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

From: Marek Maly <>
Date: Fri, 02 Dec 2011 14:36:11 +0100

Dear prof. Case, thanks for your answer !

I am also almost sure that there is enough particular functions working
on individual residues/atoms from which the proper NAB program
might be composed to do the task which I described sooner.

I was just curious if such comfortable and complex NAB program/function
was not
already composed to save lot of time to anyone who would like to simulate
a bit
unusual RNA/DNA or some hybrid molecule. That.s all.

   Best wishes,


Dne Fri, 02 Dec 2011 13:59:32 +0100 David A Case
<> napsal/-a:

> 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.
> ...dac
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