[AMBER] Cpptraj Filter of Radius of gyration

From: josephine <j.abi-ghanem.iecb.u-bordeaux.fr>
Date: Fri, 29 Jan 2016 16:02:19 +0100

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
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
Mainly what i would need, is to know the min, max and mean value of the
radgyr series.

Thanks for the help

Josephine Abi Ghanem, PhD
BiophyMS - INSERM U869 ARNA lab
Tel. +33 (5) 4000 6331
Institut européen de chimie et biologie
2, rue Robert Escarpit
33607 Pessac, France
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Received on Fri Jan 29 2016 - 07:30:04 PST
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