[Bug-gmx_MMPBSA]: gmx make_ndx failed when querying index_LIG.ndx

[dj8207]

Bug summary

gmx make_ndx failed when querying index_LIG.ndx gmx make_ndx failed when querying index_final.ndx

Terminal output

gmx_MMPBSA -O -i mmpbsa.in -cs MD.tpr -ci index_LIG.ndx -cg 1 13 -ct MD_center.xtc -cp topol.top -lm LIG.mol2
hwloc/linux: Ignoring PCI device with non-16bit domain.
Pass --enable-32bits-pci-domain to configure to support such devices
(warning: it would break the library ABI, don't enable unless really needed).
[INFO   ] Starting gmx_MMPBSA v1.6.1
[INFO   ] Command-line
  gmx_MMPBSA -O -i mmpbsa.in -cs MD.tpr -ci index_LIG.ndx -cg 1 13 -ct MD_center.xtc -cp topol.top -lm LIG.mol2

tets
[INFO   ] Checking mmpbsa.in input file...
[INFO   ] Checking mmpbsa.in input file...Done.

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

/home/ngsm/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx make_ndx failed when querying index_LIG.ndx

Check the gmx_MMPBSA.log file to report the problem.
  File "/home/ngsm/miniconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/home/ngsm/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
    app.make_prmtops()
  File "/home/ngsm/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
    self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
  File "/home/ngsm/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology
    self.gmx2pdb()
  File "/home/ngsm/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 263, in gmx2pdb
    GMXMMPBSA_ERROR('%s failed when querying %s' % (' '.join(self.make_ndx), self.FILES.complex_index))
  File "/home/ngsm/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
    raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error: 

/home/ngsm/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx make_ndx failed when querying index_LIG.ndx

Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.

gmx_MMPBSA.log

gmx_MMPBSA.log

Operating system

Linux

gmx_MMPBSA Version

gmx_MMPBSA v1.6.1

Python version

Python 3.9.12

Installation

None

[marioernestovaldes]

which gromacs version did you use to run the MD simulation?

[dj8207]

GROMACS - gmx, 2022.4-conda_forge

[marioernestovaldes]

Upgrade gromacs in the gmx_MMPBSA conda environment and it should be fine

conda install -c conda-forge gromacs==2023.1

[dj8207]

Thanks a lot it worked.

[dj8207]

resolved