计算化学公社

标题: 使用gmx_MMPBSA计算膜蛋白与配体的时候报错 [打印本页]

作者
Author: Pipi_ 时间: 2025-12-5 17:52
标题: 使用gmx_MMPBSA计算膜蛋白与配体的时候报错
(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.

欢迎光临计算化学公社 (http://bbs.keinsci.com/)