AMBER Archive (2007)

Subject: Re: AMBER: Targetted MD and ptraj analysis

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Fri Sep 21 2007 - 07:12:50 CDT

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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