AMBER: global pH variation in AMBER.

From: Osman Gani <>
Date: Tue, 8 Mar 2005 11:56:06 +0100

I seek a design of protein + ligand complex with AMBER.

I have a protein having at least 3 conserved active site residues, say X, Y and Z. Of them one residue must be negatively charged to abstarct a proton from ligand, wheras other residues may or may not be ionized in the course of reaction.

Purpose: To see which residue must be ionized to abstract proton from ligand.

Experimental results(kinetic assays):
Temperature is varied from 15 to 30 degree celsius.
pH is also varied between 6-10.

Result 1: Different kinetic constants indicates one residue(say X) is essential for abstatrcting proton but Y is also ionized for optmum orientation of ligand.

Result 2: Different dissocation constants were found for different temperature and pH.

There was no obvious conclusion to say that which residue must be ionized for proton abstarction.

AMBER design:
What I did? I manually ionized either one or combination of residues and did MD (at 300K and neutralize globally, explicit solvent), and subsequently deriving free energy for each type of protein+ ligand complex.And I could rank these ionization scenarios on delta G.

What I can't say: Which ionization scenario (as I manually prepared) corresponds to which pH. A very very obvious question haunting me for sevaral months). I went through some literatures, but they say about local and global pH variations which make little sense to me.

My question(in AMBER):
I can make temperature variations, no doubt. And I can make different ionization scenarios of these 3 residues in AMBER. But how can I correlate different ionization scenarios of these 3 residues with global(!) pH values as done in experiments?
So that, finally i can say that at specific ionization scenario (that correspponds to a specific pH) i get a specific amount of free energy.

Thanks for your patients.

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Received on Tue Mar 08 2005 - 11:53:01 PST
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