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 - 05:30:04 PST
