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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--
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Joseph Nachman Department of Biochemistry
nachman.hera.med.utoronto.ca University of Toronto
Medical Sciences Building
tel: +1 416 978-5510 Toronto, Ontario M5S 1A8
fax: +1 416 978-8548 Canada
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