AMBER Archive (2005)

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

From: David A. Case (case_at_scripps.edu)
Date: Tue Apr 05 2005 - 01:31:35 CDT


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

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu