[AMBER] cpptraj RMS calculations appear to be incorrect

From: Bellesis, Andrew G <AGB53.pitt.edu>
Date: Mon, 2 Dec 2019 17:02:50 +0000

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 trajectory.nc
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?

Andrew Bellesis
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Received on Mon Dec 02 2019 - 09:30:02 PST
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