MMPBSA ERROR

[Sridhar Kulkarni]

Can you please tell me what is the problem here.

gmx_MMPBSA -O -i mmpbsa.in -cs 2ITV_DUTA_md.tpr -ct 2ITV_DUTA_md_noPBC_180-200ns_100_frames.xtc -ci index.ndx -cg 1 13 -cp topol.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv

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

[INFO   ] Checking external programs...
[INFO   ] cpptraj found! Using /home/bif-sssihl-12/miniconda3/envs/AmberTools23/bin/cpptraj
[INFO   ] tleap found! Using /home/bif-sssihl-12/miniconda3/envs/AmberTools23/bin/tleap
[INFO   ] parmchk2 found! Using /home/bif-sssihl-12/miniconda3/envs/AmberTools23/bin/parmchk2
[INFO   ] sander found! Using /home/bif-sssihl-12/miniconda3/envs/AmberTools23/bin/sander
[INFO   ] Using GROMACS version > 5.x.x!
[INFO   ] gmx found! Using /home/bif-sssihl-12/miniconda3/envs/gmxMMPBSA/bin/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/bif-sssihl-12/miniconda3/envs/gmxMMPBSA/bin/gmx make_ndx failed when querying index.ndx

Check the gmx_MMPBSA.log file to report the problem.
  File "/home/bif-sssihl-12/miniconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/home/bif-sssihl-12/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
    app.make_prmtops()
  File "/home/bif-sssihl-12/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 682, in make_prmtops
    self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
  File "/home/bif-sssihl-12/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology
    self.gmx2pdb()
  File "/home/bif-sssihl-12/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 284, in gmx2pdb
    GMXMMPBSA_ERROR('%s failed when querying %s' % (' '.join(self.make_ndx), self.FILES.complex_index))
  File "/home/bif-sssihl-12/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/bif-sssihl-12/miniconda3/envs/gmxMMPBSA/bin/gmx make_ndx failed when querying index.ndx

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

[Sridhar Kulkarni]

The error got solved after installing recent verion of conda 2023.1 . you had already solved the issue and i just had to look and got it thank you.