Re: [AMBER] cpptraj RMS calculations appear to be incorrect

From: Carlos Simmerling <>
Date: Mon, 2 Dec 2019 13:18:09 -0500

try adding "nofit" to the end of the helix# lines. RMSD values are very
sensitive to what you use for the best-fit. if your helix1 rmsd is low that
means that internally it is not that flexible, but visually you may see it
undocking. that would be removed if you best-fit to helix1 before the rmsd
calculation. if you best-fit to you "Helices" part, and nofit to helix 1,
you'll overlap all 3 then see how much helix1 moved.

On Mon, Dec 2, 2019 at 12:03 PM Bellesis, Andrew G <> wrote:

> Dear all,
> I am trying to calculate the RMSD of subsets of residues within a protein
> during the course of a trajectory. However, I am obtaining results that
> appear to be contradictory to visual inspection of the trajectory. My
> protein is a 3-helix bundle. Helix 1 is very mobile while helices 2 and 3
> are very rigid. However, when I calculate RMSD of all 3 helices together, I
> get significantly higher numbers compared to when I calculate the RMSD of
> helix 1 by itself. In short, why does a calculation that includes rigid
> parts of a protein have a higher RMSD than a known mobile region
> calctulated by itself?
> Here is the input that I am using:
> parm topology.prmtop
> trajin
> reference equlibrated_struct.pdb
> rms RMS_Helices (:6-17,24-36,41-54)&(.CA,C,O,N,H) reference out
> RMS_Helices.dat mass
> rms RMS_Helix1 (:6-17)&(.CA,C,O,N,H) reference out RMS_Helix1.dat mass
> rms RMS_Helix2 (:24-36)&(.CA,C,O,N,H) reference out RMS_Helix2.dat mass
> rms RMS_Helix3 (:41-54)&(.CA,C,O,N,H) reference out RMS_Helix3.dat mass
> Where do you think the unexpected behavior is coming from?
> Best,
> Andrew Bellesis
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Received on Mon Dec 02 2019 - 10:30:02 PST
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