AMBER Archive (2005)

Subject: AMBER: Re:Re:single-stranded poly(rC) simulation

From: Kateryna Miroshnychenko (kateryna_mirosh_at_ire.kharkov.ua)
Date: Tue Apr 05 2005 - 12:37:54 CDT

Dear prof. Case,

Thank you for response. The problem is that the terminal conformation
of my polyrC doesn't look like a helix much. May be you can recommend how
to estimate the helicity of it? Is there any parameter ( or may be
set of parameters) that could distinguish between "random coil" and
distorted helical conformation?

With many thanks in advance,
 Kateryna

mailto:kateryna_mirosh_at_ire.kharkov.ua

>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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