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

From: Marek Maly <marek.maly.ujep.cz>
Date: Thu, 01 Dec 2011 11:53:53 +0100

Hello all,
I have just question regarding study of eventual ssDNA dimerization.

Let say that I would like to study stability of 5’-GCTCCCGGGCTCGACC-3’
eventual dimers.

One of the strategy might be in my opinion like this:

estimate the most favourable overlap here for example like this:


Create the 5’-GCTCCCGGGCTCGACC-3’ 3D model and then to try
prepare the optimal initial dimer configuration which here means
to satisfy Watson/Crick base pairing between complementary residue pairs
(C-G, A-T) and at least to remove the eventual atom overlaps regarding the
rest non-complementary residues.

I prepared this structure by hand (in UCSF Chimera ) using NAB just to
generate initial 5’-GCTCCCGGGCTCGACC-3’ ssDNA
 from dsDNA, however I had to do really deep minimization (+ very small dt
steps in consequent sveral MD stages)
  at the start of simulation as my input structure was not really the
"optimal" one.

After the breef check of NAB description I am almost sure that it should
be possible to
use it for this task to automate the whole procedure and provide much
better input structure. I also
see several useful functions for this task like wc_basepair() etc.

But what I was looking for it was some NAB function to which I could
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.

I breefly checked the NAB description and found there several useful
functions like wc_basepair() etc. but
it seems to me, that I have to create my own NAB program where I will use
several relevant functions to accomplish
my task, but I did not find any simple function like for example bdna() to
which I simply provide input sequence
and it generates relevant 3D structure of dsDNA, but maybe I just
overlooked it ...

Any relevant comments welcomed !

      Best wishes,


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Received on Thu Dec 01 2011 - 03:00:03 PST
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