Re: [AMBER] ptraj, alignment, and rmsd

From: Carlos Simmerling <>
Date: Wed, 15 Jun 2011 16:17:06 -0400

if you don't specify a reference, then you need to tell it what
structure to use (such as the "first" keyword). For nofit, no fitting
is done at all and if a fit was never done earlier in the script, the
results can be arbitrary. When a fit is done, it is only to minimize
the rmsd for the atoms in the mask. Tom Cheatham would have to say the
specific algorithm but likely it's the standard kabsch one. you can
select mass weighting I believe, but otherwise all pairs are treated

On Wed, Jun 15, 2011 at 4:13 PM, Michael Zimmermann
<> wrote:
> 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
> important.
> 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

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Received on Wed Jun 15 2011 - 13:30:05 PDT
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