Skip to content

gmx rms complains about missing atom masses even with -nomw flag

Summary

 -[no]mw                    (yes)
           Use mass weighting for superposition

Setting -nomw should force gmx rms to ignore atom masses. Yet it still tries to read them, and, if it fails, the program refuses to work.

Using an example from #3368 (comment 721329831):

Command line:
  gmx rms -s mol.pdb -f mol.xtc -f2 mol.xtc -o mol-rmsd.xvg -nomw

WARNING: second trajectory (-f2) useless when not calculating matrix (-m/-bm),
         will not read from mol.xtc

WARNING: Masses and atomic (Van der Waals) radii will be guessed
         based on residue and atom names, since they could not be
         definitively assigned from the information in your input
         files. These guessed numbers might deviate from the mass
         and radius of the atom type. Please check the output
         files if necessary.

Can not find mass in database for atom AR in residue 1 AR
Can not find mass in database for atom AR in residue 2 AR
Can not find mass in database for atom AR in residue 3 AR
Can not find mass in database for atom AR in residue 4 AR

-------------------------------------------------------
Program:     gmx rms, version 2022-beta2-dev-20220122-31f6f1eaf6
Source file: src/gromacs/fileio/confio.cpp (line 515)

Fatal error:
Masses were requested, but for some atom(s) masses could not be found in the
database. Use a tpr file as input, if possible, or add these atoms to the mass
database.

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

Exact steps to reproduce

See above.

For developers: Why is this important?

We have at least two user reports about poor guessing of the atomic masses (#3368 (closed), #4288 (closed)), so the situation can happen relatively often.

If this is a bug, (1) what happens, and (2) what did you expect to happen?

(1) gmx rms -nomw complains about missing atom masses.

(2) gmx rms -nomw works fine, because it does not need atom masses.

Relevant input files, logs and/or screenshots

See above.

Possible fixes

If you have any suggestion, or even finished fix or merge request, that's awesome!