AMBER Archive (2006)

Subject: AMBER: How to built the deprotonated form of lysine and tyrosine

From: jitrayut jitonnom (jitrayut.018_at_gmail.com)
Date: Wed May 24 2006 - 21:49:04 CDT

---------- Forwarded message ----------
From: Amber admin <amber-admin_at_scripps.edu>
Date: 25 ¾.¤. 2006, 3:44 ¹.
Subject: Re: BOUNCE amber_at_scripps.edu: Non-member submission from
["jitrayut jitonnom" <jitrayut.018_at_gmail.com>]
To: jitrayut.018_at_gmail.com

On Wed, May 24, 2006, owner-amber_at_scripps.edu wrote:

> Date: Wed, 24 May 2006 18:16:58 +0700
> From: "jitrayut jitonnom" <jitrayut.018_at_gmail.com>
> To: amber_at_scripps.edu
> Subject: How to build the structure of Lysine and Tyrosine in deprotonated
form
>
> Dear amber staff
> I was wondering that what is the model of deprotonated form of tyrosine
and
> lysine. Because when I use the database library of amino acid in
HyperChem,
> I see the NH-C(R)-CO which should be NH3-C(R)-COOH instead. So,which form
=
> I
> should be selected for the deprotonated form or the correct deprotonated
> form. Since I want to create the prepin file for deprotonated tyrosine and
> lysine in leap.
> To check my idea, Is it right that the NH3(+) should be changed to NH2 in
> the deprotonated form and also COO- including the side chain ,in case of
> lysine ? If I think wrong please tell me and tell the right ?
>

> Thanks
>
> Mr. Jitrayut Jitonnom
> Chiang Mai University
> Thailand
> 50200
>
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