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

From: Hector A. Baldoni <hbaldoni.unsl.edu.ar>
Date: Tue, 12 Jan 2021 13:44:05 -0300 (ARGSL-ST)

Dear Dixit,

Please try something similar to the following commands, where files
"rmsd_cplx_P1.txt"
are the regular cpptraj outputs.

#===================
set terminal pngcairo truecolor nocrop enhanced size 1600,800 font "arial
bold,22"
set yrange [0.0 : 6.0]
set xlabel "Time (ns)"
set ylabel "RMSD (angstroms)"

set output "CPLX.png"
plot 'rmsd_cplx_P1.txt' w l dt 1 title 'P1', 'rmsd_cplx_P2.txt' w l dt 1
title 'P2', 'rmsd_cplx_P3.txt' w l dt 1 title 'P3', 'rmsd_cplx_P4.txt' w l
dt 1 title 'P4'

#====================

Greeting,
Hector.


> 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 <david.case.rutgers.edu>
> wrote:
>
>> 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 prot.nc
>> >reference prot.inpcrd
>> >trajin prot1.nc 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
>>
>>
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>>
>
>
> --
>
> Regards,
>
> Dr. Vaibhav A. Dixit,
>
> Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
> University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
> AND
> Assistant Professor,
> Department of Pharmacy,
> ‚–„‚–„‚–„‚–„‚–„‚–„‚–„‚–„‚–„‚–„‚–„‚–„‚–„‚–„‚–„‚–„‚–„‚–„‚–„‚–„‚–„‚–„‚–„‚–„‚–„‚–„‚–„‚–„‚–„‚–„‚–„‚–„‚–„‚–„‚–„‚–„‚–„‚–„‚–„‚–„‚–„‚–„‚–„‚–„‚–„
> Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
> VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
> India.
> Phone No. +91 1596 255652, Mob. No. +91-7709129400,
> Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
> ‚Äčhttp://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
> https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
>
> ORCID ID: https://orcid.org/0000-0003-4015-2941
>
> http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
>
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>


--------------------------------------
 Dr. Hector A. Baldoni
 Profesor Titular (FQByF-UNSL)
 Investigador Adjunto (IMASL-CONICET)
 Area de Quimica General e Inorganica
 Universidad Nacional de San Luis
 Chacabuco 917 (D5700BWS)
 San Luis - Argentina
 hbaldoni at unsl dot edu dot ar
 Tel.:+54-(0)266-4520300 ext. 6157
--------------------------------------


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Received on Tue Jan 12 2021 - 09:00:03 PST
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