MMPBSA error in query index.ndx

[Research Boulevard]

Hi,

We used CHARMgui for generating the input files, as such the index.ndx file from CHARMgui contained only three groups (Solute, Solvent and System), therefore we created updated the index file with all the defaults groups (the protein in the 1 and ligand in 13th position). Now the simulation runs are completed using the input files from CHARMgui, however gmx_MMPBSA throws errors at index file query.

Below is the information from the log file

[INFO   ] Starting gmx_MMPBSA v1.6.2
[DEBUG  ] WDIR          : /home/boulevard/Documents/charmm-gui/charmm-gui-0685766525/gromacs
[DEBUG  ] AMBERHOME     : /home/boulevard/miniconda3/envs/gmxMMPBSA
[DEBUG  ] PYTHON EXE    : /home/boulevard/miniconda3/envs/gmxMMPBSA/bin/python
[DEBUG  ] PYTHON VERSION: 3.9.15 | packaged by conda-forge | (main, Nov 22 2022, 08:45:29) [GCC 10.4.0]
[DEBUG  ] MPI           : /home/boulevard/miniconda3/envs/gmxMMPBSA/bin/mpirun
[DEBUG  ] ParmEd        : 3.4.3+11.g41cc9ab
[DEBUG  ] OS PLATFORM   : Linux-6.5.0-17-generic-x86_64-with-glibc2.35
[DEBUG  ] OS SYSTEM     : Linux
[DEBUG  ] OS VERSION    : #17~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Tue Jan 16 14:32:32 UTC 2
[DEBUG  ] OS PROCESSOR  : x86_64

[INFO   ] Command-line
  gmx_MMPBSA -O -i mmpbsa.in -cs step4.0_minimization.tpr -ct no_pbc_trajectory.xtc -ci index.ndx -cg 1 13 -cp topol.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv

[DEBUG  ] |Input file:
[DEBUG  ] |--------------------------------------------------------------
[DEBUG  ] |Sample input file for PB calculation
[DEBUG  ] |This input file is meant to show only that gmx_MMPBSA works. Although, we tried to use the input files as recommended
[DEBUG  ] |in the Amber manual, some parameters have been changed to perform more expensive calculations in a reasonable amount of time. Feel free to change the
[DEBUG  ] |parameters according to what is better for your system.
[DEBUG  ] |
[DEBUG  ] |&general
[DEBUG  ] |sys_name="Prot-Lig-CHARMM",
[DEBUG  ] |startframe=1,
[DEBUG  ] |endframe=4,
[DEBUG  ] |# In gmx_MMPBSA v1.5.0 we have added a new PB radii set named charmm_radii. This radii set should be used only
[DEBUG  ] |# with systems prepared with CHARMM force fields. Uncomment the line below to use charmm_radii set
[DEBUG  ] |PBRadii=7,
[DEBUG  ] |/
[DEBUG  ] |&pb
[DEBUG  ] |# radiopt=0 is recommended which means using radii from the prmtop file for both the PB calculation and for the NP
[DEBUG  ] |# calculation
[DEBUG  ] |istrng=0.15, fillratio=4.0, radiopt=0
[DEBUG  ] |/
[DEBUG  ] |--------------------------------------------------------------
[DEBUG  ]
[INFO   ] Checking mmpbsa.in input file...
[INFO   ] Checking mmpbsa.in input file...Done.

[INFO   ] Checking external programs...
[INFO   ] cpptraj found! Using /home/boulevard/miniconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO   ] tleap found! Using /home/boulevard/miniconda3/envs/gmxMMPBSA/bin/tleap
[INFO   ] parmchk2 found! Using /home/boulevard/miniconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO   ] sander found! Using /home/boulevard/miniconda3/envs/gmxMMPBSA/bin/sander
[INFO   ] Using GROMACS version > 5.x.x!
[INFO   ] gmx found! Using /home/boulevard/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO   ] Checking external programs...Done.

[INFO   ] Building AMBER topologies from GROMACS files...
[INFO   ] Get PDB files from GROMACS structures files...
[INFO   ] Making gmx_MMPBSA index for complex...
[DEBUG  ] Running command: echo -e "name 1 GMXMMPBSA_REC\n name 13 GMXMMPBSA_LIG\n  1 | 13\n q\n" | /home/boulevard/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx make_ndx -n index.ndx -o _GMXMMPBSA_COM_index.ndx -f step4.0_minimization.tpr
[DEBUG  ]                :-) GROMACS - gmx make_ndx, 2022.4-conda_forge (-:
[DEBUG  ]
[DEBUG  ] Executable:   /home/boulevard/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[DEBUG  ] Data prefix:  /home/boulevard/miniconda3/envs/gmxMMPBSA
[DEBUG  ] Working dir:  /home/boulevard/Documents/charmm-gui/charmm-gui-0685766525/gromacs
[DEBUG  ] Command line:
[DEBUG  ]   gmx make_ndx -n index.ndx -o _GMXMMPBSA_COM_index.ndx -f step4.0_minimization.tpr
[DEBUG  ]
[DEBUG  ]
[DEBUG  ] Reading structure file
[DEBUG  ] Reading file step4.0_minimization.tpr, VERSION 2024 (single precision)
[DEBUG  ] Reading file step4.0_minimization.tpr, VERSION 2024 (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/boulevard/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx make_ndx failed when querying index.ndx

Check the gmx_MMPBSA.log file to report the problem.

Please help

[Mario E. Valdes-Tresanco]

Since GROMACS 2024 is not in conda yet (I believe), you need to specify where the bin executable folder is in your machine through the gmx_path variable in the input file, something like this:

&general
sys_name="Prot-Prot",
startframe=1,
endframe=10,
gmx_path="/home/programs/gromacs/bin"
/
&gb
igb=2, saltcon=0.150,
/

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