AMBER Archive (2007)

Subject: AMBER: single solvated glycine simulation - zwitterion, cation, anion parameters? 2nd try

From: Nicolas Lux Fawzi (fawzin_at_berkeley.edu)
Date: Tue Apr 17 2007 - 16:50:07 CDT

I sent this a few hours ago, but it doesn't seem to have gone through --
apologies if you are receiving this twice.
_________

Hi 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)

Thanks
-Nick
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