AMBER Archive (2006)

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

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Sat Mar 11 2006 - 12:37:16 CST

> I checked the types of these atoms. All N atoms are of nh type,
> and C1 are of c2 type. So I think they should be in a plane. But
> after minimization of the whole protein, H21 and H22 rotate along
> C1-N2 bond. I guess this should not happen.
> Can you help me to solve it?
>
> H21 H22
> \ /
> C2 N2
> \ //
> N1--C1 (+1 charge)
> / \
> C3 N3
> / \
> H31 H32

An improper around N2 would keep C1/N2/H21/H22 planar, which
doesn't prevent rotation of the NH2 group around the C1-N2 bond.
That rotation would be controlled by the torsion parameters like
H21-N2-C1-N1 and H21-N2-C1-N3.

Bill
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