AMBER Archive (2009)

Subject: Re: [AMBER] Custom RNA modeling

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Mon Dec 14 2009 - 15:55:20 CST

Amber is not the right tool for RNA 3D structure prediction from sequence.
perhaps in the future.
I think the best approach for you to take is to find articles in the
literature that were successful at what you want to do and see what methods
they used, and perhaps use those in putting together some documents on the
protocols.
carlos

On Mon, Dec 14, 2009 at 4:49 PM, Wallace Kunin <kunin_at_marshall.edu> wrote:

> What we are trying to do is to input a nucleotide sequence and predict the
> 3D RNA structure for it. Since it is not an exact science, we want to
> compare the results from different programs. So, for example, we would get
> a prediction from both AMBER and MCSYM and compare the results. After
> that,
> we would like to do MD simulations on that RNA structure. Hopefully, that
> helps in describing what I am looking for.
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