Gromacs error when running gmx_mmpbsa

[nikpekbook]

I have used gmx_mmpbsa as was recommended on the examples page. But I get the following error: 

[DEBUG  ] Running command: echo -e "name 21 GMXMMPBSA_REC\n name 22 GMXMMPBSA_LIG\n  21 | 22\n q\n" | /home/user/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx make_ndx -n index.ndx -o _GMXMMPBSA_COM_index.ndx -f md100.tpr
[DEBUG  ]                :-) GROMACS - gmx make_ndx, 2022.4-conda_forge (-:
[DEBUG  ]
[DEBUG  ] Executable:   /home/nikita/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[DEBUG  ] Data prefix:  /home/nikita/miniconda3/envs/gmxMMPBSA
[DEBUG  ] Working dir:  /home/nikita/moldyn/coronavirus/pig-purdue
[DEBUG  ] Command line:
[DEBUG  ]   gmx make_ndx -n index.ndx -o _GMXMMPBSA_COM_index.ndx -f md100.tpr
[DEBUG  ]
[DEBUG  ]
[DEBUG  ] Reading structure file
[DEBUG  ] Reading file md100.tpr, VERSION 2023.3 (single precision)
[DEBUG  ] Reading file md100.tpr, VERSION 2023.3 (single precision)
[DEBUG  ]
[DEBUG  ] -------------------------------------------------------
[DEBUG  ] Program:     gmx make_ndx, version 2022.4-conda_forge
[DEBUG  ]
[DEBUG  ] Standard library logic error (bug):
[DEBUG  ] (exception type: St12length_error)
[DEBUG  ] vector::_M_default_append
[DEBUG  ]
[DEBUG  ] For more information and tips for troubleshooting, please check the GROMACS
[DEBUG  ] website at http://www.gromacs.org/Documentation/Errors
[DEBUG  ] -------------------------------------------------------
[ERROR  ] MMPBSA_Error

/home/user/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx make_ndx failed when querying index.ndx

[nikpekbook]

Perhaps this error is happening because gmx_mmpbsa is using the gromacs 2022.4 version installed via conda by default? And the trajectory was created using Gromacs 2023.3. Is it possible to fix this error by redirecting the path to a newer version of Gromacs installed on my computer and how to do this?

воскресенье, 28 января 2024 г. в 15:21:48 UTC+2, nikpekbook:

[gmx_MMPBSA]

Yes. Check the variable gmx_path in the input file (https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/input_file/#miscellaneous-options)

But, also you can install gromacs v2023.3 (even gromacs v2023.4) (https://anaconda.org/conda-forge/gromacs)

[nikpekbook]

Thanks a lot. 

Adding of gmx_path variable helped me.

воскресенье, 28 января 2024 г. в 20:57:49 UTC+2, gmx_MMPBSA: