On Fri, Jul 07, 2017, Garima Singh wrote:
>
> How do I calculate binding free energy of a
> metalloprotein complex interacting with Cd ion using Amber14?
Short answer: you can't do this sort of calculation in any version of Amber.
Longer answer: If you really want to do this, start with a thorough literature
search for similar calculations. You will probably need some combination of
quantum electronic structure theory plus statistical averaging. A lot would
depend on the details of the coordination geometry around the Cd site. You
would have to invest a *lot* of time to do a good job; hence, you would want
to be sure that estimating a single number (the binding free energy) would be
worth the effort.
....dac
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Received on Fri Jul 07 2017 - 07:00:05 PDT
