AMBER Archive (2006)

Subject: AMBER: force fiels for a-rna

From: asli ertekin (asliertekin_at_gmail.com)
Date: Fri Oct 13 2006 - 17:28:58 CDT

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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