Re: [AMBER] RMSD on two slightly different structures

From: Guillaume Roellinger <>
Date: Fri, 26 Sep 2014 10:56:30 +0000


Thanks a lot! I was indeed using an older version of cpptraj (14.01). I updated and recompiled and it is working now.
I took a deeper look at my output and just as you said both masks are processed: the reference mask when the action is initialized and the target mask in the 'ACTION SETUP FOR PARM' section during processing, so it was working as well.

Thank you for your help!



Von: Daniel Roe <>
Gesendet: Donnerstag, 25. September 2014 17:14
An: AMBER Mailing List
Betreff: Re: [AMBER] RMSD on two slightly different structures


What version of cpptraj are you using? It should be 14.09. The
segfault you describe sounds a lot like an issue that was fixed in
update 6 for AmberTools 14.

On Thu, Sep 25, 2014 at 2:39 AM, Guillaume Roellinger <> wrote:
> About Daniel's answer:
> The statement [rms reference :1-265.CA :6-270.CA] works however I have no idea how cpptraj knows which mask is related to which structure. I tried to add parmindex for each mask but it did not work. Switching both masks did not work [rms reference :6-270.CA :1-265.CA] and the output let me think that only the first mask is taken into account and the second mask is just ignored:
> [0: [rms reference :1-265.CA :6-270.CA out RMSD.dat]
> Mask [:1-265.CA] corresponds to 265 atoms.]

Both masks are processed. The first mask is always the target mask,
and the second mask is always the reference mask (as stated in the
manual). The reference mask for 'reference' is processed when the
action is initialized (near the top of your output). The target mask
is processed in the 'ACTION SETUP FOR PARM' section during processing,
which is what you were reporting.

> It would then explain why the mask switching did not work: if only the first mask matters, it is looking in both structures for :6-270.CA. In the structure with 271 residues, the masks corresponds to more atoms than in the second structure with 265 residues. Mismatch in the number of atom will cause rms to fail.

Without seeing your entire output I can't be sure what is happening.
Can you send it in an email or as an attachment?


> Best regards,
> Guillaume
> ___________________________________
> Von: Jason Swails <>
> Gesendet: Montag, 22. September 2014 14:23
> An:
> Betreff: Re: [AMBER] RMSD on two slightly different structures
> 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 structureB.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.
> HTH,
> Jason
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list
> _______________________________________________
> 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 Fri Sep 26 2014 - 04:00:02 PDT
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