Error while running MMPBSA for protein-protein complex

[Shivananda Kandagalla]

Hi sir,

I am getting an error while trying to run MMPBSA for the analysis of the MD. I am interested in calculating the binding free energy between two chain (A and B). 

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  gmx_MMPBSA -O -i mmpbsa.in -cs md_0_2.tpr -ct md_0_2_noPBC.xtc -ci index.ndx -cg 3 4 -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 /root/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO   ] tleap found! Using /root/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO   ] parmchk2 found! Using /root/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO   ] sander found! Using /root/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO   ] Using GROMACS version > 5.x.x!
[INFO   ] gmx found! Using /root/anaconda3/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 C-alpha_Backbone (3_4) 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 C-alpha (3) 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 Backbone (4) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
  File "/root/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/root/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
    app.make_prmtops()
  File "/root/anaconda3/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 "/root/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology
    self.gmx2pdb()
  File "/root/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 492, in gmx2pdb
    self.resi, self.resl, self.orderl = res2map(self.indexes, self.complex_str)
  File "/root/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/utils.py", line 601, in res2map
    for e in value['num']:
TypeError: string indices must be integers
Exiting. All files have been retained.

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Please find attached my input files and the log file. I will really appreaciate if you come through for me.

 Kind Regards

Shivananda

[Mario Sergio Valdes]

You are selecting the wrong groups in the index file. Groups 3 and 4 correspond to C-alpha and Backbone respectively, not to the protein chain. You must create the proper groups using gmx make_ndx and then define them in the -cg option