AMBER Archive (2004)

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

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Wed May 19 2004 - 13:34:08 CDT

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

The carnal version allows simply "rmsid%residues" to get the
per-residue rms in a table, where the protein can be positioned
to fit to any subset of atoms in the reference frame including
(default) all atoms.

Bill
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