在能量最小化的时候报错moleculetype H is redefined

Lemon97z

我使用packmol建了盒子pdb转换为了gro文件，使用0.8 OPLS-2009IL 中TFSI-和NO3-的拓扑文件，用ligpargen产生了FEC、DMC、DMA分子的拓扑，把atomtypes中内容剪切到另一个新的itp文件中include到了主top， 在进行gmx grompp -f em.mdp -c mix_ele.gro -p mix_topol.top -o em.tpr 的时候出现了以下警告和报错 ，把H改为FEC仍有moleculetype FEC is redefined的报错，请问是为什么呢 ？附件提供了我的参数文件

1. WARNING 1 [file FEC_atomtypes.itp, line 2]:
   
2.   Overriding atomtype opls_802
   
3. 
   
4. 
   
5. WARNING 2 [file FEC_atomtypes.itp, line 3]:
   
6.   Overriding atomtype opls_801
   
7. 
   
8. 
   
9. WARNING 3 [file FEC_atomtypes.itp, line 4]:
   
10.   Overriding atomtype opls_809
    
11. 
    
12. 
    
13. WARNING 4 [file FEC_atomtypes.itp, line 5]:
    
14.   Overriding atomtype opls_803
    
15. 
    
16. 
    
17. WARNING 5 [file FEC_atomtypes.itp, line 6]:
    
18.   Overriding atomtype opls_808
    
19. 
    
20. 
    
21. WARNING 6 [file FEC_atomtypes.itp, line 7]:
    
22.   Overriding atomtype opls_805
    
23. 
    
24. 
    
25. WARNING 7 [file FEC_atomtypes.itp, line 8]:
    
26.   Overriding atomtype opls_804
    
27. 
    
28. 
    
29. WARNING 8 [file FEC_atomtypes.itp, line 9]:
    
30.   Overriding atomtype opls_807
    
31. 
    
32. WARNING 9 [file FEC_atomtypes.itp, line 10]:
    
33.   Overriding atomtype opls_806
    
34. 
    
35. 
    
36. WARNING 10 [file FEC_atomtypes.itp, line 11]:
    
37.   Overriding atomtype opls_800
    
38. 
    
39. 
    
40. WARNING 11 [file DMA_atomtypes.itp, line 3]:
    
41.   Overriding atomtype opls_807
    
42. 
    
43. 
    
44. WARNING 12 [file DMA_atomtypes.itp, line 4]:
    
45.   Overriding atomtype opls_802
    
46. 
    
47. 
    
48. WARNING 13 [file DMA_atomtypes.itp, line 5]:
    
49.   Overriding atomtype opls_806
    
50. 
    
51. 
    
52. WARNING 14 [file DMA_atomtypes.itp, line 6]:
    
53.   Overriding atomtype opls_803
    
54. 
    
55. 
    
56. WARNING 15 [file DMA_atomtypes.itp, line 8]:
    
57.   Overriding atomtype opls_809
    
58. 
    
59. 
    
60. WARNING 16 [file DMA_atomtypes.itp, line 9]:
    
61.   Overriding atomtype opls_801
    
62. 
    
63. WARNING 17 [file DMA_atomtypes.itp, line 10]:
    
64.   Overriding atomtype opls_804
    
65. 
    
66. 
    
67. WARNING 18 [file DMA_atomtypes.itp, line 11]:
    
68.   Overriding atomtype opls_808
    
69. 
    
70. 
    
71. WARNING 19 [file DMA_atomtypes.itp, line 14]:
    
72.   Overriding atomtype opls_800
    
73. 
    
74. 
    
75. WARNING 20 [file DMA_atomtypes.itp, line 16]:
    
76.   Overriding atomtype opls_805
    
77. 
    
78. Generated 349030 of the 349030 non-bonded parameter combinations
    
79. Generating 1-4 interactions: fudge = 0.5
    
80. Generated 349030 of the 349030 1-4 parameter combinations
    
81. 
    
82. ERROR 1 [file FEC.itp, line 8]:
    
83.   moleculetype H is redefined
    
84. 
    
85. There were 20 warnings
    
86. 
    
87. -------------------------------------------------------
    
88. Program:     gmx grompp, version 2018.8
    
89. Source file: src/gromacs/gmxpreprocess/toppush.cpp (line 1469)
    
90. 
    
91. Fatal error:
    
92. There was 1 error in input file(s)
    

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Lemon97z

sobereva 发表于 2022-11-5 21:57
始终记住grompp看到的是所有include的文件全都展开后的文件
肯定是原子类型和moleculetype都被重复定义了 ...

谢谢老师的回答，问题解决了！
C:\Users\86133\Desktop\processed.png

sobereva

始终记住grompp看到的是所有include的文件全都展开后的文件
肯定是原子类型和moleculetype都被重复定义了，仔细检查拓扑文件便知，搞清楚各个文件都有哪些字段
另外，grompp加-pp选项可以输出一个processed.top，是预处理器处理top文件后的结果，所有include的文件都会被展开，有助于你检查