[gmx-users] strange RMSD output
mailmd2011 at gmail.com
Sun Oct 28 17:55:22 CET 2012
I've got several individual .pdb file and I use the following command to merge it input .xtc and calculate the rmsd by g_rms:
trjcat -cat -keeplast -f *.pdb -o out.xtc
g_rms -f out.xtc -s 001.pdb -o rmsd.xvg
However, I find a problem with the results. Since most part of each PDB
file overlapped very well only a small loop is different. I first
calculate the rmsd of backbone and got:
@ subtitle "Backbone after lsq fit to Backbone"
Then I calculate the loop region and got:
@ subtitle "Backbone_&_r_120-131 after lsq fit to Backbone"
As we can see, the rmsd of loop region is smaller than the backbone
which I think it should be reversed.......
thank you very much.
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