Index out of range error

[N Sridhara Devi]

 after properly visualizing the trajectory I have run the command but got the following error

File "/home/saiprasad/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/home/saiprasad/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
    app.make_prmtops()
  File "/home/saiprasad/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 548, in make_prmtops
    self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
  File "/home/saiprasad/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 118, in buildTopology
    tops = self.gmxtop2prmtop()
  File "/home/saiprasad/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 513, in gmxtop2prmtop
    action = ChRad(com_amb_prm, PBRadii[self.INPUT['PBRadii']])
  File "/home/saiprasad/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/tools/changeradii.py", line 295, in ChRad
    _call_method[radii_set](parm)
  File "/home/saiprasad/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/tools/changeradii.py", line 145, in mbondi2
    if atom.bond_partners[0].atomic_number == 7:
IndexError: list index out of range
Exiting. All files have been retained.

please help me with this

[Mario Sergio Valdes]

This looks like your system has an unbound atom. Please, send me your files to check them

[Mario Sergio Valdes]

The problem here is that the LP pseudo-atom is not supported. Please, check this example:

https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/examples/Protein_ligand_LPH_atoms_CHARMMff/

I think the protonation state of the ligand is incorrect. The ligand has some nitrogens whose configuration should be sp2 as sp3. I recommend you check it.