Re: [AMBER] cpptraj RMSD reference

From: Mac Kevin Braza <>
Date: Sat, 16 Oct 2021 16:28:02 -0700

Hi I was able to fix it by adding

'ref' in the "rms :11-23.CA [ref2] :14-26.CA out RMSD_LOOP1.dat" >>> "rms
:11-23.CA ref [ref2] :14-26.CA out RMSD_LOOP1.dat"

Thank you!


On Sat, Oct 16, 2021 at 4:16 PM Mac Kevin Braza <> wrote:

> Hi folks,
> I am experiencing a reference error when I am implementing RMSD analysis
> in cpptraj. It says that my [ref2] reference contains no data despite that
> it is present there I wanna ask on what is this error about and what I can
> do about this:
> [rms :11-23.CA [ref2] :14-26.CA out /tmp/tmp.9O7m9mY1bm]
> RMSD: (:11-23.CA), reference is first frame (:14-26.CA).
> Best-fit RMSD will be calculated, coords will be rotated and
> translated.
> [rms :118-127.CA [ref2] :121-130.CA out /tmp/tmp.gUvdc0imCD]
> Warning: DataSet '[ref2]' already present.
> Warning: Set '[ref2]' contains no data.
> Warning: File 'RMSD_LOOP1.dat' has no sets containing data.
> Warning: File 'RMSD_LOOP7.dat' has no sets containing data.
> TIME: Total execution time: 0.1839 seconds.
> I have my cpptraj script here
> parm CONFIG/
> trajin CONFIG/closed.rst
> trajin CONFIG/0001.rst
> autoimage
> parm /CONFIG/ [ref2parm]
> reference $WEST_SIM_ROOT/CONFIG/firstfr.ncrst parm [ref2parm] [ref2]
> rms :11-23.CA [ref2] :14-26.CA out RMSD_LOOP1.dat
> rms :118-127.CA [ref2] :121-130.CA out RMSD_LOOP7.dat
> Thank you for your help, I appreciate this!
> Sincerely,
> Kevin
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Received on Sat Oct 16 2021 - 16:30:02 PDT
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