AmberParm does not support all of the parameters defined in the input Structure. Try ChamberParm

[Jonathan]

Hi Collegues, 

I prepared my gromacs files using Charmm GUI and used defaults AMBER forcefields. My gromacs ran well and i  able to carry out analysis. Upon running gmxMMPBSA i came across this error

"AmberParm does not support all of the parameters defined in the input Structure. Try ChamberParm"

may you kindly kelp me solve it. Please find below the full log from the terminal.

$~/Desktop/Trachoma/100ns/owe/gromacs$ mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md_100.tpr -ci index.ndx -cg 1 13 -ct 100ns_noPBC.xtc -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -cp topol.top
[INFO   ] Starting gmx_MMPBSA v1.5.2+20.g83afa51
[INFO   ] Command-line
  mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md_100.tpr -ci index.ndx -cg 1 13 -ct 100ns_noPBC.xtc -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -cp topol.top

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

[INFO   ] Checking external programs...
[INFO   ] cpptraj found! Using /home/d2i/miniconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO   ] tleap found! Using /home/d2i/miniconda3/envs/gmxMMPBSA/bin/tleap
[INFO   ] parmchk2 found! Using /home/d2i/miniconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO   ] sander found! Using /home/d2i/miniconda3/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 1_13 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 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 13 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 "/home/d2i/miniconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/home/d2i/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 101, in gmxmmpbsa
    app.make_prmtops()
  File "/home/d2i/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 538, in make_prmtops
    self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
  File "/home/d2i/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 118, in buildTopology
    tops = self.gmxtop2prmtop()
  File "/home/d2i/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 480, in gmxtop2prmtop
    com_amb_prm = parmed.amber.AmberParm.from_structure(com_top)
  File "/home/d2i/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/amber/_amberparm.py", line 317, in from_structure
    raise TypeError('AmberParm does not support all of the parameters '
TypeError: AmberParm does not support all of the parameters defined in the input Structure. Try ChamberParm
Exiting. All files have been retained.
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0

thanks 

[Mario Sergio Valdes]

Use the -cp topol.top option. Please, consider using the latest version (v1.5.6)

Mario S.

[Tatenda Bvunzawabaya]

Thank you Mario, 

I have installed the latest version. However, the error hasn't gone. I have also included the -cp topol.top command but nothing has changed. Is there anything wrong with my files somehow?.

Best regards 

[INFO   ] Starting gmx_MMPBSA v1.5.6
[DEBUG  ] WDIR          : /home/d2i/Desktop/Trachoma/100ns/owe/gromacs
[DEBUG  ] AMBERHOME     : /home/d2i/miniconda3/envs/gmxMMPBSA
[DEBUG  ] PYTHON EXE    : /home/d2i/miniconda3/envs/gmxMMPBSA/bin/python
[DEBUG  ] PYTHON VERSION: 3.9.12 (main, Apr  5 2022, 06:56:58) [GCC 7.5.0]
[DEBUG  ] MPI           : /home/d2i/miniconda3/envs/gmxMMPBSA/bin/mpirun
[DEBUG  ] ParmEd        : 3.4.3
[DEBUG  ] OS PLATFORM   : Linux-5.15.0-46-generic-x86_64-with-glibc2.31
[DEBUG  ] OS SYSTEM     : Linux
[DEBUG  ] OS VERSION    : #49~20.04.1-Ubuntu SMP Thu Aug 4 19:15:44 UTC 2022
[DEBUG  ] OS PROCESSOR  : x86_64

  File "/home/d2i/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 537, in make_prmtops

    self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
  File "/home/d2i/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 118, in buildTopology
    tops = self.gmxtop2prmtop()
  File "/home/d2i/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 480, in gmxtop2prmtop
    com_amb_prm = parmed.amber.AmberParm.from_structure(com_top)
  File "/home/d2i/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/amber/_amberparm.py", line 317, in from_structure
    raise TypeError('AmberParm does not support all of the parameters '
TypeError: AmberParm does not support all of the parameters defined in the input Structure. Try ChamberParm
Exiting. All files have been retained.
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0

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[marioe911116]

could you please send us the files you re suing to see what's going wrong?

[marioe911116]

As discussed offline:

update Parmed as follows:

python -m pip install git+https://github.com/Valdes-Tresanco-MS/ParmEd.git@v3.4