Re: [AMBER] Mass-weighted RMSD one-liner with cpptraj - possible?

From: Daniel Roe <>
Date: Tue, 5 May 2020 09:08:34 -0400


On Mon, May 4, 2020 at 9:23 AM Martin Mielke <> wrote:
> It seems like calculating a mass-weighted RMSD is possible too, so I was
> wondering if someone would point me to the right direction in telling me
> how to use cpptraj in a way that it yields the mass-weighted RMSD for 2
> given PDB files? All I want is the final value shown on screen, no graph
> files etc needed.
> For example:
> $ cpptraj [options for mass-weighted RMSD here] file1.pdb file2.pdb [hit
> enter]
> 10.874

This will require a short input file. Something like a file named e.g.

# load reference pdb
parm pdb1.pdb
reference pdb1.pdb parmindex 0
# load target pdb
parm pdb2.pdb
trajin pdb2.pdb parmindex 1
# Calculate RMSD
rmsd RMS reference mass
printdata RMS

Then run 'cpptraj -i'.

This will be a best-fit RMSD by default, assumes that pdb1.pdb and
pdb2.pdb have the exact same atoms, and that you want the final RMSD
to include every atom. If the PDBs are different you would have to
give mask expressions that describe the regions you want to use in the
RMSD calculation. There needs to be a 1 to 1 correspondence between
the atoms in the target and reference structures for the RMSD to be

Please let me know if you have more questions. It's probably also a
good idea to look at the 'rmsd' command section of the cpptraj manual,
and maybe do 1 or 2 of the basic cpptraj tutorials
( If you run
cpptraj interactively (by just typing cpptraj with no other input) and
type 'help rmsd', it will show you the command syntax.

Hope this helps,


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Received on Tue May 05 2020 - 06:30:02 PDT
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