AMBER Archive (2006)

Subject: Re: AMBER: Charge fitting in Amber

From: FyD (fyd_at_u-picardie.fr)
Date: Wed Nov 29 2006 - 01:16:38 CST

Quoting Changge Ji <jcg_at_itcc.nju.edu.cn>:

> In 2003 amber force field (Duan et al) , during the fitting
> procedure, "charge of each amino acid was represented by a
> dipeptide fragment consisting of the amino acid residue and the
> terminal groups (Ace- and -Nme)". And charge of each atom in molecue
> (Ace- and -Nme) was fitted using RESP method .
>
> What technique was used to guarantee total charge for each amino
> acid residue was 0 ,-1 or +1.

Intra- and inter-molecular charge constraints used during the RESP or
ESP fit allows to set 0 ,-1 or +1 charge values in molecule fragments.

You are going to find many examples of charge derivation for
(+)NH3-terminal, (-)OOC-terminal, and central fragments of aminoacids
in R.E.DD.B.: projects F-1 up to F-44

You will also find examples of charge derivation for Duan et al FF :
projects F-65 up to F-70. See for instance
http://www.u-picardie.fr/labo/lbpd/REDDB/up/F-70/

regards, Francois

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