使用gmx_MMPBSA计算膜蛋白与配体的时候报错

Pipi_

(gmxMMPBSA) [shuyun@mu02 gmx_MMPBSA_run]$ gmx_MMPBSA -O \
>   -i mmpbsa.in \
>   -cs step7_production_run3.tpr \
>   -ct fit.xtc \
>   -ci index_mmpbsa.ndx \
>   -cg 1 13 \
>   -cp topol.top \
>   -o FINAL_RESULTS_MMPBSA.dat \
>   -eo FINAL_RESULTS_MMPBSA.csv
[INFO   ] Starting gmx_MMPBSA 1.6.4
[INFO   ] Command-line
  gmx_MMPBSA -O -i mmpbsa.in -cs step7_production_run3.tpr -ct fit.xtc -ci index_mmpbsa.ndx -cg 1 13 -cp topol.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv

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

[INFO   ] Checking external programs...
[INFO   ] cpptraj found! Using /home/shuyun/.conda/envs/gmxMMPBSA/bin/cpptraj
[INFO   ] tleap found! Using /home/shuyun/.conda/envs/gmxMMPBSA/bin/tleap
[INFO   ] parmchk2 found! Using /home/shuyun/.conda/envs/gmxMMPBSA/bin/parmchk2
[INFO   ] sander found! Using /home/shuyun/.conda/envs/gmxMMPBSA/bin/sander
[INFO   ] Using GROMACS version > 5.x.x!
[INFO   ] gmx found! Using /home/shuyun/.conda/envs/gmxMMPBSA/bin.AVX2_256/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_LIG (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 LIG (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...
/home/shuyun/.conda/envs/gmxMMPBSA/lib/python3.11/site-packages/parmed/gromacs/gromacstop.py:627: GromacsWarning: pairs funct != 1; unknown functional
  warnings.warn('pairs funct != 1; unknown functional',
/home/shuyun/.conda/envs/gmxMMPBSA/lib/python3.11/site-packages/parmed/gromacs/gromacstop.py:627: GromacsWarning: pairs funct != 1; unknown functional
  warnings.warn('pairs funct != 1; unknown functional',
/home/shuyun/.conda/envs/gmxMMPBSA/lib/python3.11/site-packages/parmed/gromacs/gromacstop.py:627: GromacsWarning: pairs funct != 1; unknown functional
  warnings.warn('pairs funct != 1; unknown functional',
/home/shuyun/.conda/envs/gmxMMPBSA/lib/python3.11/site-packages/parmed/gromacs/gromacstop.py:627: GromacsWarning: pairs funct != 1; unknown functional
  warnings.warn('pairs funct != 1; unknown functional',
/home/shuyun/.conda/envs/gmxMMPBSA/lib/python3.11/site-packages/parmed/gromacs/gromacstop.py:627: GromacsWarning: pairs funct != 1; unknown functional
  warnings.warn('pairs funct != 1; unknown functional',
/home/shuyun/.conda/envs/gmxMMPBSA/lib/python3.11/site-packages/parmed/gromacs/gromacstop.py:627: GromacsWarning: pairs funct != 1; unknown functional
  warnings.warn('pairs funct != 1; unknown functional',
/home/shuyun/.conda/envs/gmxMMPBSA/lib/python3.11/site-packages/parmed/gromacs/gromacstop.py:627: GromacsWarning: pairs funct != 1; unknown functional
  warnings.warn('pairs funct != 1; unknown functional',
/home/shuyun/.conda/envs/gmxMMPBSA/lib/python3.11/site-packages/parmed/gromacs/gromacstop.py:627: GromacsWarning: pairs funct != 1; unknown functional
  warnings.warn('pairs funct != 1; unknown functional',
/home/shuyun/.conda/envs/gmxMMPBSA/lib/python3.11/site-packages/parmed/gromacs/gromacstop.py:627: GromacsWarning: pairs funct != 1; unknown functional
  warnings.warn('pairs funct != 1; unknown functional',
/home/shuyun/.conda/envs/gmxMMPBSA/lib/python3.11/site-packages/parmed/gromacs/gromacstop.py:627: GromacsWarning: pairs funct != 1; unknown functional
  warnings.warn('pairs funct != 1; unknown functional',
/home/shuyun/.conda/envs/gmxMMPBSA/lib/python3.11/site-packages/parmed/gromacs/gromacstop.py:627: GromacsWarning: pairs funct != 1; unknown functional
