ONIOM结构优化中遇到的问题

zcf · 发表于 Post on 2015-1-16 20:19:36

求助个ONIOM结构优化中的问题：
配体与蛋白分子的金属中心作用，用ONIOM结构优化，初始结构从晶体结构中提取，
关键词： #p opt oniom(hf/6-31g*:amber=hardfirst) nosymm geom=connectivity iop(2
/15=3,1/8=2) scf=(maxcycle=100,xqc) test
错误提示： Largest displacement in micro-iterations: 0.00D+00
Max number of microiteration restarts exceeded.
Error termination via Lnk1e in l103.exe

尝试过用PM6，b3lyp，M06等方法都不行，不知道是什么原因？？？

sobereva · 发表于 Post on 2015-1-16 21:17:41

最好把输入输出文件都贴上来

zcf · 发表于 Post on 2015-1-16 22:59:01

谢谢Sobereva老师！输入文件：
%chk=4exs1b_part3b.chk
%mem=3700MB
%nprocshared=16
#p opt=quadmac oniom(pm6:amber=hardfirst) nosymm geom=connectivity
iop(2/15=3,5/13=1,1/8=2)

ONIOM

-9 1 -2 1 -2 1
O-O1--0.933389 0  -53.99300000 11.20900000  -29.32000000 H
C-C1-1.705329 0  -54.52700000 12.05600000  -30.02700000 H
C-C2-0.063733 0  -53.67000000 12.95700000  -30.88900000 H
C-C3--0.228318 0  -52.67500000 13.84600000  -30.13300000 H
S-S1--0.851277 0  -53.25000000 14.73700000  -28.66000000 H
C-C4--0.442602 0  -52.86300000 12.08200000  -31.84900000 H
N-N1--0.665757 0  -55.87000000 12.16300000  -30.11000000 H
C-C5--0.378208 0  -56.73700000 11.26400000  -29.33200000 H
C-C6-1.045541 0  -56.57300000 9.82100000  -29.75600000 H
O-O2--0.764080 0  -56.04800000 9.56600000  -30.86900000 H
O-O3--0.764080 0  -56.95800000 8.91600000  -28.97500000 H
C-C7-0.166268 0  -56.65200000 13.09500000  -30.93300000 H
C-C8-0.545014 0  -58.11900000 12.83900000  -30.60700000 H
C-C9--0.089004 0  -58.17400000 11.69600000  -29.61400000 H
H-H1--0.097172 0  -58.57100000 12.08900000  -28.70100000 H
H-H2--0.097172 0  -58.66100000 10.87700000  -30.10100000 H
H-H3--0.134768 0  -58.48800000 13.71000000  -30.10700000 H
H-H4--0.134768 0  -58.58800000 12.49900000  -31.50700000 H
H-H5--0.151293 0  -56.41900000 14.08600000  -30.60300000 H
H-H6--0.151293 0  -56.50000000 12.82300000  -31.95700000 H
H-H7-0.135219 0  -56.48300000 11.32700000  -28.29500000 H
....坐标参数
输出文件
。。。。
0.22763780 38.3408599 ----
409 0 0 T F  3.57D-02 0.94207591 0.03683907 0.14220102 0.00812089 6.1809801 ----
410 0 0 T F  2.93D-01 0.94207591 0.03683907 0.04171637 0.00238236 1.5876850 ----
411 0 0 F F  2.32D-02 0.94207591 0.03683907 0.00096613 0.00005517 1.5701006 ---+
412 0 0 F T  1.00D+00 1.08162483 0.03770794 1.97441248 0.11412456 1.5700995 ----
413 0 0 T F  1.29D-01 1.08162483 0.03770794 0.25521933 0.01475213 6.9839759 ----
414 0 0 F F -1.86D-02 1.08162483 0.03770794 0.00475230 0.00027469 1.0319903 ----
415 0 0 F F -3.95D-01 1.08162483 0.03770794 0.00187566 0.00010842 1.0318259 ---+
Large rigid frag rotational dispacement found.
Stepping infringing coordinate back!
416 0 0 F T  1.00D+00 5.80607809 0.1788723841.43167396 2.38720002 1.0317156 XXXX
Largest displacement in micro-iterations:  8.74D+00
Fragment:  1 Trans scale: 1.0000 Rot scale: 0.0345
NRF= 1 NRA=  89 NVA= 877 HaveQM=F NVQ=    0
Convergence limit is  0.300E-04 MaxStp=  8313 StMxLn= 1.00D-04 StpMin= 1.00D-06.
Convergence criteria          0.00014584 0.00003000 0.00018000 0.00012000
  Step  NS  ND Rises OKQ Scale  Max. Force  RMS Force Max. Disp.  RMS Disp.    Energy Flag
   1 0 0 F T  1.00D+00 5.80607809 0.17887238 5.80607809 0.11263328 1.0317156 ----
   2 0 0 T F  6.58D-01 5.80607809 0.17887238 3.81916246 0.07408870************* ----
   3 0 0 T F  6.34D-01 5.80607809 0.17887238 2.42169260 0.0469789015056.9959892 ----
   4 0 0 T F  4.69D-01 5.80607809 0.17887238 1.13554286 0.02202862 24.6959511 ----
   5 0 0 T F  2.60D-01 5.80607809 0.17887238 0.29492424 0.00572129 4.0952638 ----
   6 0 0 T F  2.80D-01 5.80607809 0.17887238 0.08246401 0.00159974 1.5848267 ----
Large rigid frag rotational dispacement found.
Stepping infringing coordinate back!
   7 0 0 F T  1.00D+0057.19983141 1.53900648***********10.70549462 -1.9392434 XXXX
Largest displacement in micro-iterations:  8.25D-02
Fragment:  1 Trans scale: 1.0000 Rot scale: 0.0345
NRF= 1 NRA=  89 NVA= 877 HaveQM=F NVQ=    0
Convergence limit is  0.300E-04 MaxStp=  8313 StMxLn= 1.00D-04 StpMin= 1.00D-06.
Convergence criteria          0.00014584 0.00003000 0.00018000 0.00012000
  Step  NS  ND Rises OKQ Scale  Max. Force  RMS Force Max. Disp.  RMS Disp.    Energy Flag
   1 0 0 F T  1.00D+0057.19983141 1.5390064857.19983141 1.07193564 -1.9392434 ----
   2 0 0 T F  1.65D-0157.19983141 1.53900648 9.41720800 0.17648026 8291.1790555 ----
   3 0 0 T F  5.00D-0157.19983141 1.53900648 4.70860400 0.08824013************* ----
   4 0 0 T F  6.37D-0157.19983141 1.53900648 3.00067793 0.05623327************* ----
   5 0 0 T F  6.19D-0157.19983141 1.53900648 1.85662022 0.03479341  775.6774860 ----
   6 0 0 T F  3.19D-0157.19983141 1.53900648 0.59169872 0.01108855 11.9334453 ----
   7 0 0 T F  2.94D-0157.19983141 1.53900648 0.17408014 0.00326229 3.0133270 ----
