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标题: 用oniom做QMMM时候，提取键连接方式时出错 [打印本页]

作者
Author: Emma_Zzz 时间: 2019-1-17 23:17
标题: 用oniom做QMMM时候，提取键连接方式时出错
(, 下载次数 Times of downloads: 46) (, 下载次数 Times of downloads: 34) 请问一下，我在提取键的连接方式的过程中出现了图中提示，意思是找不到键的参数所以赋予了虚拟值吗？请问这个虚拟值可以用吗。然后我将这些键信息帖在了输入文件末尾，gjf文件如下
%chk=13E1.chk
%nprocshared=8
# p oniom(b3lyp/6-311G**:amber=hardfirst) nosymm geom=connectivity iop(2/15=3) test opt=quadmac

remark line goes here

0 1 0 1 0 1
C-ca--0.136271                                           -1 4.74000000 8.42000000 0.17500000 L
C-ca--0.217096                                           -1 5.21000000 7.46000000 1.07500000 L
H-ha-0.191740                                           -1 4.46000000 6.94000000 1.67500000 L
H-ha-0.143885                                           -1 3.67000000 8.56000000 0.05500000 L
C-ca--0.095101                                           -1 5.57000000 9.28000000 -0.49500000 L
H-ha-0.137482                                           -1 5.19000000 10.11000000 -1.07500000 L
C-ca--0.235974                                           -1 6.96000000 9.13000000 -0.31500000 L
H-ha-0.163227                                           -1 7.57000000 9.82000000 -0.88500000 L
C-ca-0.068796                                           -1 7.48000000 8.17000000 0.53500000 L
C-ca-0.048744                                           -1 8.89000000 7.92000000 0.66500000 L
C-ca-0.081330                                           -1 9.36000000 6.92000000 1.53500000 L
.

.
.
HrmBnd1 ca cc cf    0.0000    0.0000
HrmBnd1 ca cc cc 67.7000 111.0400
HrmBnd1 cc cc cf 65.6000 123.9200
HrmBnd1 cc cf ha 49.3000 119.1600
HrmBnd1 cc cf cd    0.0000    0.0000
HrmBnd1 cf cd ss    0.0000    0.0000
HrmBnd1 cf cd cc    0.0000    0.0000
HrmBnd1 ha cf cd    0.0000    0.0000
HrmBnd1 cd ss cd 67.0000 89.9100
HrmBnd1 cd cc ha 48.4000 122.8900
HrmBnd1 cd cc cc 68.2000 114.1900
HrmBnd1 ss cd cc 63.6000 118.1700
HrmBnd1 ss cd cd 63.8000 115.0200
HrmBnd1 cc cc ss 63.8000 115.0200
HrmBnd1 ha cc cc 46.6000 123.7400
HrmBnd1 cc ss cc 67.0000 89.9100
HrmBnd1 cc cd cd 68.2000 114.1900
HrmBnd1 ss cc cd 63.6000 118.1700
HrmBnd1 ss cc ca 64.9000 111.0900
HrmBnd1 cd cd c3 64.7000 115.9700
HrmBnd1 cd c3 ca 65.2000 108.0800
HrmBnd1 cd cc ca 68.2000 113.5100
HrmBnd1 c3 cd cc 64.8000 119.4500
HrmBnd1 c3 ca ca 63.8000 120.6300
HrmBnd1 ca c3 ca 63.6000 112.4700
HrmBnd1 ca c3 hc 47.0000 110.1500
HrmBnd1 hc c3 hc 39.4000 108.3500

