[AMBER] ptraj, alignment, and rmsd

From: Michael Zimmermann <michaelz.iastate.edu>
Date: Wed, 15 Jun 2011 15:13:35 -0500

Dear AMBER users,

I have a ptraj question that is not detailed in the users guide. the rms
routine in ptraj has an input option "nofit" which suppresses fitting, but
when rms does perform fitting, what algorithm is used? Does it minimize
total RMSD relative to the reference frame, global RMSD to the reference
frame for only the mask, or something else? There are many alignment
protocols that exist, many of which refine the fit by ignoring poorly
aligned pairs in the selection. So, knowing what method ptraj is using and
which atoms are being aligned for each frame (all or just the mask) is

This question assumes there have been no "reference" calls, as the users
guide details that the rmsd is then to the tagged atoms in the reference
structure. However, it is still good to know the precise algorithm used when
a reference state is used.

Thank you,

Michael Zimmermann
Ph.D. student in Bioinformatics and Computational Biology
Department of Biochemistry, Biophysics and Molecular Biology
Iowa State University
AMBER mailing list
Received on Wed Jun 15 2011 - 13:30:03 PDT
Custom Search