   8 0 0 T F  2.60D-0157.19983141 1.53900648 0.04524374 0.00084788 1.3390475 ----
   9 0 0 F F -2.69D-0157.19983141 1.53900648 0.01218517 0.00022835  -20.8527917 ----
10 0 0 F F -3.15D-0157.19983141 1.53900648 0.00383815 0.00007193  -30.1047872 ---+
Large rigid frag rotational dispacement found.
Stepping infringing coordinate back!
11 0 0 F T  1.00D+00******************************************** -119.9943353 XXXX
Largest displacement in micro-iterations:  3.71D-02
Fragment:  1 Trans scale: 1.0000 Rot scale: 0.0345
NRF= 1 NRA=  89 NVA= 877 HaveQM=F NVQ=    0
Convergence limit is  0.300E-04 MaxStp=  8313 StMxLn= 1.00D-04 StpMin= 1.00D-06.
Convergence criteria          0.00014584 0.00003000 0.00018000 0.00012000
  Step  NS  ND Rises OKQ Scale  Max. Force  RMS Force Max. Disp.  RMS Disp.    Energy Flag
Large rigid frag rotational dispacement found.
Stepping infringing coordinate back!
   1 0 0 F T  1.00D+00******************************************** -119.9943353 XXXX
Largest displacement in micro-iterations:  0.00D+00
Fragment:  1 Trans scale: 1.0000 Rot scale: 0.0345
NRF= 1 NRA=  89 NVA= 877 HaveQM=F NVQ=    0
Convergence limit is  0.300E-04 MaxStp=  8313 StMxLn= 1.00D-04 StpMin= 1.00D-06.
Convergence criteria          0.00014584 0.00003000 0.00018000 0.00012000
  Step  NS  ND Rises OKQ Scale  Max. Force  RMS Force Max. Disp.  RMS Disp.    Energy Flag
Large rigid frag rotational dispacement found.
Stepping infringing coordinate back!
   1 0 0 F T  1.00D+00******************************************** -119.9943353 XXXX
Largest displacement in micro-iterations:  0.00D+00
Fragment:  1 Trans scale: 1.0000 Rot scale: 0.0345
NRF= 1 NRA=  89 NVA= 877 HaveQM=F NVQ=    0
Convergence limit is  0.300E-04 MaxStp=  8313 StMxLn= 1.00D-04 StpMin= 1.00D-06.
Convergence criteria          0.00014584 0.00003000 0.00018000 0.00012000
  Step  NS  ND Rises OKQ Scale  Max. Force  RMS Force Max. Disp.  RMS Disp.    Energy Flag
Large rigid frag rotational dispacement found.
Stepping infringing coordinate back!
   1 0 0 F T  1.00D+00******************************************** -119.9943353 XXXX
Largest displacement in micro-iterations:  0.00D+00
Fragment:  1 Trans scale: 1.0000 Rot scale: 0.0345
NRF= 1 NRA=  89 NVA= 877 HaveQM=F NVQ=    0
Convergence limit is  0.300E-04 MaxStp=  8313 StMxLn= 1.00D-04 StpMin= 1.00D-06.
Convergence criteria          0.00014584 0.00003000 0.00018000 0.00012000
  Step  NS  ND Rises OKQ Scale  Max. Force  RMS Force Max. Disp.  RMS Disp.    Energy Flag
Large rigid frag rotational dispacement found.
Stepping infringing coordinate back!
   1 0 0 F T  1.00D+00******************************************** -119.9943353 XXXX
Largest displacement in micro-iterations:  0.00D+00
Fragment:  1 Trans scale: 1.0000 Rot scale: 0.0345
NRF= 1 NRA=  89 NVA= 877 HaveQM=F NVQ=    0
Convergence limit is  0.300E-04 MaxStp=  8313 StMxLn= 1.00D-04 StpMin= 1.00D-06.
Convergence criteria          0.00014584 0.00003000 0.00018000 0.00012000
  Step  NS  ND Rises OKQ Scale  Max. Force  RMS Force Max. Disp.  RMS Disp.    Energy Flag
Large rigid frag rotational dispacement found.
Stepping infringing coordinate back!
   1 0 0 F T  1.00D+00******************************************** -119.9943353 XXXX
Largest displacement in micro-iterations:  0.00D+00
Fragment:  1 Trans scale: 1.0000 Rot scale: 0.0345
NRF= 1 NRA=  89 NVA= 877 HaveQM=F NVQ=    0
Convergence limit is  0.300E-04 MaxStp=  8313 StMxLn= 1.00D-04 StpMin= 1.00D-06.
Convergence criteria          0.00014584 0.00003000 0.00018000 0.00012000
  Step  NS  ND Rises OKQ Scale  Max. Force  RMS Force Max. Disp.  RMS Disp.    Energy Flag
Large rigid frag rotational dispacement found.
Stepping infringing coordinate back!
   1 0 0 F T  1.00D+00******************************************** -119.9943353 XXXX
Largest displacement in micro-iterations:  0.00D+00
Fragment:  1 Trans scale: 1.0000 Rot scale: 0.0345
NRF= 1 NRA=  89 NVA= 877 HaveQM=F NVQ=    0
Convergence limit is  0.300E-04 MaxStp=  8313 StMxLn= 1.00D-04 StpMin= 1.00D-06.
Convergence criteria          0.00014584 0.00003000 0.00018000 0.00012000
  Step  NS  ND Rises OKQ Scale  Max. Force  RMS Force Max. Disp.  RMS Disp.    Energy Flag
Large rigid frag rotational dispacement found.
Stepping infringing coordinate back!
   1 0 0 F T  1.00D+00******************************************** -119.9943353 XXXX
Largest displacement in micro-iterations:  0.00D+00
Max number of microiteration restarts exceeded.
Error termination via Lnk1e in /g09/l103.exe at Fri Jan 16 20:54:08 2015.
Job cpu time:  0 days  0 hours  4 minutes 28.5 seconds.
File lengths (MBytes):  RWF= 138 Int=    0 D2E=    0 Chk= 104 Scr=    1
完整的文件太大了，这是相关的部分。