最后Log文件的报错信息如下：

1025       6       1000       1.160000 -3.250000  -19.235000
1026       7 90000002       0.650000 -2.280000  -19.045000
1027       6       1000       2.680000 -4.410000  -20.545000
1028       7 90000002       3.260000 -4.390000  -21.515000
1029       6 20001003       2.010000 -7.000000  -19.085000
1030       6 20001003       1.130000 -7.950000  -18.645000
1031       6 20001003       1.210000 -9.310000  -19.135000
1032       6 20001003       0.180000  -10.260000  -18.925000
1033       6 20001003       0.200000  -11.510000  -19.545000
1034       6 20001003       1.220000  -11.890000  -20.385000
1035       6 20001003       2.260000  -10.960000  -20.555000
1036       1 20001033       3.050000  -11.280000  -21.235000
1037       1 20001033       1.170000  -12.830000  -20.935000
1038       1 20001033    -0.720000  -12.090000  -19.465000
1039       1 20001033    -0.740000  -10.040000  -18.395000
1040       6 20001003       2.330000 -9.690000  -19.915000
1041       6 20001003       3.430000 -8.780000  -20.025000
1042       6 20001003       3.280000 -7.420000  -19.465000
1043       6 20001003       4.400000 -6.580000  -19.425000
1044       1 20001033       4.310000 -5.550000  -19.075000
1045       6 20001003       5.650000 -7.080000  -19.845000
1046       1 20001033       6.490000 -6.390000  -19.905000
1047       6 20001003       5.800000 -8.270000  -20.415000
1048       1 20001033       6.750000 -8.600000  -20.805000
1049       6 20001003       4.710000 -9.160000  -20.515000
1050       1 20001033       4.850000  -10.140000  -20.945000
---------------------------------------------------------------------
Rotational constants (GHZ):    0.0006196    0.0003837    0.0003317
ONIOM: saving gridpoint 17
ONIOM: generating point  3 -- low level on real system.
Standard basis: Dummy (5D, 7F)
  1050 basis functions,  1050 primitive gaussians,  1050 cartesian basis functions
833 alpha electrons    833 beta electrons
   nuclear repulsion energy    53619.7660872314 Hartrees.
NAtoms= 1050 NActive= 1050 NUniq= 1050 SFac= 1.00D+00 NAtFMM= 60 NAOKFM=T Big=T
Integral buffers will be 131072 words long.
Raffenetti 1 integral format.
Two-electron integral symmetry is turned off.
AMBER calculation of energy and first derivatives.
Atom I= 27 has type=       1000.
MMAtmC is confused about an atom type.
Error termination via Lnk1e in /opt/soft/g09/G09E/g09e/l402.exe at Wed Jan  2 23:00:29 2019.

请问究竟是哪一步做错了呢，怎样改进

（新手不太懂望谅解）

作者
Author: 柒月小鱼 时间: 2019-1-18 09:59
我不太知道哈，我也是用好久的TAO感觉总是过不去
你这个有什么特殊的原子么，MMAtmC is confused about an atom type.
我感觉TAO补的参数不一定完全合适，可以用AMBER自己对照着参数看看哈

作者
Author: Emma_Zzz 时间: 2019-1-21 09:14

柒月小鱼发表于 2019-1-18 09:59
我不太知道哈，我也是用好久的TAO感觉总是过不去
你这个有什么特殊的原子么，MMAtmC is confused about an ...

没有什么特殊原子啊，C,H,O,N,S。
Atom I= 27 has type= 1000.
MMAtmC is confused about an atom type.
根据这个报错信息，找到是氰基里面的碳原子有问题，但是不知道怎么改啊

作者
Author: 柒月小鱼 时间: 2019-1-21 15:10

Emma_Zzz 发表于 2019-1-21 09:14
没有什么特殊原子啊，C,H,O,N,S。
Atom I= 27 has type= 1000. ...

你用parmchk2输出所有的AMBER参数看看
然后对照着http://bbs.keinsci.com/thread-942-1-1.html
看看有没有收获，不管怎么样，告诉我下结果哈

作者
Author: SimoneSan 时间: 2022-7-7 16:51
Hi,
Sorry I don't speak Chinese, so I'm writing here in english:

I'm trying to perform the ONIOM method for an enzymatic reaction: I've prepared all used TAO toolkit and Molup VMD tool (https://biosim.pt/molup/). All the parameters seems ok, the calculation begin but after few second give this kind of error:
"MMAtmC is confused about an atom type
Atom I= 4691 has type= 1000."

I don't know why Gaussian assign a strange code to the atom type of some of the carbon of my ligand
I'm attaching here the input and output I've obtained. https://easyupload.io/m/228w2z
Thank you

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