MMPBSA_Error

[Shilpa Sharma]

Can anyone help to solve this error. gmx_MMPBSA_test file is running successfully.

But when running " gmx_MMPBSA -O -i mmpbsa.in -cs md2.tpr -ct md1_noPBC.xtc -ci index.ndx -cg 1 13 -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv" encountering the error as shown below.

INFO   ] Splitting  receptor and ligand in PDB files..

[INFO   ] Building tleap input files...
[ERROR  ] MMPBSA_Error

/home/ncd/miniconda3/envs/gmxMMPBSA/bin/tleap failed when querying _GMXMMPBSA_leap.in

Check the gmx_MMPBSA.log file to report the problem.
tets
  File "/home/ncd/miniconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/home/ncd/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
    app.make_prmtops()
  File "/home/ncd/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 682, in make_prmtops
    self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
  File "/home/ncd/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 128, in buildTopology
    tops = self.makeToptleap()
  File "/home/ncd/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 1581, in makeToptleap
    self._run_tleap(tleap, 'leap.in', data_path)
  File "/home/ncd/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 1708, in _run_tleap
    GMXMMPBSA_ERROR('%s failed when querying %s' % (tleap, self.FILES.prefix + arg1))
  File "/home/ncd/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
    raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error:

/home/ncd/miniconda3/envs/gmxMMPBSA/bin/tleap failed when querying _GMXMMPBSA_leap.in

[Mario Sergio Valdes]

Please, use the topology (-cp topol.top)

[Shilpa Sharma]

Not working i have tried with topol.top also

[Shilpa Sharma]

I have attached log file from both commands with -cp topol.top and without topol.top

[Mario Sergio Valdes]

What is the error when you use the topology file?

[Shilpa Sharma]

A lot of warnings and parameters were not found.

/home/ncd/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py:556: GromacsWarning: angles funct != 1 or 5; unknown functional

  warnings.warn('angles funct != 1 or 5; unknown '
/home/ncd/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py:556: GromacsWarning: angles funct != 1 or 5; unknown functional
  warnings.warn('angles funct != 1 or 5; unknown '
/home/ncd/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py:556: GromacsWarning: angles funct != 1 or 5; unknown functional
  warnings.warn('angles funct != 1 or 5; unknown '
/home/ncd/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py:556: GromacsWarning: angles funct != 1 or 5; unknown functional
  warnings.warn('angles funct != 1 or 5; unknown '
/home/ncd/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py:556: GromacsWarning: angles funct != 1 or 5; unknown functional
  warnings.warn('angles funct != 1 or 5; unknown '
/home/ncd/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py:556: GromacsWarning: angles funct != 1 or 5; unknown functional
  warnings.warn('angles funct != 1 or 5; unknown '
/home/ncd/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py:556: GromacsWarning: angles funct != 1 or 5; unknown functional
  warnings.warn('angles funct != 1 or 5; unknown '

  File "/home/ncd/miniconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/home/ncd/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
    app.make_prmtops()
  File "/home/ncd/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 682, in make_prmtops
    self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()

  File "/home/ncd/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 125, in buildTopology
    tops = self.gmxtop2prmtop()
  File "/home/ncd/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 555, in gmxtop2prmtop
    com_top = self.cleantop(self.FILES.complex_top, self.indexes['COM']['COM'])
  File "/home/ncd/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 843, in cleantop
    rtemp_top = parmed.gromacs.GromacsTopologyFile(ttp_file.as_posix())
  File "/home/ncd/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 251, in __init__
    self.read(fname, defines, parametrize)
  File "/home/ncd/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 461, in read
    self.parametrize()
  File "/home/ncd/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 1021, in parametrize
    raise ParameterError('Not all bond parameters found')
ParameterError: Not all bond parameters found
Exiting. All files have been retained.

[marioe911116]

Which force field did you use in the MD simulation?

[Shilpa Sharma]

I used GROMOS96 54a7 force field for these files.

[Shilpa Sharma]

problem resolved

[João Victor Piloto]

shilpa how do you solved this problem?

i have tha same problem

[gmx_MMPBSA]

Probably the solution is to change the forcefield since gromos is not supported