Re: [AMBER] NAB possibility for automatic creation of initial configurations of unusual DNA/RNA "duplexes" ?

From: David A Case <>
Date: Fri, 2 Dec 2011 07:59:32 -0500

On Thu, Dec 01, 2011, Marek Maly wrote:
> Let say that I would like to study stability of 5’-GCTCCCGGGCTCGACC-3’
> eventual dimers.
> But what I was looking for it was some NAB function to which I could
> provide some initial double strand sequence (as in #1) no matter how
> "exotic" one and this function just generate the "optimal" initial
> configuration of ds molecule in the sense mentioned above (first
> paragraph of #2) + eventually some small initial energy minimization/MD.

The wc_helix() routine is extensively documented in the Users' Manual. It
would need to be extended for "exotic" structures like you are describing, but
it sounds like that should be possible once you understand in detail what the
routine is doing.


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Received on Fri Dec 02 2011 - 05:00:03 PST
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