AMBER Archive (2004)

Subject: Re: AMBER: Molecular Frame

From: Byungchan Kim (bk385_at_columbia.edu)
Date: Sat Jan 03 2004 - 13:00:20 CST

On Fri, 2 Jan 2004, Bill Ross wrote:

> > I want to calculate order parameter (S2) of backbone N-H.
> > To calculate rotation correlation function of N-H bond vector,
> > I need to calculate the bond vector respect to molecular frame.
> > Is there any pre-set way or program to do this easily?
>
> If you want to measure the angle of the bond vector with some
> vector derived from the overall molecule, you will need to
> define the latter vector. One possibility might be the line
> drawn between centers of mass of two groups of atoms. Another
> possibility might be to use the vector N-{molecule center of mass}
> as the measurement vector. These two could be done with carnal
> and possibly ptraj. Or you could take the angle of N-H with
> respect to the principle axis of the molecule, which might
> require some programming to accomplish. I am not familiar
> with the mathematical definition of "molecular frame", so
> am just throwing out some ideas.
>
> In any case, it sounds like you are interested in per-snapshot
> 'internal' measurements, so superimposing snapshots may not be
> relevant except to perform an approximate measurement whereby
> the N-H vector of the positioned molecule could be used for
> further calculations.
>

Actually, my favorate is to use principal axis of a molecule as the
molecular frame. If the molecule is rigid, I would not hesitate to use
the principal axis. But if the molecule is flexible during the simulation,
principal axis would also change and that is I am wondering if I can use
principal axis.

> Bill Ross
>
>
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Thank You So Much
Byungchan Kim

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