AMBER Archive (2008)

Subject: AMBER: how to calculate the interaction energy

From: Wang,Ying (
Date: Tue Jun 10 2008 - 09:52:10 CDT

Hi, dear all,

I'm trying to calculate the interaction energy of a small organic
molecule bind to a big protein. I saw there is a equation in the
literature: Einter=Ecom-Eprotein-Eligand, in which Einter is the
interaction energy, Ecom is the energy of the whole system after
they bind together, Eprotein and Eligand are the energy of the
isolated protein and the small molecule.
My question is, if anybody know the procedure to get the
interaction energy? My understanding is that I put these two
molecules together with a suitable distance then let them move to
close to each other then I can get the energy of every step. and
then I delete one of the molecule from the whole system and
perform the same MD on this molecule then I can get the energy of
these two molecules individually in every md step then I can minus
them from the energy of the whole system to get the interaction
energy. But I use the explicit water, like tip3p water box, so the
energy contain the water contribution. How can I deal with it?
Could anybody tell me how to do that? Or I should perform this in
vacuum or implicit solvent?

Thanks a lot in advance!


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