Re: [AMBER] Enquiring about RMSD of small and large proteins

From: Daniel Roe <>
Date: Mon, 8 Sep 2014 07:54:02 -0600


On Sun, Sep 7, 2014 at 8:52 PM, Yip Yew Mun <> wrote:
> Hi, I recently ran a simulation of a small alpha helix (~12 residues) with REMD and I did a RMSD analysis using just the backbone atoms (N,CA,C). Usually for simulations of large proteins, an RMSD of 3 Angstroms is usually enough to quantify that there are no major conformational changes. However, I realised for small protein systems like mine, an RMSD of 3 Angstroms isn’t a good criterion to say that I have folded my protein successfully. Therefore, I wish to ask:
> 1) Does the number of atoms affect the RMSD calculation?

For folded conformations not really. Average RMSD is not correlated
with chain length, although the distribution tends to get narrower for
longer chains.

> 2) Is there a need for the reference structure to be protonated before using it for RMSD analysis since in this case, I’m just using the backbone atoms (N,CA,C).

No, as long as the number of atoms and the atom ordering in your
target and reference structures are the same. Jed Pitera has recently
done some very interesting work looking at intrinsic characteristics
of RMSD distributions that I recommend checking out:

Hope this helps,


> Thanks.
> Yip Yew Mun (Mr) | PhD Research Scholar | Division of Chemistry & Biological Chemistry
> School of Physical & Mathematical Sciences | Nanyang Technological University | Singapore 639798
> Tel: (+65) 97967803 | Email: | GMT+8h
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Mon Sep 08 2014 - 07:00:06 PDT
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