AMBER Archive (2006)

Subject: Re: AMBER: double stranded polyribocytidylic acid

From: Jiri Sponer (
Date: Wed Feb 15 2006 - 07:16:46 CST

Hi Bill,
in this case she likely attempts to simulate a nonexisting
molecule. The difraction experiment on polyC is old, not much data, and
oligoC in recent experiments form selfintercalated tetraplexes,
not duplexes,
no duplex has ever been seen at atomic resolution.


> > I'm trying to perform the simulation of double stranded
> > polyribocytidylic acid but I haven't succeded yet.
> > I start with the structure built according to the Langridge and Rich
> > data(Nature,1963): helical rise=3.11 A, helical twist=30 degrees, parralel
> > strands, each strand consisting of alternating cytosine, protonated
> > cytosine residues, so that each pair of the double helix contains one
> > protonated cytosine. But even during the minimization my structure
> > distorts greatly: bases in pairs become nonplanar and the whole
> > structure looks rather like two single-stranded helices twisted one on
> > the another, than a double stranded helix. The more steps of the
> > minimization I perform, the more distorted structure I obtain.
> Small, relatively inconsequential errors in the starting structure
> can induce such problems. Energy minimization is not the best
> procedure for fixing the model - better would be to use positional
> restraints on the bases and run dynamics in vacuum, e.g. at 10-100K.
> (Because of the classic local minimum problem.)
> It is quite impressive to see a nucleic acid backbone equilibrate
> under such conditions. After this procedure, solvate, minimize
> 100-500 steps, and continue with careful equilibration of volume
> and temperature.
> Bill
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