AMBER Archive (2004)

Subject: Re: AMBER: RMSD calculations in ptraj and Carnal

From: Joseph Nachman (nachman_at_hera.med.utoronto.ca)
Date: Wed Jun 16 2004 - 15:16:52 CDT

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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