AMBER Archive (2006)

Subject: Re: Re: AMBER: bond parameters for positively charged guanidine group

From: FyD (fyd_at_u-picardie.fr)
Date: Thu Mar 09 2006 - 02:22:05 CST

Quoting Ye Mei <ymei_at_itcc.nju.edu.cn>:

> Thank you very much for your reply. Maybe I have not made myself clear.
> H21 H22
> \ /
> N2
> //
> -N1--C1 (+1 charge)
> | \
> H1 N3
> / \
> H31 H32

Why don't you look at the ARG residue available in the AMBER FF topology DB ?

Here are the imporper taken from /usr/local/amber8/dat/leap/prep/all_amino94.in
used for ARG
IMPROPER
 -M CA N H
 CA +M C O
 NE NH1 CZ NH2
 CD CZ NE HE
 CZ HH11 NH1 HH12
 CZ HH21 NH2 HH22

regards, Francois

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