由smiles字符串直接生成gromacs文件的脚本

Puying

分享一个由smiles字符串直接生成跑分子动力学所有的文件的脚本。

需要电脑安装若干软件，分别是sobtop，xtb，gromacs，obabel，packmol和Multiwfn

obabel负责把字符串转为3d结构，然后交给xtb进行优化。优化完成的分子交给sobtop生成gaff力场结构，以及交给packmol来塞进模拟盒子。脚本同时也会生成gaussian的输入文件，计算完成后交给Multiwfn进行resp电荷计算。电荷仍然需要手动粘贴进itp文件里面。

目前脚本写的比较简单，只支持一种分子。可以根据脚本改进支持多种分子。

1. ╰─$ ./smiles2box-bash.sh                                       
   
2. please input the SMILES:
   
3. cccccc
   
4. please input the number of molecules:
   
5. 50
   
6. please input the cell length:
   
7. 50
   
8. Paths of packages:
   
9. the path of obabel is /opt/openbabel/bin/obabel
   
10. 
    
11. the path of packmol is /opt/packmol/packmol
    
12. 
    
13. the path of xtb is /opt/xtb-6.6.1/bin/xtb
    
14. 
    
15. the path of gmx is /opt/gmx2022/bin/gmx
    
16. 
    
17. the path of sobtop is /opt/sobtop_1.0(dev3.1)/sobtop
    
18. 
    
19. Please confirm that the paths are all right.
    
20. ============= generating xyz file with obabel =============
    
21. 1 molecule converted
    
22. mol1.xyz generated
    
23. ============= optimizing xyz file with xtb =============
    
24. normal termination of xtb
    
25. xtb optimization finished
    
26. 
    
27. 
    
28. 
    
29. ===============gaussian gjf file generation================
    
30. =================================================
    
31. 
    
32. 
    
33. ================ Packmol part ======================
    
34. 1 molecule converted
    
35.                      :-) GROMACS - gmx editconf, 2022.5 (-:
    
36. 
    
37. Executable:   /opt/gmx2022/bin/gmx
    
38. Data prefix:  /opt/gmx2022
    
39. Working dir:  /home/chenxi/Templates/smiles2box/pack_mol
    
40. Command line:
    
41.   gmx editconf -f ./mol1_multi.pdb -o mol1_multi.gro -box 5 5 5
    
42. 
    
43. Note that major changes are planned in future for editconf, to improve usability and utility.
    
44. WARNING: all CONECT records are ignored
    
45. Read 700 atoms
    
46. No velocities found
    
47.     system size :  4.945  4.863  4.899 (nm)
    
48.     center      :  2.836  2.467  2.505 (nm)
    
49.     box vectors :  0.000  0.000  0.000 (nm)
    
50.     box angles  :   0.00   0.00   0.00 (degrees)
    
51.     box volume  :   0.00               (nm^3)
    
52.     shift       : -0.336  0.033 -0.005 (nm)
    
53. new center      :  2.500  2.500  2.500 (nm)
    
54. new box vectors :  5.000  5.000  5.000 (nm)
    
55. new box angles  :  90.00  90.00  90.00 (degrees)
    
56. new box volume  : 125.00               (nm^3)
    
57. 
    
58. GROMACS reminds you: "Is That a Real Poncho ?" (F. Zappa)
    
59. 
    
60. =================packmol finished================
    
61. 
    
62. 
    
63. ================top file generation=================
    
64. 1 molecule converted
    
65. mol2 file generated
    
66. the path of sobtop is /opt/sobtop_1.0(dev3.1)/
    
67. ===========================================
    

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exity

越来越多的脚本被开发出来了，越点越开心，感觉自己像一个废物。T_T

Puying

加入了for循环，可以支持多种分子packing