AMBER Archive (2006)

Subject: Re: AMBER: double stranded polyribocytidylic acid

From: Bill Ross (
Date: Tue Feb 14 2006 - 14:35:19 CST

> 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.


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