AMBER: Is MM-PBSA doable for transition metals ?

From: Cenk Andac <>
Date: Mon, 24 Oct 2005 09:55:27 -0700 (PDT)

Dear Amber community,

I have been currently working on binding energetics of
copper ions in complex with a protein using the
following simple equation

Delta G (binding) = Abs G (complex) - Abs G
(protein/receptor) - Abs G copper (ion/ligand).

I have done several explicit solvent simulations for
the receptor and computed its Abs G in MM-PBSA. I am
about to carry out the same procedure for the complex
as well.

My question here is about the copper ion.
How do I get an Abs G value for the copper ion?
Is it obtained from empirical literature values or is
it just that I run another explicit solvent simulation
for the copper ion alone and compute its energy in
MM-PBSA? Is the letter case doable in AMBER 8?




Cenk Andac, M.S., Ph.D. Dissertator
at the University of Wisconsin-Madison
Currently a faculty candidate in Turkey
Guleryuz cad. 37/15, Ankara, Turkey

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Received on Mon Oct 24 2005 - 18:53:00 PDT
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