ptraj does this very well. use 2 rms commands,
one for the best-fit and another for the rmsd. the second should end with
"nofit"
>
> > --------------------------------------------
> > Unfortunately, this does not work. I am trying to analyze a targetted MD
> > simulation, and wondering if it is possible in ptraj to (1) first
> > alligning the structure on specified atoms, and then (2) calculating the
> > rmsd of the chosen atoms. Thanks.
> >
> > Best,
> > --
> > Ilyas Yildirim
>
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Received on Sun Sep 23 2007 - 06:07:41 PDT
