Memory allocation error

[Aiman Parvez]

Hello,

i am trying to do MMPBSA energy calculation but it showed memory allocation error,

i have used (gmx_MMPBSA -O -i mmpbsa.in -cs md_0_10.tpr -ci index.ndx -cg 1 13 -ct md_0_10.xtc -cp topol.top) command  i am also attaching th .log file and screen shot to this conversation.

please guid me to solve this error...

[ERROR  ] MMPBSA_Error

/home/aiman/anaconda3/envs/gmx-mmpbsa/bin.AVX2_256/gmx make_ndx failed when querying index.ndx

Check the gmx_MMPBSA.log file to report the problem.
  File "/home/aiman/anaconda3/envs/gmx-mmpbsa/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/home/aiman/anaconda3/envs/gmx-mmpbsa/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
    app.make_prmtops()
  File "/home/aiman/anaconda3/envs/gmx-mmpbsa/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/aiman/anaconda3/envs/gmx-mmpbsa/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology
    self.gmx2pdb()
  File "/home/aiman/anaconda3/envs/gmx-mmpbsa/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/aiman/anaconda3/envs/gmx-mmpbsa/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/aiman/anaconda3/envs/gmx-mmpbsa/bin.AVX2_256/gmx make_ndx failed when querying index.ndx

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

[Mario E. Valdes-Tresanco]

Usually this is related to the GROMACS version:

Try updating gromacs 

conda install -c conda-forge gromacs==2023.2

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