Re: [AMBER] RMS fit

From: Eliac Brown <>
Date: Tue, 14 Aug 2012 10:06:03 -0700 (PDT)

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?
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).
Any comment would be highly appreciated

----- Original Message -----
From: Daniel Roe <>
To: Eliac Brown <>; AMBER Mailing List <>
Sent: Tuesday, August 14, 2012 4:04 PM
Subject: Re: [AMBER] RMS fit


The RMS command by default performs a best-fit rotation on coordinates
(unless 'nofit' is specified) in addition to centering, while the
center command performs centering only. So in the second command the
coordinates are being rotated to minimize the RMSD to the coordinates
in the first frame, so you are in essence performing 'atomicfluct' on
different coordinates than in the first case, which is why you get
different answers.

Hope this helped,


On Tue, Aug 14, 2012 at 8:45 AM, Eliac Brown <> wrote:
> Dear All
> I was wondering what is the difference between the RMS fitting and the usual fitting command of (center :X-XX mass origin).
> The Center command beside it reallocates the atoms into the origin of the box, it does also perform RMS fit (see page 112 AMBERTOOLS 1.4 manual).
> So, why I got different answers when I calculated the RMSF per residue with the following jobs:
> Job I
> trajin 1ns.mdcrd
> atomicfluct out RMSF :1-100 byres
> Job II
> trajin 1ns.mdcrd
> rms first  :1-100
> atomicfluct out RMSF :1-100 byres
> Note that the 1ns.mdcrd is already centers in both cases using
> center :1-100 mass origin
> image origin center
> Any kind of explanation would be highly appreciated
> Cheers
> _______________________________________________
> AMBER mailing list

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 - 10:30:02 PDT
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