Hi,
You can't do it in the same cpptraj run, but you can certainly do it
in the same script. The cpptraj analysis command 'avg' will calculate
the average, standard deviation, Y min and max for a specified data
set. So you could do something like:
parm leap/K1_ions.prmtop
trajin MD/k1MMD.nobox.nowat.img.crd
reference leap/K1_ions.pdb
radgyr R1 :1-18 out radgyr_noions.out
avg R1 out average.dat
The format of output from 'avg' is:
#Set Average Stdev Ymin YminIdx Ymax YmaxIdx Name
So just grab the values from columns 4 and 6 and plug them into your
second cpptraj run with 'filter'. Hope this helps!
-Dan
PS - The plan in future releases is to have data from commands like
'avg' also be stored in data sets, so things like this can be done in
one run.
On Fri, Jan 29, 2016 at 8:02 AM, josephine
<j.abi-ghanem.iecb.u-bordeaux.fr> wrote:
> Hello Amber users,
>
> I want to use cpptraj to perform some systematic analysis for the radius
> of gyration of an RNA molecule.
> Then I would like to filter this results to obtain the frames with a low
> radius of gyration.
> Something like this works fine:
>
> cpptraj leap/K1_ions.prmtop
> trajin MD/k1MMD.nobox.nowat.img.crd
> reference leap/K1_ions.pdb
> rmsd :1-18 reference
> radgyr R1 :1-18 out radgyr_noions.out
> filter R1 min 10 max 11.4 out radgyr_10_11.4.out
> trajout radgyr_10_11.4.crd
>
> Then I use the .crd file to cluster and get a representative strutcure.
>
> However, I do not know a priori the min and the max to use in the filter
> command.
> Is there a way to do the whole treatment in one script or should i just
> generate the radgyr_noions.out file, calculate the range i need and then
> filter?
> Mainly what i would need, is to know the min, max and mean value of the
> radgyr series.
>
> Thanks for the help
> Josephine
>
>
> --
> ---------------------------------------
> Josephine Abi Ghanem, PhD
> Postdoc
> BiophyMS - INSERM U869 ARNA lab
> j.abi-ghanem.iecb.u-bordeaux.fr
> Tel. +33 (5) 4000 6331
> Institut européen de chimie et biologie
> 2, rue Robert Escarpit
> 33607 Pessac, France
> www.iecb.u-bordeaux.fr
> -----------------------------------------
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Fri Jan 29 2016 - 08:00:04 PST
