> 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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Received on Tue Jun 15 2004 - 22:53:01 PDT
