AMBER Archive (2004)

Subject: RE: AMBER: rmsd over residues using ptraj

From: Ty Curtis (tcrex2000_at_hotmail.com)
Date: Wed May 19 2004 - 11:23:50 CDT

>   Is there any way to get RMSD over each residues using ptraj after a MD
>simulation?
 
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!
 
-Ty

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