RE: AMBER: rmsd over residues using ptraj

From: Ty Curtis <>
Date: Wed, 19 May 2004 10:23:50 -0600
>   Is there any way to get RMSD over each residues using ptraj after a MD
I suppose you could do it for each residue, one at a time. You can specify the part of the molecule in the mask. For example, you could do something like this:
trajin production.1.mdcrd
trajin production.2.mdcrd
reference average.inpcrd
rms reference mass out rmsdFromAverageResidue1.txt :1 nofit
rms reference mass out rmsdFromAverageResidue2.txt :2 nofit
rms reference mass out rmsdFromAverageResidues3-8.txt :3-8 nofit
Hope this helps!

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