On Mon, Apr 04, 2005, Kateryna Miroshnychenko wrote:
>
> I've modelled single-stranded poly(rC) with explicit water and
> counterions starting from its helical conformation. But after 2.1 ns
> production simulation my poly(rC) seems to be gone quite far from its
> initial helical conformation (first snapshot). Backbone RMSD is
> around 3 A (see attachment)).
A 3 Ang. rms deviation is really pretty small, especially for a
single-stranded piece of RNA. My understanding of the general feeling of the
community is that single-stranded RNA has a significant helical tendency (it
is very far from "random coil") but that it certainly should not be expected
to look like a duplex with the second strand just removed. So, what you
describe is about what I would have expected to see.
....hope this helps...dac
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Received on Tue Apr 05 2005 - 07:53:01 PDT
