Re: [AMBER] RMS fit

From: Jason Swails <>
Date: Tue, 14 Aug 2012 13:29:29 -0400

On Tue, Aug 14, 2012 at 1:06 PM, Eliac Brown <> wrote:

> Dear Daniel
> Your answer is really helpful, thanks for that.
> So, does it mean it is wrong to calculate the RMSF without prior RMS
> fitting step? in other words, are the calculated RMSF data without prior
> RMS fitting meaningless values?

Without RMS fitting prior to running the atomicfluct calculation, all of
the atomic fluctuations contain effects not only from the inherent
flexibility of the protein at that location, but also the effects of
whatever rotational motion the system displays (since the translational
effects were removed by the centering).

I can't think of many analyses where the RMSF of the un-fitted trajectory
would be any more interesting than the RMSF of the fitted trajectory, but
it's important to base your approach on the actual question you're trying
to answer.

> I think in my case the two RMSF data (with and without RMS fitting) are
> taken nearly the same curves with a difference in the corresponding values
> (around 15 A without fitting and around 1 A with fitting).

This is not entirely surprising to me. A rigid-body rotation will have the
same effect on all residues equidistant from the center. For a spherical
protein, I wouldn't expect the interior residues to show as much RMSF as
surface residues due to rotation, simply because rotation doesn't move them
as far laterally. The rotation present in un-fitted snapshots will have a
similar effect on every residue, such that the original trend may still be
visible above the noise.

Hopefully that last part made sense...

All the best,

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
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Received on Tue Aug 14 2012 - 10:30:04 PDT
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