Error in running gmx_MMPBSA (simulation performed using Charmm forcefield)

[Syed Jawad Ali shah]

I ran into problem while running gmx_MMPBSA. The command line i used and the error i encountered was following:

[INFO   ] Starting

[INFO   ] Command-line

  gmx_MMPBSA -O -i mmpbsa.in -cp ../topol.top -cs ../md_50ns.tpr -ci ../index.ndx -cg 1 14 -ct ../md_50ns_fit.xtc

[WARNING] protein_forcefield and ligand_forcefield variables are deprecate since version 1.4.1 and will be remove in the next version. Please, use forcefield instead.

[WARNING] entropy_seg variable is deprecate since version 1.4.2 and will be remove in v1.5.0. Please, use ie_segment instead.

[INFO   ] Checking external programs...

[INFO   ] cpptraj found! Using /home/khan/softwares/amber20/bin/cpptraj

[INFO   ] tleap found! Using /home/khan/softwares/amber20/bin/tleap

[INFO   ] parmchk2 found! Using /home/khan/softwares/amber20/bin/parmchk2

[INFO   ] sander found! Using /home/khan/softwares/amber20/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   ] Checking gmxMMPBSA data folder exists in Amber data...

[INFO   ] Get PDB files from GROMACS structures files...

[INFO   ] Making gmx_MMPBSA index for complex...

[INFO   ] Normal Complex: Saving group 1_14 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 Complex: Saving group 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 14 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb

[INFO   ] Building Normal Complex Amber Topology...

  File "/home/khan/softwares/amber20/miniconda/bin/gmx_MMPBSA", line 8, in <module>

    sys.exit(gmxmmpbsa())

  File "/home/khan/softwares/amber20/miniconda/lib/python3.8/site-packages/GMXMMPBSA/app.py", line 95, in gmxmmpbsa

    app.make_prmtops()

  File "/home/khan/softwares/amber20/miniconda/lib/python3.8/site-packages/GMXMMPBSA/main.py", line 576, in make_prmtops

    self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()

  File "/home/khan/softwares/amber20/miniconda/lib/python3.8/site-packages/GMXMMPBSA/make_top.py", line 116, in buildTopology

    tops = self.gmxtop2prmtop()

  File "/home/khan/softwares/amber20/miniconda/lib/python3.8/site-packages/GMXMMPBSA/make_top.py", line 317, in gmxtop2prmtop

    com_top = self.cleantop(self.FILES.complex_top, self.indexes[0] + self.indexes[1])

  File "/home/khan/softwares/amber20/miniconda/lib/python3.8/site-packages/GMXMMPBSA/make_top.py", line 597, in cleantop

    rtemp_top = parmed.gromacs.GromacsTopologyFile(ttp_file.as_posix())

  File "/home/khan/softwares/amber20/lib/python3.8/site-packages/parmed/gromacs/gromacstop.py", line 251, in __init__

    self.read(fname, defines, parametrize)

  File "/home/khan/softwares/amber20/lib/python3.8/site-packages/parmed/gromacs/gromacstop.py", line 289, in read

    for line in f:

  File "/home/khan/softwares/amber20/lib/python3.8/site-packages/parmed/gromacs/_gromacsfile.py", line 44, in __iter__

    for line in self._handle:

  File "/home/khan/softwares/amber20/lib/python3.8/site-packages/parmed/gromacs/_cpp.py", line 175, in __iter__

    self._ppcmdmap[cmd](self, args)

  File "/home/khan/softwares/amber20/lib/python3.8/site-packages/parmed/gromacs/_cpp.py", line 30, in wrapper

    return func(self, args)

  File "/home/khan/softwares/amber20/lib/python3.8/site-packages/parmed/gromacs/_cpp.py", line 279, in _pp_include

    raise PreProcessorError('Bad #include syntax')

PreProcessorError: Bad #include syntax

Exiting. All files have been retained.

Any suggestions will be of great help. 

Thank you

[Mario Sergio Valdes]

Hi and welcome!

This error is probably related to the #include files statement of the topology.

Check that the files defined in such declarations are accessible. If you still can't solve it, consider sending us a copy of the files (top + itps + charmm parm folder [if exists], xtc [10 frames], tpr, ndx, groups)

Mario S.