AMBER Archive (2004)

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

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Tue Jun 15 2004 - 15:55:31 CDT

> 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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