Error in indexing

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Raj Choudhary

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Jun 22, 2025, 10:59:11 AMJun 22

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Dear Sir

While running the gmx_MMPBSA for the protein-ligand complex, I am getting the following error. AMBER99SB-ILDN was the force field used on GROMACS 2023.3 for the simulation

gmx_MMPBSA -O -i mmpbsa.in -cs md_lig.tpr -ct md_lig_center_fit.xtc -ci index.ndx -cg 1 13 -cp protein.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -do FINAL_DECOMP_MMPBSA.dat -deo FINAL_DECOMP_MMPBSA.csv
[INFO ] Starting gmx_MMPBSA v1.6.3
[INFO ] Command-line
gmx_MMPBSA -O -i mmpbsa.in -cs md_lig.tpr -ct md_lig_center_fit.xtc -ci index.ndx -cg 1 13 -cp protein.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -do FINAL_DECOMP_MMPBSA.dat -deo FINAL_DECOMP_MMPBSA.csv

[INFO ] Checking mmpbsa.in input file...
[WARNING] The startframe variable must be >= 1. Changing startframe from 0 to 1
[INFO ] Checking mmpbsa.in input file...Done.

[INFO ] Checking external programs...
[INFO ] cpptraj found! Using /home/raj/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] tleap found! Using /home/raj/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] parmchk2 found! Using /home/raj/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] sander found! Using /home/raj/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /home/raj/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 Protein_LIG (1_13) 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 (1) 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 LIG (13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
[INFO ] Checking the structures consistency...
[INFO ]
[INFO ] Using topology conversion. Setting radiopt = 0...
[INFO ] Building Normal Complex Amber topology...
File "/home/raj/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
^^^^^^^^^^^
File "/home/raj/anaconda3/envs/gmxMMPBSA/lib/python3.11/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/raj/anaconda3/envs/gmxMMPBSA/lib/python3.11/site-packages/GMXMMPBSA/main.py", line 681, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
^^^^^^^^^^^^^^^^^^^^^^^
File "/home/raj/anaconda3/envs/gmxMMPBSA/lib/python3.11/site-packages/GMXMMPBSA/make_top.py", line 124, in buildTopology
tops = self.gmxtop2prmtop()
^^^^^^^^^^^^^^^^^^^^
File "/home/raj/anaconda3/envs/gmxMMPBSA/lib/python3.11/site-packages/GMXMMPBSA/make_top.py", line 565, in gmxtop2prmtop
com_top = self.cleantop(self.FILES.complex_top, self.indexes['COM']['COM'])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/raj/anaconda3/envs/gmxMMPBSA/lib/python3.11/site-packages/GMXMMPBSA/make_top.py", line 854, in cleantop
rtemp_top = parmed.gromacs.GromacsTopologyFile(ttp_file.as_posix())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/raj/anaconda3/envs/gmxMMPBSA/lib/python3.11/site-packages/parmed/gromacs/gromacstop.py", line 346, in __init__
self.read(fname, defines, parametrize)
File "/home/raj/anaconda3/envs/gmxMMPBSA/lib/python3.11/site-packages/parmed/gromacs/gromacstop.py", line 472, in read
attype, typ = self._parse_atomtypes(line)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/raj/anaconda3/envs/gmxMMPBSA/lib/python3.11/site-packages/parmed/gromacs/gromacstop.py", line 828, in _parse_atomtypes
if len(words[3]) == 1 and words[3] in ascii_letters:
~~~~~^^^
IndexError: list index out of range
Exiting. All files have been retained.

I am attaching the relevant files for your reference. Can you please help me to resolve this issue?

Thank you in anticipation

Kind Regards

Raj