I am sorry, I know I said it worked, it did but I just wanted to know which
is more correct regarding rmsd line
rmsd first (without any mask)
OR
rmsd first :1-431.C,CA,N (my protein has 431 residues)
Many thanks
Mahmood
On 5 December 2013 13:54, Jason Swails <jason.swails.gmail.com> wrote:
> On Thu, 2013-12-05 at 13:32 +0000, John Smith wrote:
> > Sorry if I was not so clear. What I meant is atomic fluctuation for
> which I
> > used the following command
> >
> > atomicfluct out back.apf .C,CA,N byres
> >
> > and I got the dat file. Waht I am trying to do now is to align all the
> > frames to the first frame and then calculate the atomic fluctuation. How
> > can I do this?
>
> My last email provided the answer. Here it is again:
>
> On Thu, 2013-12-05 at 12:41 +0000, John Smith wrote:
> > Hi Amber users
> >
> > I am trying to align my trajecotry to get an rmsf using ptraj. I
> managed to
> > get rmsf but what I could not do is to align the trajectory to the
> first
> > frame and then claculate the rmsf
>
> You need to do an RMSD fit first. For example:
>
> rmsd first <mask>
> atomicfluct out <filename> <mask>
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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Received on Thu Dec 05 2013 - 07:30:04 PST
