On Wed, Feb 3, 2016 at 2:39 AM, Atila Petrosian <atila.petrosian.gmail.com>
wrote:
> Dear amber users,
>
> I have obtained rmsd values using ccptraj for my protein trajectory. I want
> to have standard deviation of rmsd values.
>
If you specify an output file or write the RMSD data set to a file, you
will have a file with two columns of numbers -- the frame number and the
RMSD. Then you can write a script that reads that file and computes a
standard deviation (with Python and numpy, you can actually do it in a
single line, you can also do it quite easily with grep/sed/awk, or even
just awk). There's also the approach of loading the text file into a
spreadsheet program (like Excel or OpenOffice/LibreOffice) and calculating
an average and/or standard deviation inside there.
Inside cpptraj, the "statistics" analysis will also do it. For example,
this is a cpptraj script I wrote really quickly:
rmsd bbrmsd .CA,C,N first
run
statistics bbrmsd
runanalysis
The printout I get to the screen shows both the average and standard
deviation. However, I would still recommend learning how to write these
kinds of simple scripts to use in your analysis if you don't already know
how as it will be an invaluable tool for carrying out interesting
computations.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Feb 03 2016 - 06:00:08 PST
