Re: [AMBER] RMSD on two slightly different structures

From: Daniel Roe <>
Date: Mon, 22 Sep 2014 08:03:16 -0600


Just to add a bit to Jason's answer, you can alternatively specify a
second mask to the RMS command that describes what you want selected
in your reference, e.g.

rms reference :1-265.CA :6-270.CA

If you have gaps in your sequences you need to specify your masks such
that corresponding atoms are selected. As Jason mentioned the
'atommap' command may help with this, but keep in mind this command
will have trouble if the structures differ too much.


On Mon, Sep 22, 2014 at 1:18 AM, 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.
> 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)?
> 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!) ?
> Thanks in advance for your answer,
> Guillaume
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Mon Sep 22 2014 - 07:30:02 PDT
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