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.musc.edu
phone: (843) 792 5029
fax: (843) 792 4322
________________________________________
From: owner-amber.scripps.edu [owner-amber.scripps.edu] On Behalf Of Carlos Simmerling [carlos.simmerling.gmail.com]
Sent: Friday, January 02, 2009 9:08 AM
To: amber.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.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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Received on Tue Jan 06 2009 - 15:33:11 PST
