Group Protein_UNK referenced in the .mdp file was not found in the index file.

I have used GROMACS - gmx, 2020.1-Ubuntu-2020.1-1. I runned this command. “gmx grompp -f nvt.mdp -c em.gro -r em.gro -p -n index.ndx -o nvt.tpr”
But I got this error while running this command.
WARNING 1 [file, line 27620]:
The GROMOS force fields have been parametrized with a physically
incorrect multiple-time-stepping scheme for a twin-range cut-off. When
used with a single-range cut-off (or a correct Trotter
multiple-time-stepping scheme), physical properties, such as the density,
might differ from the intended values. Since there are researchers
actively working on validating GROMOS with modern integrators we have not
yet removed the GROMOS force fields, but you should be aware of these
issues and check if molecules in your system are affected before
proceeding. Further information is available at , and a longer explanation of our
decision to remove physically incorrect algorithms can be found at
On The Importance of Accurate Algorithms for Reliable Molecular Dynamics Simulations | Theoretical and Computational Chemistry | ChemRxiv | Cambridge Open Engage .

Setting gen_seed to 237804172
Velocities were taken from a Maxwell distribution at 300 K

NOTE 1 [file, line 27620]:
The bond in molecule-type UNK between atoms 20 C4 and 21 C3 has an
estimated oscillational period of 1.9e-02 ps, which is less than 10 times
the time step of 2.0e-03 ps.
Maybe you forgot to change the constraints mdp option.

Program: gmx grompp, version 2020.1-Ubuntu-2020.1-1
Source file: src/gromacs/gmxpreprocess/readir.cpp (line 2701)

Fatal error:
Group Protein_UNK referenced in the .mdp file was not found in the index file.
Group names must match either [moleculetype] names or custom index group
names, in which case you must supply an index file to the ‘-n’ option
of grompp.

For more information and tips for troubleshooting, please check the GROMACS
website at Common Errors — GROMACS webpage documentation

Hi @Anitha

This forum is focused on running tools in the Galaxy ecosystem.

Command-line usage would be better asked at general bioinformatics forums or the author’s resources.

  • Abraham, M. J., Murtola, T., Schulz, R., Páll, S., Smith, J. C., Hess, B., & Lindahl, E. (2015). GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX, 1–2, 19–25.

If you want to try in Galaxy, or to just review our example data and curated information, please see: