You can take a look on:
Nan-Jie Deng, P.Cieplak
Molecular Dynamics and Free Energy Study of the Conformational Equilibria
in the UUUU RNA Hairpin:
J.Comput.Theor.Chem., 3, 1435-1450, 2007.
Maybe it helps a little.
Piotr
-
> On Mon, Jun 25, 2012, barb fr wrote:
>>
>> I'm trying to estimate the free energy difference associated to the
>> formation of a duplex B-DNA from the two single strand
>> oligonucleotides within the mm-PBSA approach.
>>
>> A quick search in the literature pointed out that such a method has
>> been extensively applied to dDNA-ligand system, but I could not find
>> any attempt to calculate the free energy associated to the formation
>> of the duplex from the two single strands sequence. So my first
>> question is: are there some severe limitations of these method just
>> considering one dna-strand like receptor and the other like ligand?
>
> Yes, there are some severe limiations: first, no one knows what the
> ensemble
> of conformations is that represents single-stranded DNA; second, the
> single
> strands are presumably much more flexible than are double helices, but
> there
> is no easy way to estimate the change in configurational entropy.
>
> Most angels have feared to tread here. If you hope to learn things, look
> carefully at the configurations you have that represent the single strand.
>
> ....dac
>
>
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Received on Tue Jun 26 2012 - 14:30:02 PDT
