运行oniom计算
运行oniom计算
UFF
最省事的一集
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# opt oniom(hf/3-21g:uff) geom=connectivity
Title Card Required
0 1 0 1 0 1
C-C_3 0 0.26396373 -0.76918113 1.35914510 L
S-S_3+2 0 0.26396373 0.42288469 0.00000000 L
...
H-H_ 0 3.09572041 3.06530397 -3.12155991 H
H-H_ 0 4.11373536 1.90760083 -2.19496084 H
H-H_ 0 2.30436088 1.82578593 -2.08403683 H
1 2 1.0 5 1.0 6 1.0 7 1.0
2 3 1.0 4 2.0
...
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Amber
首先，原子类型的指定是第一个问题：
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# opt oniom(hf/3-21g:amber=SoftFirst) geom=connectivity
Title Card Required
0 1 0 1 0 1
C-CT 0 -1.77321200 -1.40136100 -0.60878200 L
S- 0 -1.78789000 0.09788200 0.43239600 L
C-CT 0 -1.96683100 1.25588300 -0.96720800 L
O- 0 -3.30457900 0.01966700 0.67268000 L
H-H1 0 -0.82770000 -1.43975400 -1.18771800 L
H-H1 0 -1.82487700 -2.29705200 0.04405400 L
...
像这个S- 就是没能指认S的原子类型，需要手动指认。既然指认不了基本上就是缺参数，填上默认的拉倒吧。
继续提交，显然，刚刚瞎指认的类型是找不到力场参数的：
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Include all MM classes
Bondstretch undefined between atoms 2 4 S-O [L,L]
Bondstretch undefined between atoms 12 14 S-O [H,H] *
Angle bend undefined between atoms 1 2 4 CT-S-O [L,L,L]
Angle bend undefined between atoms 3 2 4 CT-S-O [L,L,L]
Angle bend undefined between atoms 11 12 14 CT-S-O [H,H,H] *
Angle bend undefined between atoms 13 12 14 CT-S-O [H,H,H] *
* These undefined terms cancel in the ONIOM expression.
MM function not complete
Error termination via Lnk1e in /apps/gaussian16//g16/l101.exe at Wed May 14 09:22:55 2025.
Job cpu time: 0 days 0 hours 0 minutes 9.1 seconds.
Elapsed time: 0 days 0 hours 0 minutes 0.3 seconds.
File lengths (MBytes): RWF= 6 Int= 0 D2E= 0 Chk= 2 Scr= 1
这个时候就要手动补力场参数了。
使用sobtop导出参数文件，找到缺的项：
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Number of bonds: 9
...
5 2S 3C 1.807843 1766.744 422.262
⇒ 6 2S 4O 1.515343 4175.575 997.986
7 3C 8H 1.097269 3163.068 755.991
8 3C 9H 1.098274 3140.462 750.588
9 3C 10H 1.098522 3134.395 749.138
Number of angles: 15
# Atoms Angle (Deg.) k (kJ/mol/rad^2 kcal/mol/rad^2)
...
7 1C 2S 3C 97.4939 1768.385 422.654
⇒ 8 1C 2S 4O 105.7596 1191.309 284.730
9 3C 2S 4O 105.7596 1191.309 284.730
...
力场参数写在拓扑关系的后面，同时加上amber=SoftFirst读取参数：
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# opt oniom(hf/3-21g:amber=SoftFirst) geom=connectivity
...
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HrmStr1 S O 997.986 1.515343
HrmBnd1 CT S O 284.730 105.7596
这样理论上就应当可以正常进行计算了。
电荷
但是这样还不够好，因为没有考虑静电相互作用，也没有考虑L层对H层的极化作用。
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# opt oniom(hf/3-21g:amber=SoftFirst)=embedcharge geom=connectivity
Title Card Required
0 1 0 1 0 1
C-CT--0.4129283248 0 -1.77321200 -1.40136100 -0.60878200 L
S-S-0.2986990408 0 -1.78789000 0.09788200 0.43239600 L
C-CT--0.4129283248 0 -1.96683100 1.25588300 -0.96720800 L
O-O--0.5383306306 0 -3.30457900 0.01966700 0.67268000 L
H-H1-0.1775813732 0 -0.82770000 -1.43975400 -1.18771800 L
H-H1-0.1775813732 0 -1.82487700 -2.29705200 0.04405400 L
H-H1-0.1775813732 0 -2.63192200 -1.42173900 -1.31341400 L
H-H1-0.1775813732 0 -2.15631500 2.27544300 -0.57262200 L
H-H1-0.1775813732 0 -1.02614700 1.27321300 -1.55500900 L
H-H1-0.1775813732 0 -2.80708200 0.96822800 -1.63471300 L
C-CT--0.4129283248 0 2.24434100 -0.20697400 -1.54439600 H
S-S-0.2986990408 0 2.53418900 -0.20802300 0.29493600 H
C-CT--0.4129283248 0 1.96508900 1.52928300 0.64961100 H
O-O--0.5383306306 0 1.34982000 -1.20819000 0.93358300 H
H-H1-0.1775813732 0 2.89248300 0.52457100 -2.00021900 H
H-H1-0.1775813732 0 2.47729800 -1.19881200 -1.89775700 H
H-H1-0.1775813732 0 1.20386600 0.01131400 -1.72598400 H
H-H1-0.1775813732 0 2.02074400 1.66406400 1.71810200 H
H-H1-0.1775813732 0 2.61804700 2.22118900 0.14168700 H
H-H1-0.1775813732 0 0.94256900 1.62879000 0.32082900 H
...
解决方法是给每个原子设置使用multiwfn计算的RESP电荷，并使用oniom=embedcharge设置电子嵌入。
其他问题
虽然历时半年终于能把ONIOM跑起来了，但水依然很深。
连原子类型都不认识怎么办？
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