[AMBER] cpptraj RMSD reference

From: Mac Kevin Braza <mebraza.up.edu.ph>
Date: Sat, 16 Oct 2021 16:16:54 -0700

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
  [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/apo.top
trajin CONFIG/closed.rst
trajin CONFIG/0001.rst
parm /CONFIG/reference.top [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!

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Received on Sat Oct 16 2021 - 16:30:02 PDT
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