Amber uses different force field parameters for different amino acids, so
if the sequence changes then the interaction does too. If you mean
something more complex, then you need to clarify the question.
On Oct 12, 2012 11:28 PM, "Acoot Brett" <acootbrett.yahoo.com> wrote:
> Dear All,
>
> A protein contain 2 chains. Chain A is ----FKY-----, Chain B is
> -----E----. Chain A and B are binding by the salt affinity between K in
> chain A and E in chain B.
>
> Another protein is the mutation form of the first protein. Chain A is
> ----AKA-----, Chain B is -----E----. A and E still forms salt bridge.
>
> As I know, AMBER has the same force field (can we regard it as homogeneous
> force field?) for the first protein and the second protein.
>
> But there is another explanation, even maybe from the text book. It says
> for the first protein, the F and Y hydrophobic environment makes the
> binding affinity between K in Chain A and E in chain B much higher. I think
> this explanation contradicts the homogeneous force field for the 2 proteins
> used by AMBER.
>
> What is your explanation?
>
> I am looking forward to getting your reply.
>
> Cheers,
>
> Acoot
>
>
>
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Received on Sat Oct 13 2012 - 06:30:03 PDT
