i dont really know the answer, but clearly including the chain entropy
part is going to be difficult with the methods you propose. the
unfolded state is not a single structure, which makes most pathway
calculation methods very hard to use for protein stability.
On Mon, Apr 11, 2011 at 5:12 PM, Jose Borreguero <borreguero.gmail.com> wrote:
> Dear Amber users,
>
> I want to estimate the free energy upon unfolding of the C-terminal from the
> rest of the protein. I either do a bunch of pulling simulations or do a set
> of umbrella simulations with reaction coordinate as the distance between tip
> of the C-terminal and point of contact with the protein in the native state.
> I don't know which method would be better. Any suggestions are welcomed.
>
> Jose M. Borreguero
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Received on Mon Apr 11 2011 - 14:30:05 PDT
