AMBER Archive (2007)

Subject: Re: AMBER: Can I measure improper torsion by ptarj?

From: Chengwen Chen (chenchengwen_at_gmail.com)
Date: Mon Mar 12 2007 - 22:18:24 CST


In fact, I would like to know the angle formed by J atom and the plane
K-I-L

                               J
                                |
                                K
                               / \
                              I L

On 3/13/07, David A. Case <case_at_scripps.edu> wrote:
>
> On Tue, Mar 13, 2007, Chengwen Chen wrote:
> >
> > I would like to get a improper torsion angle of a md trajactory. But it
> > seems that ptraj only provide measuring torstion angle, right? How can I
> get
> > the improper torsion angle with ptraj, or any other method? Thank you .
>
> I don't think ptraj knows if a torsion is "proper" or "improper". Have
> you
> tried any experiments to see what happens if you just provide the four
> atoms
> you have in mind?
>
> ...dac
>
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