mmpbsa analysis error

[Shweata Maurya]

Hi there!

I am currently working on an all-atom MD simulation using GROMACS and have been attempting to calculate binding energy between two chains using the gmx_MMPBSA tool. Unfortunately, I've encountered an error during the execution, and I'm seeking assistance to resolve it.  

(gmxMMPBSA) aditya@ws2:~$ gmx_MMPBSA -O -i mmpbsa.in -cs /data/Shweata/all-atom-WT/mmpbsa/wtallatommdformmpbsa/protein.tpr -ct /data/Shweata/all-atom-WT/removepbc.xtc -ci /data/Shweata/all-atom-WT/mmpbsa/wtallatommdformmpbsa/index.ndx -cg 10 11 -cp /data/Shweata/all-atom-WT/mmpbsa/wtallatommdformmpbsa/topol.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv
[INFO   ] Starting gmx_MMPBSA v1.6.1
[INFO   ] Command-line
  gmx_MMPBSA -O -i mmpbsa.in -cs /data/Shweata/all-atom-WT/mmpbsa/wtallatommdformmpbsa/protein.tpr -ct /data/Shweata/all-atom-WT/removepbc.xtc -ci /data/Shweata/all-atom-WT/mmpbsa/wtallatommdformmpbsa/index.ndx -cg 10 11 -cp /data/Shweata/all-atom-WT/mmpbsa/wtallatommdformmpbsa/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/aditya/miniconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO   ] tleap found! Using /home/aditya/miniconda3/envs/gmxMMPBSA/bin/tleap
[INFO   ] parmchk2 found! Using /home/aditya/miniconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO   ] sander found! Using /home/aditya/miniconda3/envs/gmxMMPBSA/bin/sander
[INFO   ] mmpbsa_py_nabnmode found! Using /home/aditya/miniconda3/envs/gmxMMPBSA/bin/mmpbsa_py_nabnmode
[INFO   ] gbnsr6 found! Using /home/aditya/miniconda3/envs/gmxMMPBSA/bin/gbnsr6
[INFO   ] Using GROMACS version > 5.x.x!
[INFO   ] gmx found! Using /home/aditya/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/aditya/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx make_ndx failed when querying /data/Shweata/all-atom-WT/mmpbsa/wtallatommdformmpbsa/index.ndx

Check the gmx_MMPBSA.log file to report the problem.
  File "/home/aditya/miniconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/home/aditya/miniconda3/envs/gmxMMPBSA/lib/python3.8/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
    app.make_prmtops()
  File "/home/aditya/miniconda3/envs/gmxMMPBSA/lib/python3.8/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
    self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
  File "/home/aditya/miniconda3/envs/gmxMMPBSA/lib/python3.8/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology
    self.gmx2pdb()
  File "/home/aditya/miniconda3/envs/gmxMMPBSA/lib/python3.8/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/aditya/miniconda3/envs/gmxMMPBSA/lib/python3.8/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/aditya/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx make_ndx failed when querying /data/Shweata/all-atom-WT/mmpbsa/wtallatommdformmpbsa/index.ndx

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

I would greatly appreciate any insights or suggestions on resolving this issue. If you require additional information or specific details about my setup, please let me know.

Thank you in advance for your time and assistance.

[gmx_MMPBSA]

Usually this is related to the GROMACS version:

Try updating gromacs 

conda install -c conda-forge gromacs==2023.2

[Shweata Maurya]

Thank you for your prompt response and suggestion regarding updating GROMACS to version 2023.2. 
However, I have a follow-up question regarding the compatibility of the updated version with my existing simulation files. As you rightly pointed out, the files I currently have were generated using GROMACS version 2022. Given this, I am concerned about potential compatibility issues and whether it would be necessary to rerun the simulations with the updated software.

Could you please advise on the best course of action in this scenario? I would greatly appreciate any insights or recommendations you can provide regarding ensuring the compatibility of my existing files with the updated GROMACS version.

Thank you for your attention to this matter, and I look forward to your guidance.

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[Mario E. Valdes-Tresanco]

No need to worry about compatibility. GROMACS 2023 is able to process v2022 files

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