AMBER Archive (2006)

Subject: Fwd: AMBER: How to build N-terminal of alanine : NH2

From: jitrayut jitonnom (jitrayut.018_at_gmail.com)
Date: Thu Jun 08 2006 - 07:32:22 CDT


Dear FYD

Thank for your advise but I am new for R.E.DD.B so please give me an idea to
do. Now I already download file (F-40). By the way, I want to do leap with
the N-terminal (neutral fragment :F-40) so what I should do next ?

,Thank

Jitrayut Jitonnom, PhD
Computational Simulation,
and Modeling Laboratory (CSML),
Chiang Mai University, Thailand.
Email: jitrayut.018_at_gmail.com <shafinaz_at_bri.nrc.ca>
Tel: 66 6 613 4218

---------- Forwarded message ----------
From: FyD <fyd_at_u-picardie.fr>
Date: 8 .. 2006, 15:27 .
Subject: Re: AMBER: How to build N-terminal of alanine : NH2
To: amber_at_scripps.edu

Quoting jitrayut jitonnom <jitrayut.018_at_gmail.com>:

> I want to build the N-terminal of ALA that was usually generated to NALA
> when do leap but acctually I want NH2- instead of NH3- . How to do this ?
> Please suggest me.

See R.E.DD.B. Then "List projects" Then "Molecule fragment"
Select the projects as examples:

F-40 N-terminal neutral fragment of O-methyl-L-tyrosine
F-39 N-terminal neutral fragment of O-methyl-L-tyrosine
F-38 N-terminal neutral fragment of O-methyl-L-tyrosine
F-37 N-terminal neutral fragment of O-methyl-L-tyrosine

Or

F-18 N-terminal neutral fragment of alpha-aminoisobutyric acid
F-17 N-terminal neutral fragment of alpha-aminoisobutyric acid
F-16 N-terminal neutral fragment of alpha-aminoisobutyric acid
F-15 N-terminal neutral fragment of alpha-aminoisobutyric acid

regards, Francois

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