Error in gmx_MMPBSA Calculation

[SM]

Hi there,

I am currently working on a coarse-grain simulation usiing GROMACS and have been attempting to perform MMPBSA analysis using the gmx_MMPBSA tool. Unfortunately, I've encountered an error during the execution, and I'm seeking assistance to resolve it.

Here is the command I used: gmx_MMPBSA -O -i /data/akshit/CG-wild-type/mmpbsa-analysis/mmpbsa.in -cs /data/akshit/CG-wild-type/protein.tpr -ct /data/akshit/CG-wild-type/removepbc.xtc -ci /data/akshit/CG-wild-type/test2.ndx -cg 10 11 -cp /data/akshit/CG-wild-type/topol.top -o /data/akshit/CG-wild-type/mmpbsa-analysis/FINAL_RESULTS_MMPBSA-WT.dat

The error message I received is as follows: [INFO   ] Checking /data/akshit/CG-wild-type/mmpbsa-analysis/mmpbsa.in input file...
[INFO   ] Checking /data/akshit/CG-wild-type/mmpbsa-analysis/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   ] 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...
[INFO   ] Normal Complex: Saving group r_1-590_r_595-790 (10_11) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO   ] No receptor structure file was defined. Using ST approach...
[INFO   ] Using receptor structure from complex to generate AMBER topology
[INFO   ] Normal Receptor: Saving group r_1-590 (10) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[INFO   ] No ligand structure file was defined. Using ST approach...
[INFO   ] Using ligand structure from complex to generate AMBER topology
[INFO   ] Normal Ligand: Saving group r_595-790 (11) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
  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 489, in gmx2pdb
    self.indexes = get_indexes(com_ndx=self.FILES.complex_index,
  File "/home/aditya/miniconda3/envs/gmxMMPBSA/lib/python3.8/site-packages/GMXMMPBSA/utils.py", line 410, in get_indexes
    com_indexes = {'COM': ndx['COM']['index'][comind], 'REC': ndx['COM']['index'][crecind],
IndexError: list index out of range
Exiting. All files have been retained.

I have attached the mmpbsa.in file for your reference.

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

Thank you in advance for your time and assistance.

[gmx_MMPBSA]

Currently, gmx_MMPBSA doesn't support processing coarse-grained systems. Have you tried and succeeded with other coarse grained systems so far?

[Shweata Maurya]

Thank you for your prompt response. I appreciate your assistance.

I wasn't aware that gmx_MMPBSA doesn't currently support processing coarse-grained systems. This is my first attempt with MMPBSA analysis, and I haven't worked on any other coarse-grained systems before.

Given this limitation, could you please suggest an alternative approach or tool that I can use to calculate the binding energy for my coarse-grained system? Alternatively, is there a method to convert the necessary files from coarse-grain trajectories for MMPBSA analysis?

I'm eager to explore any possible solutions you may have.

Thank you once again for your help.

--
You received this message because you are subscribed to the Google Groups "gmx_MMPBSA" group.
To unsubscribe from this group and stop receiving emails from it, send an email to gmx_mmpbsa+...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/gmx_mmpbsa/01a6578a-7531-4175-830e-9304047baf4fn%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

[gmx_MMPBSA]

I don't think MMPBSA is the way to go when it comes to coarse-grained models. As far as I understand, there are other methods more suitable for coarse-grained models 

https://pubs.acs.org/doi/10.1021/acs.jctc.9b00548