Re: AMBER: RMSD calculations in ptraj and Carnal

From: Joseph Nachman <nachman.hera.med.utoronto.ca>
Date: Tue, 15 Jun 2004 15:37:18 -0400 (EDT)

The trajectories are fitted, beafuase I keep the protein and part pof the
peptide fixed - basically 90% of the structure - so there is no CM
displacement. And sicne I'm looking at CAs, the mass weighting shouldn't
matter.

The way I discovered something was fishy was that I looked at a structure
in which all but one CA were 2Ang and more away from the reference
structure (up to 7Ang), yet ptraj listed an rmsd of less than 1Ang. When I
calculated by hand I got a figure of about 4Ang, which was more inline
with what I was observing visually.

Joseph


 On Tue, 15 Jun 2004, Bill Ross wrote:

> > whether RMSD means the same thing in ptraj and Carnal.
>
> Carnal does mass-weighted RMS and ptraj didn't, but ptraj
> may have this facility now, and anyway it shouldn't matter
> if all the atoms being compared are carbons.
>
> Are you fitting in all 3 cases? As a further test you could
> produce a fitted trajectory by one method, and then measure
> RMS by ptraj, carnal, and manually.
>
>
> Bill
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Joseph Nachman				Department of Biochemistry
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Received on Tue Jun 15 2004 - 21:53:01 PDT
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