[AMBER] MMPBSA and explicit ions: what should I do?

From: <tommaso.casalini.mail.polimi.it>
Date: Thu, 01 Mar 2012 11:21:51 +0100

Dear Amber users and developers,
I am performing some simulations in order to compute the binding free
energy of hyaluronic acid and BMP2 protein.
I would like to use MMPBSA approach in order to obtain the desidered value.
However, in the simulation box I had to add 14 Cl- ions in order to
assure electroneutrality.
Since I have explicit ions, how can I consider them in MMPBSA?
Can I remove them and consider them in implicit way through ionic strenght?
Or maybe, can I consider them as a part or receptor or ligand?

Thank you so much for your help!

Tommaso Casalini, Ph.D. fellow
CFA lab, Politecnico di Milano

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Received on Thu Mar 01 2012 - 02:30:02 PST
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