Re: [AMBER] RMS fit

From: Daniel Roe <>
Date: Tue, 14 Aug 2012 11:35:30 -0600


This is covered in the 'atomicfluct' section of the manual, although
it is sort of buried near the end:

"Note that RMS fitting is not done implicitly. If you want
fluctuations without rotations or
translations (for example to the average structure), perform an RMS
fit to the average structure
(best) or the first structure (see rmsd) prior to this calculation."

On Tue, Aug 14, 2012 at 11:06 AM, Eliac Brown <> wrote:
> 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?

So, if you want to compare to B-factors you should RMS fit to an
average structure prior to 'atomicfluct'.


Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Tue Aug 14 2012 - 11:00:03 PDT
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