On Mon, Apr 03, 2017, Mary Varughese wrote:
>
> Could i use mmpbsa stability calculation to assess the stability of a
> DNA and a modified DNA structure? If i got PBtotal of DNA as 4561.23
> and that of (corresponding) modified DNA as -6297.18, could i
> interpret the modified DNA structure is more stable?
No. First, you cannot directly compare the energies of structures with
different numbers of atoms. (I'm reading your term "modified DNA" as
meaning some chemical modification.) For chemical modifications, you
always will need to construct some sort of thermodynamic cycle to generate
a consistent interpretation.
Second, if you have two numbers that differ by 10,000 kcal/mol (!) it is far
more likely that there is something wrong someplace, than it is that this
represents any true estimate of a difference in stability.
...good luck...dac
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Received on Mon Apr 03 2017 - 05:30:02 PDT
