AMBER Archive (2006)

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

From: Ye Mei (ymei_at_itcc.nju.edu.cn)
Date: Thu Mar 09 2006 - 02:40:14 CST

Dear Francois,

Thank you very much for your reply.
I ever thought about add these improper torsions, but I am not sure whether this is enough to keep them in a plane, at least not far from a plane.
I will have a try.

Ye

======= 2006-03-09 16:22:05 FyD wrote=======

>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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