  warnings.warn('pairs funct != 1; unknown functional',
/home/shuyun/.conda/envs/gmxMMPBSA/lib/python3.11/site-packages/parmed/gromacs/gromacstop.py:627: GromacsWarning: pairs funct != 1; unknown functional
  warnings.warn('pairs funct != 1; unknown functional',
/home/shuyun/.conda/envs/gmxMMPBSA/lib/python3.11/site-packages/parmed/gromacs/gromacstop.py:627: GromacsWarning: pairs funct != 1; unknown functional
  warnings.warn('pairs funct != 1; unknown functional',
/home/shuyun/.conda/envs/gmxMMPBSA/lib/python3.11/site-packages/parmed/gromacs/gromacstop.py:627: GromacsWarning: pairs funct != 1; unknown functional
  warnings.warn('pairs funct != 1; unknown functional',
/home/shuyun/.conda/envs/gmxMMPBSA/lib/python3.11/site-packages/parmed/gromacs/gromacstop.py:627: GromacsWarning: pairs funct != 1; unknown functional
  warnings.warn('pairs funct != 1; unknown functional',
/home/shuyun/.conda/envs/gmxMMPBSA/lib/python3.11/site-packages/parmed/gromacs/gromacstop.py:627: GromacsWarning: pairs funct != 1; unknown functional
  warnings.warn('pairs funct != 1; unknown functional',
/home/shuyun/.conda/envs/gmxMMPBSA/lib/python3.11/site-packages/parmed/gromacs/gromacstop.py:627: GromacsWarning: pairs funct != 1; unknown functional
  warnings.warn('pairs funct != 1; unknown functional',
/home/shuyun/.conda/envs/gmxMMPBSA/lib/python3.11/site-packages/parmed/gromacs/gromacstop.py:627: GromacsWarning: pairs funct != 1; unknown functional
  warnings.warn('pairs funct != 1; unknown functional',
/home/shuyun/.conda/envs/gmxMMPBSA/lib/python3.11/site-packages/parmed/gromacs/gromacstop.py:627: GromacsWarning: pairs funct != 1; unknown functional
  warnings.warn('pairs funct != 1; unknown functional',
/home/shuyun/.conda/envs/gmxMMPBSA/lib/python3.11/site-packages/parmed/gromacs/gromacstop.py:627: GromacsWarning: pairs funct != 1; unknown functional
  warnings.warn('pairs funct != 1; unknown functional',
/home/shuyun/.conda/envs/gmxMMPBSA/lib/python3.11/site-packages/parmed/gromacs/gromacstop.py:627: GromacsWarning: pairs funct != 1; unknown functional
  warnings.warn('pairs funct != 1; unknown functional',
  File "/home/shuyun/.conda/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 7, in <module>
    sys.exit(gmxmmpbsa())
             ^^^^^^^^^^^
  File "/home/shuyun/.conda/envs/gmxMMPBSA/lib/python3.11/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
    app.make_prmtops()
  File "/home/shuyun/.conda/envs/gmxMMPBSA/lib/python3.11/site-packages/GMXMMPBSA/main.py", line 681, in make_prmtops
    self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
                                                                          ^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/shuyun/.conda/envs/gmxMMPBSA/lib/python3.11/site-packages/GMXMMPBSA/make_top.py", line 125, in buildTopology
    tops = self.gmxtop2prmtop()
           ^^^^^^^^^^^^^^^^^^^^
  File "/home/shuyun/.conda/envs/gmxMMPBSA/lib/python3.11/site-packages/GMXMMPBSA/make_top.py", line 585, in gmxtop2prmtop
    com_amb_prm = parmed.amber.AmberParm.from_structure(com_top)
                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/shuyun/.conda/envs/gmxMMPBSA/lib/python3.11/site-packages/parmed/amber/_amberparm.py", line 288, in from_structure
    raise TypeError('Cannot instantiate an AmberParm from unknown functional')
TypeError: Cannot instantiate an AmberParm from unknown functional
Exiting. All files have been retained.