Dear users,
I have multiple RNA helices of 36 base-pairs that i am simulating using
ff12sb(chi OL3 corrections). These structures differ in the identity of
their central two base-pairs.
My doubt is that in some sets, the terminal base-pair fraying effect is
very large, to the extent that the base-pair completely opens up and then
reforms, while in other cases this effect is not observed at all..i.e. the
pair remains quite stable.
Is this fraying quite random in nature? because i can't see how change in
the central base-pair will affect the terminal one sitting 18 base-pairs
away..
Or does it has to do with force field.Again, i am using only ff12sb for all
calculations?So it doesn't make sense..
i don't want to apply any artificial restraints at the terminals of the
helices.
Thank you
Asmita
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Received on Thu Aug 01 2013 - 23:00:02 PDT