sobereva · 发表于 Post on 2015-1-17 00:18:52

你就用论坛的附件方式发上来就行了（最好先压缩一下），不要直接贴内容。

zcf · 发表于 Post on 2015-1-17 00:38:04

这是输入和输出文件

zcf · 发表于 Post on 2015-1-17 00:38:44

添加不了附件呢？点击添加附件，没反应？？

sobereva · 发表于 Post on 2015-1-17 00:47:22

估计是你的浏览器问题，换个浏览器吧

zcf · 发表于 Post on 2015-1-17 00:51:26

我给您传到思想家公社了，麻烦您去看一下吧，可能宿舍的网太慢了吧

zcf · 发表于 Post on 2015-1-17 11:32:21

sobereva 发表于 2015-1-17 00:18
你就用论坛的附件方式发上来就行了（最好先压缩一下），不要直接贴内容。

这是ONIOM的输入和输出文件，麻烦Sob老师帮忙解答一下，谢谢！

sobereva · 发表于 Post on 2015-1-17 21:47:49

你的体系太大了，很难说原因，最好先简化简化，把距离高层比较远的残基全都先删掉试试。
即便是ONIOM，直接计算这么大的体系也不妥，也照样需要先简化一下体系，而不是直接就算整个蛋白。
或者先尝试直接用MM计算来优化整个体系，看看能否顺利进行。能行的话再转到ONIOM处理。

zcf · 发表于 Post on 2015-1-19 15:57:42

谢谢Sobereva老师！这里提取的12A以内的部分，我改成6A试试吧。再次感谢！

jackieiii · 发表于 Post on 2018-8-28 09:07:21

想问一下你最后怎么解决的？我也遇到了相同的问题。

Emma_Zzz · 发表于 Post on 2019-1-25 09:35:36

你好，请问你最后是怎么解决的？我简化体系之后，依然出现了这样的报错信息

Emma_Zzz · 发表于 Post on 2019-3-5 17:20:52

jackieiii 发表于 2018-8-28 09:07
想问一下你最后怎么解决的？我也遇到了相同的问题。

你好，请问你的这个问题解决了吗

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[新手求助] ONIOM结构优化中遇到的问题

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