AMBER: During the Sander process, does the pH of the solution change orr not

From: Fenghui Fan <>
Date: Mon, 3 Dec 2007 17:58:44 -0800 (PST)

Dear all,

In order to do a MD by Sander, we need to neutralize the solution by Na+ or Cl-. But during the MD process, the exposure extent or the ionization content of the charged residues can change due to conformational change, and this should change the pH of the protein water solution, as there is H+ couple and decouple to the charged residue. However the AMBER does not consider the pH change. My understanding of the Amber MD is that we can say the protein-water solution change continuously on the pH value, do you agree on that? What will be the pH of the water-protein solution?

I am looking forward to getting a message from you.

Best regards.

Fenghui Fan

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Received on Wed Dec 05 2007 - 06:07:23 PST
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