On Wed, Dec 07, 2022, laura zhang via AMBER wrote:
>
>lg1 has 29 atoms. But I only wanted to calculate the binding energy between
>receptor and lg2.
Do you really want this: the binding energy between (protein + lg1) and
lg2? In that case, you would define "receptor" as protein + lg1, and the
"ligand" as lg2. Atom numbers should the add up.
It's actually not clear what simulations you have actually done. If you
just have (protein + lg1 + lg2) and the two ligands, you could proceed with
the calculation outlined in the paragraph above, but you don't have enough
information (simulations) to compute the binding energy between just the
protein and lg2.
Put another way: "receptor" has to include everything except the ligand of
interest. The term "receptor" is often treated as a synonym for "protein",
but that only works if there is just a single ligand.
I hope this clarifies things, but I recognize that I may have made things
worse. If it's not clear, tell us exactly which simulations you have
carried out.
....dac
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Received on Thu Dec 08 2022 - 05:30:03 PST
