error in running gmx_mmpbsa

[Ketan Rohilla]

I am getting the following error. I have generated the input files from charmm-gui and simulated them in GROMACS.

gmx_MMPBSA -O -i mmpbsa.in -cs md_0_1.tpr -ci index.ndx -cg 18 19 -ct md_nopbc_cluster_fit.xtc -cp topol.top -eo Energy.csv -o FINAL_RESULTS_MMPBSA.dat
[INFO   ] Starting gmx_MMPBSA v1.5.0.3+37.g67bd79a
[INFO   ] Command-line
  gmx_MMPBSA -O -i mmpbsa.in -cs md_0_1.tpr -ci index.ndx -cg 18 19 -ct md_nopbc_cluster_fit.xtc -cp topol.top -eo Energy.csv -o FINAL_RESULTS_MMPBSA.dat

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

[INFO   ] Checking external programs...
[INFO   ] cpptraj found! Using /root/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO   ] tleap found! Using /root/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO   ] parmchk2 found! Using /root/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO   ] sander found! Using /root/anaconda3/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 18_19 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 18 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 19 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 "/root/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/root/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 101, in gmxmmpbsa
    app.make_prmtops()
  File "/root/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 533, in make_prmtops
    self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
  File "/root/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 118, in buildTopology
    tops = self.gmxtop2prmtop()
  File "/root/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 442, in gmxtop2prmtop
    com_top = self.cleantop(self.FILES.complex_top, self.indexes['COM']['COM'])
  File "/root/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 713, in cleantop
    rtemp_top = parmed.gromacs.GromacsTopologyFile(ttp_file.as_posix())
  File "/root/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 251, in __init__
    self.read(fname, defines, parametrize)
  File "/root/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 289, in read
    for line in f:
  File "/root/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/_gromacsfile.py", line 44, in __iter__
    for line in self._handle:
  File "/root/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/_cpp.py", line 175, in __iter__
    self._ppcmdmap[cmd](self, args)
  File "/root/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/_cpp.py", line 30, in wrapper
    return func(self, args)
  File "/root/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/_cpp.py", line 288, in _pp_include
    raise PreProcessorError('Could not find %s' % includefile)
PreProcessorError: Could not find toppar/forcefield.itp
Exiting. All files have been retained.

[Mario Ernesto]

Include the 'forcefield.itp' file in the toppar folder and it should be fine 

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