AMBER: single solvated glycine simulation - zwitterion, cation, anion parameters?

From: Nicolas Lux Fawzi <>
Date: Tue, 17 Apr 2007 12:00:18 -0700

I'm trying to assist someone with a single amino acid simulation in amber. Since it is a single amino acid and there are no peptide bonds, I couldn't figure out how to find the correct amino acid types in standard amber. Are the parameters for zwitterionic glycine available somewhere? How about the anionic and cationic forms are meant to be (crude?) mimics of high and low pH conditions. Sorry if this is an obvious question. See below:

> I'm interested in simulating the following things in water:
> Zwitterionic glycine (Just the amino acid, charge 0) Anionic
> glycine (Just the amino acid, charge -1) Cationic glycine
> (Just the amino acid, charge +1)


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Received on Wed Apr 18 2007 - 06:07:38 PDT
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