AMBER Archive (2006)

Subject: AMBER: double stranded polyribocytidylic acid

From: Kateryna Miroshnychenko (
Date: Tue Feb 14 2006 - 03:44:01 CST

Dear Amber users,

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.

The parial charges of protonated cytosine I've calculated using resp
methodology. I've tryed also partial charges of Dr Sponer and Dr
Spackova but the results were the same. I've used multistage
minimization with gradually removed positional restraints on the atoms
of nucleobases, but still got the distorted structure.
The test 100 ps md runs with implicit solvent starting with partially
optimized structure(where the bases in base pairs were still coplanar)
resulted also in distorted structure. When the run was carried without
restraints the edge residues were mostly distorted, when the weak
positional restraints were applied to the edge residues - the central
basepairs were mostly distorted with bases flipping out the helix.

Any suggestions on the problem would be helpful.
With many thanks in advance,

 Kateryna Miroshnychenko
post-graduate student
Department of Biological Physics,
Institute of Radiophysics and Electronics,
National Academy of Sciences of Ukraine,
12, Proskura st., Kharkiv, 61085, Ukraine

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