From: Alexei Rossokhin (alrossokhin_at_yahoo.com)
Date: Thu Nov 25 2021 - 02:15:39 CST
Dear NAMD users, While browsing the NAMD tutorial I found the residue_rmsd.tcl script to calculate RMSD for individual residues. When I tried to run it, the results puzzled me a little.
When I used the selection "protein and chain A and resid 174 and name CA and noh" for my MD calculations I got the following result
RMSD of residue 174 is 1.3978458595465855
Average rmsd per residue: 1.3978458595465855
When I used the selection "protein and chain A and resid 174 and name CA CB CG CD and noh" I got the following result
RMSD of residue 174 is 5.591383438186342
RMSD of residue 174 is 0.022276428040583034
RMSD of residue 174 is 8.875070932503201e-5
RMSD of residue 174 is 3.535884833666614e-7
Average rmsd per residue: 1.4034372426311832
Using "protein and chain A and resid 174 and name CB and noh" I got
RMSD of residue 174 is 1.3978458595465855
Average rmsd per residue: 1.3978458595465855
If to run the script separately for CA or CB result is the same. If to run the script with the selection "name CA CB CG CD", the result for individual atoms is strange, although the average is close in all cases.
What does it mean, any bug in the script?Thank you for help.
Alexey
PS I attached the residue_rmsd.tcl script.
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