Error gmx_mmpbsa: LP pseudo-atom is not supported

Question

[bhavya2269]

Hi, I want to perform MMPBSA for complex file

Command:

gmx_MMPBSA -O -i mmpbsa.in -cs md_100.tpr -ct md_center.xtc -ci index.ndx -cg 1 13 -cp topol.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv

Error:

[INFO   ] Starting gmx_MMPBSA v1.6.2
[INFO   ] Command-line
  gmx_MMPBSA -O -i mmpbsa.in -cs md_100.tpr -ct md_center.xtc -ci index.ndx -cg 1 13 -cp topol.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv

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

[INFO   ] Checking external programs...
[INFO   ] cpptraj found! Using /home/amjesh/miniconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO   ] tleap found! Using /home/amjesh/miniconda3/envs/gmxMMPBSA/bin/tleap
[INFO   ] parmchk2 found! Using /home/amjesh/miniconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO   ] sander found! Using /home/amjesh/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 Protein_UNK (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 Protein (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 UNK (13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
[INFO   ] Checking the structures consistency...
[ERROR  ] MMPBSA_Error 

The LP pseudo-atom is not supported. Please remove them following these instructions: https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/examples/Protein_ligand_LPH_atoms_CHARMMff

Check the gmx_MMPBSA.log file to report the problem.
  File "/home/amjesh/miniconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/home/amjesh/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
    app.make_prmtops()
  File "/home/amjesh/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/amjesh/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology
    self.gmx2pdb()
  File "/home/amjesh/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 514, in gmx2pdb
    self.check_structures(self.complex_str, self.receptor_str, self.ligand_str)
  File "/home/amjesh/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 1368, in check_structures
    check_str(com_str)
  File "/home/amjesh/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/utils.py", line 513, in check_str
    GMXMMPBSA_ERROR('The LP pseudo-atom is not supported. Please remove them following these instructions: '
  File "/home/amjesh/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:

**The LP pseudo-atom is not supported.** Please remove them following these instructions: https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/examples/Protein_ligand_LPH_atoms_CHARMMff

Check the gmx_MMPBSA.log file to report the problem.

We followed the instruction that mentioned in above link. Still the error didn't resolve. How to solve this error?

[namck]

Hi @bhavya2269, did you find any solution to this? I'm getting a similar error.