IndexError: list index out of range

[Hanah Ali]

[INFO   ] Starting gmx_MMPBSA v1.6.2
[INFO   ] Command-line
  gmx_MMPBSA -O -i mmpbsa.in -cs md.tpr -ct md_noPBC.xtc -ci index.ndx -cg 2 3 -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 /Users/hanahnasifaali/amber22/bin/cpptraj
[INFO   ] tleap found! Using /Users/hanahnasifaali/amber22/bin/tleap
[INFO   ] parmchk2 found! Using /Users/hanahnasifaali/amber22/bin/parmchk2
[INFO   ] sander found! Using /Users/hanahnasifaali/amber22/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 UNK_UNL (2_3) 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 UNK (2) 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 UNL (3) in _GMXMMPBSA_COM_index.ndx file as 

Hi,

While performing some calculations, i got the following error. I hope you can help me. 

Kind regards, 

Hanah

_GMXMMPBSA_LIG.pdb
[INFO   ] Checking the structures consistency...
[INFO   ]
[INFO   ] Using topology conversion. Setting radiopt = 0...
[INFO   ] Building Normal Complex Amber topology...
  File "/Users/hanahnasifaali/amber22/miniconda/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
             ^^^^^^^^^^^
  File "/Users/hanahnasifaali/amber22/miniconda/lib/python3.11/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
    app.make_prmtops()
  File "/Users/hanahnasifaali/amber22/miniconda/lib/python3.11/site-packages/GMXMMPBSA/main.py", line 682, in make_prmtops
    self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
                                                                          ^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/hanahnasifaali/amber22/miniconda/lib/python3.11/site-packages/GMXMMPBSA/make_top.py", line 125, in buildTopology
    tops = self.gmxtop2prmtop()
           ^^^^^^^^^^^^^^^^^^^^
  File "/Users/hanahnasifaali/amber22/miniconda/lib/python3.11/site-packages/GMXMMPBSA/make_top.py", line 555, in gmxtop2prmtop
    com_top = self.cleantop(self.FILES.complex_top, self.indexes['COM']['COM'])
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/hanahnasifaali/amber22/miniconda/lib/python3.11/site-packages/GMXMMPBSA/make_top.py", line 843, in cleantop
    rtemp_top = parmed.gromacs.GromacsTopologyFile(ttp_file.as_posix())
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/hanahnasifaali/amber22/miniconda/lib/python3.11/site-packages/parmed/gromacs/gromacstop.py", line 251, in __init__
    self.read(fname, defines, parametrize)
  File "/Users/hanahnasifaali/amber22/miniconda/lib/python3.11/site-packages/parmed/gromacs/gromacstop.py", line 379, in read
    attype, typ = self._parse_atomtypes(line)
                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/hanahnasifaali/amber22/miniconda/lib/python3.11/site-packages/parmed/gromacs/gromacstop.py", line 734, in _parse_atomtypes
    if len(words[3]) == 1 and words[3] in letters:
           ~~~~~^^^
IndexError: list index out of range

[Hanah Ali]

Hi,

While performing some calculations, i got the following error. I hope you can help me. 

Kind regards, 

Hanah

[Mario E. Valdes-Tresanco]

Seems there is an error in the topology format... could you please send the topology files?

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[Mario Sergio Valdes]

Please check that you have the correct parmed version specified in the installation instructions

[Hanah Ali]

Hi,

It worked. Thank you very much for the help.

Best,

Hanah