IndexError: list index out of range

[SANDRA KP 21903032]

Hi, I'm trying to run mmgbsa analysis of receptor (protein+cofactor) and ligand (substrate), but I'm getting error. When I run gb just between protein and substrate, it works well. As cofactor also contribute to the system, I need to run gb/pbsa for whole system. I performed MD simulation using CHARMM36 forcefield and index file contains the preferred receptor group as well. I'm getting the following error:

[INFO   ] Starting gmx_MMPBSA v1.6.3
[INFO   ] Command-line
  gmx_MMPBSA -O -i mmgbsa.in -cs md1.tpr -ci index.ndx -cg 28 20 -ct analysis-fit.xtc -cp topol.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv

[INFO   ] Checking mmgbsa.in input file...
[INFO   ] Checking mmgbsa.in input file...Done.

[INFO   ] Checking external programs...
[INFO   ] cpptraj found! Using /home/puneet/miniconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO   ] tleap found! Using /home/puneet/miniconda3/envs/gmxMMPBSA/bin/tleap
[INFO   ] parmchk2 found! Using /home/puneet/miniconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO   ] sander found! Using /home/puneet/miniconda3/envs/gmxMMPBSA/bin/sander
[INFO   ] Using GROMACS version > 5.x.x!
[INFO   ] gmx found! Using /usr/local/gromacs/bin/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 Protein_PPI1_JZ4 (28_20) 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 Protein_PPI1 (28) 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 JZ4 (20) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
[INFO   ] Checking the structures consistency...
[WARNING] No reference structure was found and the complex structure not contain any chain ID. Assigning chains ID automatically...
  File "/home/puneet/miniconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/home/puneet/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
    app.make_prmtops()
  File "/home/puneet/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 681, in make_prmtops
    self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
  File "/home/puneet/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 122, in buildTopology
    self.gmx2pdb()
  File "/home/puneet/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 524, in gmx2pdb
    self.check_structures(self.complex_str, self.receptor_str, self.ligand_str)
  File "/home/puneet/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 1436, in check_structures
    self._assign_chains_IDs(com_str, rec_str, lig_str)
  File "/home/puneet/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 1492, in _assign_chains_IDs
    if self.resl[c + 1].is_receptor():
IndexError: list index out of range
Exiting. All files have been retained.

How can I rectify this?

[mariosergi...@gmail.com]

This may be due to incorrect groups or to groups that have artifacts in their sequence. It's important that the selected group (in this case, it appears to be the receptos) fully matches the structure and the topology. In this case, it appears that the index has more registered residues than the structure. In some cases, this can be resolved by creating a new index from the TPR you're using as the structure.

[SANDRA KP 21903032]

Thank you. One of the component in the index group (receptor) was not assigned with a chain ID. Now I'm facing an another issue. I can't reproduce the same results which I got earlier. I got -19kcal/mol before and this time I'm getting 0.14 kcal/mol. I did the gb calculation for the same simulation run results.

[mariosergi...@gmail.com]

Oh, this is very strange because these calculations are deterministic, so the values ​​should be the same in both cases. Please send me the files so I can reproduce the error.

[SANDRA KP 21903032]

https://drive.google.com/file/d/1VyFYyWvTipAxkJdF3N2kla6mMwzYmHG1/view?usp=sharing

Hi, here is the link to the files. Also, when I set intdiel=10, I got enthalpy =-11kcal/mol. Is this correct to use that way. My system has protein+substrate+cofcators(ppi and Mg2+).