AMBER Archive (2004)

Subject: Re[2]: AMBER: rmsd over residues using ptraj

From: Qiang Lu (qiangl_at_uci.edu)
Date: Wed May 19 2004 - 12:19:38 CDT

Hi Ty,

    That will align the proteins only based on the marked residue
but not the whole protein. That will cause error. 

-- 
Best regards,
 Qiang Lu
=================Original message text===============
> 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

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