Index Failure

[Omar Casanova Alvarez]

I am having this, 

[DEBUG  ] Executable:   /opt/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[DEBUG  ] Data prefix:  /opt/anaconda3/envs/gmxMMPBSA
[DEBUG  ] Working dir:  /home/omar/Dynamic_Alex/charmm-gui-6615763234/gromacs
[DEBUG  ] Command line:
[DEBUG  ]   gmx make_ndx -n index.ndx -o _GMXMMPBSA_COM_index.ndx -f step6.tpr
[DEBUG  ]
[DEBUG  ]
[DEBUG  ] Reading structure file
[DEBUG  ] Reading file step6.tpr, VERSION 2025.4-conda_forge (single precision)
[DEBUG  ] Reading file step6.tpr, VERSION 2025.4-conda_forge (single precision)
[DEBUG  ]
[DEBUG  ] -------------------------------------------------------
[DEBUG  ] Program:     gmx make_ndx, version 2024.3-conda_forge
[DEBUG  ] Source file: listoflists.h (line 98)
[DEBUG  ] Function:    gmx::ListOfLists< <template-parameter-1-1> >::ListOfLists(std::vector<>
[DEBUG  ]
[DEBUG  ] Inconsistency in user input:
[DEBUG  ] listRanges does not have a first element with value 0
[DEBUG  ]
[DEBUG  ] For more information and tips for troubleshooting, please check the GROMACS
[DEBUG  ] website at https://manual.gromacs.org/current/user-guide/run-time-errors.html
[DEBUG  ] -------------------------------------------------------
[ERROR  ] MMPBSA_Error

/opt/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx make_ndx failed when querying index.ndx

Check the gmx_MMPBSA.log file to report the problem.

How I can fix it?

[mariosergi...@gmail.com]

Please, check first that you are using the same or a superior gromacs version, since gromacs guarantees retrocompatibility. Here, your index seems to have been generated by gromacs v2025.4, but you are processing it with v2024.3.
You can freely upgrade the gromacs version from conda and try again