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 - 06:00:03 PST
