Dear Carlos,
Your suggestion worked, thank you. As far as I understood, the ptraj
commands 'principal' and 'rms' cannot be used together. If someone wants
to calculate the rmsd by first aligning some atoms, the command 'rms'
needs to be used (not 'principal'). That means that the algorithm used for
'principal' and 'rms' to align the atoms are different. I wonder what the
purpose of 'principal' is. It looks like that it helps to create a movie
file for the trajectory, which is aligned according to the specified
atoms. Other than that I dont see any use of it. Thanks again.
Best,
On Fri, 21 Sep 2007, Carlos Simmerling wrote:
> 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
> >
>
--
Ilyas Yildirim
---------------------------------------------------------------
= Department of Chemistry - =
= University of Rochester - =
= Rochester, NY 14627-0216 - Ph.:(585) 275 67 66 (Office) =
= http://www.pas.rochester.edu/~yildirim/ =
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Received on Sun Sep 23 2007 - 06:07:45 PDT
