AMBER Archive (2009)

Subject: RE: AMBER: RMS plot

From: Duggan, Brendan M. (bmduggan_at_musc.edu)
Date: Tue Jan 06 2009 - 13:54:04 CST


I too have been trying to get per residue RMSDs from trajectories. After looking at the ptraj manual I was using commands like:

trajin ./ligand.traj
rms first :1-85
atomicfluct out backbone.rmsd @N,CA,C byres

This gave me numbers that seemed reasonable, but I'm not sure if its correct. Can anyone tell me the difference between these commands and what Carlos proposed?

brendan

email: bmduggan_at_musc.edu
phone: (843) 792 5029
fax: (843) 792 4322

________________________________________
From: owner-amber_at_scripps.edu [owner-amber_at_scripps.edu] On Behalf Of Carlos Simmerling [carlos.simmerling_at_gmail.com]
Sent: Friday, January 02, 2009 9:08 AM
To: amber_at_scripps.edu
Subject: Re: AMBER: RMS plot

probably the easiest way is to make a script that creates a ptraj
input for this, like the following. then you'll need to average the
outputs, again a script will do that. maybe there is an easier way or
someone else might have a better program- I don't think ptraj does it
directly. hopefully you can use the example below as a starting place
and modify it for your needs. make sure to watch out for the "nofit"
parts and change the masks to what you want.

#!/bin/csh

set i=1
set last = 100
echo "ptraj prmtop << EOF"
echo "trajin ./mdcrd.gz"
echo "reference ./ref.crd"

echo "rmsd reference mass out rmsd.res.ALL.dat :$i-$last"
while ($i < 10)
        echo "rmsd reference mass out rmsd.res.all.00$i.dat :$i nofit"
        @ i++
end
while ($i < 100)
        echo "rmsd reference mass out rmsd.res.all.0$i.dat :$i nofit"
        @ i++
end
while ($i <= $last)
        echo "rmsd reference mass out rmsd.res.all.$i.dat :$i nofit"
        @ i++
end

echo "EOF"

On Wed, Dec 31, 2008 at 2:11 PM, Beale, John <jbeale_at_stlcop.edu> wrote:
> I need to make a plot of C-alpha RMS deviations (in Angstroms) vs. residue number for a protein that I am studying with MD. Is it possible to do this in ptraj? If so, how do I set it up?
>
> John Beale
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