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error while running gmx_MMPBSA #84

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hima111997 opened this issue Oct 6, 2021 · 4 comments
Closed

error while running gmx_MMPBSA #84

hima111997 opened this issue Oct 6, 2021 · 4 comments
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Inconsistent input files Problems with user-defined files. i.e, number of atoms mismatch between tpr and trajectory unsupported force field wontfix This will not be worked on

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@hima111997
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Describe the issue
I have run a simulation for a protein-ligand complex using GROMOS96 43a1 force field in GROMACS and when I tried to run gmx_MMPBSA it gave me this error
[ERROR ] MMPBSA_Error Unknown force field in GROMACS topology in line: #include "gromos43a1.ff/forcefield.itp" . Check the gmx_MMPBSA.log file to report the problem. File "/home/cairo029u1/.local/bin/gmx_MMPBSA", line 8, in <module> sys.exit(gmxmmpbsa()) File "/home/cairo029u1/.local/lib/python3.8/site-packages/GMXMMPBSA/app.py", line 95, in gmxmmpbsa app.make_prmtops() File "/home/cairo029u1/.local/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/cairo029u1/.local/lib/python3.8/site-packages/GMXMMPBSA/make_top.py", line 117, in buildTopology tops = self.gmxtop2prmtop() File "/home/cairo029u1/.local/lib/python3.8/site-packages/GMXMMPBSA/make_top.py", line 318, in gmxtop2prmtop com_top = self.cleantop(self.FILES.complex_top, self.indexes[0] + self.indexes[1]) File "/home/cairo029u1/.local/lib/python3.8/site-packages/GMXMMPBSA/make_top.py", line 580, in cleantop GMXMMPBSA_ERROR(f'Unknown force field in GROMACS topology in line:\n {line}') File "/home/cairo029u1/.local/lib/python3.8/site-packages/GMXMMPBSA/exceptions.py", line 169, in __init__ raise exc(msg + '. Check the gmx_MMPBSA.log file to report the problem.') MMPBSA_Error: Unknown force field in GROMACS topology in line: #include "gromos43a1.ff/forcefield.itp" . Check the gmx_MMPBSA.log file to report the problem. Exiting. All files have been retained.

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To Reproduce
Steps to reproduce the behavior:

  1. Which system type are you running? (Protein-Protein, Protein-Ligand, etc)
    protein-ligand system
  2. The command-line are you using.
    gmx_MMPBSA -O -i pbs.in -cs mdsim.tpr -ci index.ndx -cg 1 13 -ct mdsim_pbc_removed_and_aligned_water.trr -lm 68M_ante.mol2 -cp topol.top -cr mdsim.pdb
    Additional context
    gmx_log.log
@Valdes-Tresanco-MS
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Hi @hima111997

Currently, gmx_MMPBSA only supports Amber (fully supported) and CHARMM (may have some limitations in rare cases) force fields.
We intend to implement APBS which is a bit more flexible and accepts more force fields. According to a brief review, g_mmpbsa can be used in your case, however, I am not sure if GROMOS has been parameterized for PB calculations, so its results may be questionable.

Cheers!
Mario S.

@Valdes-Tresanco-MS Valdes-Tresanco-MS added Inconsistent input files Problems with user-defined files. i.e, number of atoms mismatch between tpr and trajectory wontfix This will not be worked on labels Oct 6, 2021
@Valdes-Tresanco-MS
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I close this issue because it has already been answered

@347lixin
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I have run a simulation for a protein-ligand complex using amber99 force field（amber 99 for protein，acpype for ligand） in GROMACS and when I tried to run gmx_MMPBSA it gave me this error
[INFO ] Building Normal Complex Amber topology...
File "/home/lixin347/miniconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in
sys.exit(gmxmmpbsa())
File "/home/lixin347/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/lixin347/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 689, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/lixin347/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 125, in buildTopology
tops = self.gmxtop2prmtop()
File "/home/lixin347/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 534, in gmxtop2prmtop
com_top = self.cleantop(self.FILES.complex_top, self.indexes['COM']['COM'])
File "/home/lixin347/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 821, in cleantop
rtemp_top = parmed.gromacs.GromacsTopologyFile(ttp_file.as_posix())
File "/home/lixin347/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 251, in init
self.read(fname, defines, parametrize)
File "/home/lixin347/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 289, in read
for line in f:
File "/home/lixin347/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/_gromacsfile.py", line 44, in iter
for line in self._handle:
File "/home/lixin347/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/_cpp.py", line 175, in iter
self._ppcmdmap[cmd](self, args)
File "/home/lixin347/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/_cpp.py", line 30, in wrapper
return func(self, args)
File "/home/lixin347/miniconda3/envs/gmxMMPBSA/lib/python3.9/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.

Repository owner deleted a comment from ssagar61 Mar 21, 2023
@marioernestovaldes marioernestovaldes mentioned this issue Mar 21, 2023
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@marioernestovaldes
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This is a closed issue... please let's post this in a new issue

further communication here #359

Repository owner locked as resolved and limited conversation to collaborators Mar 21, 2023
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@Valdes-Tresanco-MS @marioernestovaldes @hima111997 @347lixin