Re: [AMBER] RMSD on two slightly different structures

From: Jason Swails <>
Date: Mon, 22 Sep 2014 08:23:46 -0400

On Mon, 2014-09-22 at 07:18 +0000, Guillaume Roellinger wrote:
> Dear all,
> Using cpptraj, I am computing the RMSD between two almost similar
> structures with two different topology files and then perform a PCA.
> Structure A has 265 residues and structure B: 271. The sequence in
> structure A from residue 1 to 265 is the almost the same (there are
> 2-3 mutations) as in structure B from residue 5 to 270.

Note that there is 1 more residue between residues 5 and 270 compared to
residues 1 to 265. I'll assume you really meant 6 to 270 (so the first
5 residues are different) in the rest of my answer.
> I am computing the RMSD this way and it is working:
> parm structureA.prmtop
> parm structure B.prmtop
> trajin structureA.pdb parmindex 0
> trajin structureB.pdb parmindex 1
> reference structureA.pdb parmindex 0
> rms reference :1-265.CA
> 1st question: When I am selecting the residue range 1-265, does it
> take from both structure A and B the residues 1 to 265 or does it
> select from structure A residues 1 to 265 and from structure B
> residues 5 to 270 (=the almost common sequence part)?

It selects both 1 to 265 of both residues. If you want to select
residues 6 to 270 of the reference structure, you should provide that
mask to the reference statement. For example, change the reference
command to:

reference structureA.pdb parmindex 0 :6-270

This will bring in the 265 residues starting from residue 6 (and they
should be renumbered sequentially starting from 1).

> 2nd question (related to the first one): In an other example, I have
> structures C with 278 residues and D with 277. What appends if I have
> "gaps" in both sequences and if I compute the RMSD with :1-277.CA as
> mask (this is working as well!) ?

cpptraj does not recognize "gaps" by default. You may want to look into
the "atommap" command, which may help you create a mapping between the
two structures you want to compare.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Mon Sep 22 2014 - 05:30:03 PDT
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