Re: [AMBER] PROTEIN-DNA rmsd plot

From: Syeda Amna Arshi <>
Date: Thu, 31 Dec 2020 15:23:45 +0530

first for combining the nc files i used following cpptraj input:
parm ABC_wation.prmtop
trajin md*.nc 1 last 10 # load frames in steps of 10
autoimage # automatic centre
strip :WAT # strip all residues with name WAT
trajout netcdf ! write out combined trajectory from 20.1ns run

further for the rmsd:
parm ABC_ion.prmtop
autoimage anchor :1-123
rms first out rmsd.dat .CA

and the resultant plot is attached below

[image: image.png]

*Syeda Amna Arshi*
*Ph.D. Scholar*
Multidisciplinary Centre For Advanced Research and Studies
Jamia Millia Islamia
Delhi-110025 7737638065
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Received on Thu Dec 31 2020 - 02:00:02 PST
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