AMBER Archive (2007)

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

From: Pradipta Bandyopadhyay (pradipta_at_iitg.ernet.in)
Date: Tue Apr 17 2007 - 23:33:52 CDT

Hi Nick,

 Not the answer to your question.

However, finding energetic differences among zwitterion, neutral, cation,
anion is non-trivial. Several years ago, we have investigated the energy
difference between Zwitterion and neutral using quantum mechanical methods
(+solvent) and found post-Hartree Fock methods are necessary (we didn't
examine DFT though). You may want to check

(1) J.Chem. Phys. 113, 1104, 2000

(2) J. Chem. Phys. 116, 5023, 2002

regards,

  Pradipta

> 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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Dr. Pradipta Bandyopadhyay
Assistant Professor
Dept. of Biotechnology
Indian Institute of Technology, Guwahati
Phone: 91-361-258-2213 (office)
e-mail: pradipta_at_iitg.ernet.in
web: http://202.141.80.5/~pradipta/Pradipta.htm

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