关于gmx_MMPBSA不兼容amber19SB_OL21_OL3_lipid17.ff的解决方法

AxiEJohn

本人利用amber19SB_OL21_OL3_lipid17.ff和OPC水模型进行模拟后欲gmx_MMPBSA进行自由能分析却出现报错

1. (ana) ubuntu@ubuntu-01:~/下载/MDSRC$ mpirun -np 1 gmx_MMPBSA -O -i mmpbsa.in -cs md.tpr -ct md.xtc -ci index.ndx -cg 1 13 -cp topol.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv
   
2. [INFO   ] Starting gmx_MMPBSA 1.6.4
   
3. [INFO   ] Command-line
   
4.   gmx_MMPBSA -O -i mmpbsa.in -cs md.tpr -ct md.xtc -ci index.ndx -cg 1 13 -cp topol.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv
   
5. 
   
6. [INFO   ] Checking mmpbsa.in input file...
   
7. [INFO   ] Checking mmpbsa.in input file...Done.
   
8. 
   
9. [INFO   ] Checking external programs...
   
10. [INFO   ] cpptraj found! Using /home/ubuntu/PyMOL_3.1.1_Linux_x86_64/PyMOL_3.1.1_Linux_x86_64/pymol/envs/ana/bin/cpptraj
    
11. [INFO   ] tleap found! Using /home/ubuntu/PyMOL_3.1.1_Linux_x86_64/PyMOL_3.1.1_Linux_x86_64/pymol/envs/ana/bin/tleap
    
12. [INFO   ] parmchk2 found! Using /home/ubuntu/PyMOL_3.1.1_Linux_x86_64/PyMOL_3.1.1_Linux_x86_64/pymol/envs/ana/bin/parmchk2
    
13. [INFO   ] sander found! Using /home/ubuntu/PyMOL_3.1.1_Linux_x86_64/PyMOL_3.1.1_Linux_x86_64/pymol/envs/ana/bin/sander
    
14. [INFO   ] Using GROMACS version > 5.x.x!
    
15. [INFO   ] gmx found! Using /home/ubuntu/下载/gromacs-2024.6/build/bin/gmx
    
16. [INFO   ] Checking external programs...Done.
    
17. 
    
18. [INFO   ] Building AMBER topologies from GROMACS files...
    
19. [INFO   ] Get PDB files from GROMACS structures files...
    
20. [INFO   ] Making gmx_MMPBSA index for complex...
    
21. [INFO   ] Normal Complex: Saving group Protein_MOL (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
    
22. [INFO   ] No receptor structure file was defined. Using ST approach...
    
23. [INFO   ] Using receptor structure from complex to generate AMBER topology
    
24. [INFO   ] Normal Receptor: Saving group Protein (1) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
    
25. [INFO   ] No ligand structure file was defined. Using ST approach...
    
26. [INFO   ] Using ligand structure from complex to generate AMBER topology
    
27. [INFO   ] Normal Ligand: Saving group MOL (13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
    
28. [INFO   ] Checking the structures consistency...
    
29. [INFO   ]
    
30. [INFO   ] Using topology conversion. Setting radiopt = 0...
    
31. [INFO   ] Building Normal Complex Amber topology...
    
32.   File "/home/ubuntu/PyMOL_3.1.1_Linux_x86_64/PyMOL_3.1.1_Linux_x86_64/pymol/envs/ana/bin/gmx_MMPBSA", line 7, in <module>
    
33.     sys.exit(gmxmmpbsa())
    
34.              ^^^^^^^^^^^
    
35.   File "/home/ubuntu/PyMOL_3.1.1_Linux_x86_64/PyMOL_3.1.1_Linux_x86_64/pymol/envs/ana/lib/python3.11/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
    
36.     app.make_prmtops()
    
37.   File "/home/ubuntu/PyMOL_3.1.1_Linux_x86_64/PyMOL_3.1.1_Linux_x86_64/pymol/envs/ana/lib/python3.11/site-packages/GMXMMPBSA/main.py", line 681, in make_prmtops
    
38.     self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
    
39.                                                                           ^^^^^^^^^^^^^^^^^^^^^^^
    
40.   File "/home/ubuntu/PyMOL_3.1.1_Linux_x86_64/PyMOL_3.1.1_Linux_x86_64/pymol/envs/ana/lib/python3.11/site-packages/GMXMMPBSA/make_top.py", line 125, in buildTopology
    
41.     tops = self.gmxtop2prmtop()
    
42.            ^^^^^^^^^^^^^^^^^^^^
    
43.   File "/home/ubuntu/PyMOL_3.1.1_Linux_x86_64/PyMOL_3.1.1_Linux_x86_64/pymol/envs/ana/lib/python3.11/site-packages/GMXMMPBSA/make_top.py", line 566, in gmxtop2prmtop
    
44.     com_top = self.cleantop(self.FILES.complex_top, self.indexes['COM']['COM'])
    
45.               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    
46.   File "/home/ubuntu/PyMOL_3.1.1_Linux_x86_64/PyMOL_3.1.1_Linux_x86_64/pymol/envs/ana/lib/python3.11/site-packages/GMXMMPBSA/make_top.py", line 853, in cleantop
    
47.     rtemp_top = parmed.gromacs.GromacsTopologyFile(temp_top.name)
    
48.                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    
49.   File "/home/ubuntu/PyMOL_3.1.1_Linux_x86_64/PyMOL_3.1.1_Linux_x86_64/pymol/envs/ana/lib/python3.11/site-packages/parmed/gromacs/gromacstop.py", line 346, in __init__
    
50.     self.read(fname, defines, parametrize)
    
51.   File "/home/ubuntu/PyMOL_3.1.1_Linux_x86_64/PyMOL_3.1.1_Linux_x86_64/pymol/envs/ana/lib/python3.11/site-packages/parmed/gromacs/gromacstop.py", line 407, in read
    
52.     bond, bond_type = self._parse_bonds(line, bond_types, molecule.atoms)
    
53.                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    
54.   File "/home/ubuntu/PyMOL_3.1.1_Linux_x86_64/PyMOL_3.1.1_Linux_x86_64/pymol/envs/ana/lib/python3.11/site-packages/parmed/gromacs/gromacstop.py", line 600, in _parse_bonds
    
55.     funct = int(words[2])
    
56.                 ~~~~~^^^
    
57. IndexError: list index out of range
    
58. Exiting. All files have been retained.

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捣鼓了一番找到一个解决方法。

笔者根据论坛中先前的讨论Gromacs额外水模型使用疑问6楼社长的课件，修改了从论坛中获取的适用于Gromacs2025之前版本的Amber19SB力场及其配套相关力场力场中的
opc.itp
和ffnonbonded.itp
之后便可正常进行MMPBSA分析了。在此感谢社长面对基础问题仍躬身指导和喵老师无私奉献劳动成果提供的力场。

顺带一提，由于该力场在笔者模拟时出现低浓度结晶现象，故而笔者将钠离子和氯离子的参数使用KBFF力场中的对应参数以作替代。



如各位老师发现有问题，恳请指教。