On Tue, Feb 17, 2015, Kornelius Zeth wrote:
>
> I have a short question regarding AMBER or any equivalent program: Does the
> program allow to calculate the free energy of ion binding (e.g. iron, zinc,
> manganese) to specific binding sites on protein surfaces and if so would it
> be possible to distinguish energies of e.g. Fe(II) and Fe(III) binding
> events??
There is no simple answer here. If you have no "inner-sphere" contacts
between the iron ions and the protein (i.e. the irons always have a full first
coordiantion shell of waters), then you probably use the non-bonded models
in Amber to get a rough idea of preferences for +2 vs +3 ions. (Even then,
getting a free energy of binding is a somewhat advanced topic.)
If there are inner-sphere contacts between iron and protein atoms, there will
likely be a fair amount of covalency in the interactions, and you would be
unlikely to get reliable results from the simple molecular mechanics force
fields we use.
Perhaps others on the list have better suggestions. As usual, try to find
papers where similar calculations have been carried out.
....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Feb 18 2015 - 08:00:10 PST
