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 Sun Jan 04 2009 - 01:09:09 PST
