helix conformation was distorted a lot.
> For my system (in which the ds-rna interacts with a protein) which
> force field i should use? If there are not any better force fields how
> can i restrain the conformation of the rna double helix?
> Thanks,
> Asli

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