Re: Namd with Amber ff for RNA minimization

From: Irina Tuszynska (
Date: Tue Nov 23 2010 - 09:37:59 CST

Hmm, you and Jerome are absolutely right. It could be an effect of the
huge negative charge of RNA in vacuo and perhaps addition of counterions
and water will stabilise the structure.
I actually wanted optimize conformation of RNA model, which I obtained
by another program.
Thank you for help.

Hannes Loeffler wrote:
> I think the real question is why you want to minimise a highly charged
> biomolecule in vacuo and expect it to keep a particular shape. I
> highly doubt that the AMBER force field for nucleotides has been
> parameterised for that purpose. What is the structure of RNA in vacuo,
> anyway? Your result has probably no real physical meaning (and Jérôme
> has hinted to that already).
> Cheers,
> Hannes.

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