Hi -
I'm sending you the inputs and theresuls of both the ptraj and Carnal
runs, as well as the RMSDscalculated by hand.
Thnaks again,
Joseph
On Tue, 15 Jun 2004, Bill Ross wrote:
> > 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.
>
> (or rotation, one would expect) - you are using the belly option
> I presume.
>
> > 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.
>
> I'd send ptraj input; maybe it was fitting?
>
> > When I
> > calculated by hand I got a figure of about 4Ang, which was more inline
> > with what I was observing visually.
>
> What did carnal give?
>
> 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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Received on Wed Jun 16 2004 - 22:53:00 PDT
