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?
Best,
Andrew Bellesis
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Dec 02 2019 - 09:30:02 PST
