Re: [AMBER] backbone rmsd between mutant trajectories, comparing conformational space sampled

From: Vaibhav Dixit <>
Date: Tue, 12 Jan 2021 15:52:25 +0900

Dear David and All,
I'm getting the analysis that I wanted, but xmgrace is not working on my
system and the error message looks too much out of my expertise to fix.
If I choose gnu format for rms out command that I get a display that
doesn't look like a usual rmsd plot (I think it displays 3d plot/map?)
Can you please suggest to me if there is a quick fix to the xmgrace error
or better options to display a line plot in gnuplot?

I understand this is not amber specific but useful suggestions are
highly appreciated.
thank you and best regards

(base) [exx.c107739 test]$ head rms.gnu
set pm3d map corners2color c1
set ytics 1.000, 1.000
set ytics("RMSD_00002" 1.000)
set xlabel "Frame"
set ylabel ""
set yrange [ 0.000: 3.000]
set xrange [ 0.000:2002.000]
splot "-" with pm3d title "H87Y-Fe3-rms.gnu"
   1.000 1.000 0.6856
   1.000 2.000 0

[image: image.png]

On Mon, Jan 11, 2021 at 10:18 PM David A Case <>

> On Mon, Jan 11, 2021, Vaibhav Dixit wrote:
> >I have simulated two protein structures in which only one residue was
> >mutated and thus backbone sequence is the same.
> >I'm guessing it must be possible to use cpptraj to align the backbone
> >coordinates frame-by-frame, and estimate rmsd to check if the mutants
> >sample the same conformational space.
> >
> >parm prot-top
> >trajin
> >reference prot.inpcrd
> >trajin parm
> The command you want is "rms", something like this:
> rms reference :1-141.C,CA,N out rms.dat
> The manual shows lots of keywords that can be added to the rms command, but
> this should get you going.
> ....dac
> _______________________________________________
> AMBER mailing list

Dr. Vaibhav A. Dixit,
Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
Assistant Professor,
Department of Pharmacy,
Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
Phone No. +91 1596 255652, Mob. No. +91-7709129400,
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Received on Mon Jan 11 2021 - 23:00:02 PST
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