On Tue, Sep 27, 2011, Niel Henriksen wrote:
>
> My experience with RNA simulations using GB would support the
> "GB will be terrible for highly polar systems such as DNA / RNA"
> statement.
I think there is "glass half empty/half full" thing going on here. RNA and
DNA double helices should be stable with igb=1, but they won't be as correclty
formed in their details as with explicit solvent. In addition to the recent
DNA paper that Thomas Gaillard mentioned, you might want to look at our
recent experience with RNA helices:
%A B.S. Tolbert
%A Y. Miyazaki
%A S. Barton
%A B. Kinde
%A P. Starck
%A R. Singh
%A A. Bax
%A D.A. Case
%A M.F. Summers
%T Major groove width variations in RNA structures determined by NMR and
impact of C-13 residual chemical shift anisotropy and H-1-C-13 residual
dipolar coupling on refinement
%J J. Biomol. NMR
%V 47
%P 205-219
%D 2010
"Details" (tm) like groove widths and base-pair tilt are suspect, but the
larger-scale behavior of double-helices looks quite reasonable, as, e.g. in:
%A Y. Bomble
%A D.A. Case
%T Multiscale modeling of nucleic acids: Insights into DNA flexibility
%J Biopolymers
%V 89
%P 722-731
%D 2008
But nucleic acids (in my limited experience) are on the edge of stability
with GB, and sometimes fall apart if you look at them cross-eyed. The
original post seemed(?) to involve having two separate helices with
co-axial stacking, and it was this feature that seemed to go away during
the simulation. I'm not too surpised at this, and it may well represent a
place where the improved description of hydrophobic interactions available
with explicit solvent might be a real help. It's hard to say much more
without having more information, and it is of course possible that
something is odd/wrong about the initial structure.
...hope this helps...dac
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Received on Tue Sep 27 2011 - 13:00:03 PDT
