Automated docking (DOCKER)#
自动对接（DOCKER）
Finding the right interaction pattern of various molecules can be a tedious task and is typically based on
chemical intuition. DOCKER is an energy driven algorithm to automatically dock atoms and moleuclar structures
to form encounter complexes and aggregates.
寻找各种分子间的合适相互作用模式是一项繁琐的任务，通常依赖于化学直觉。DOCKER 是一种能量驱动算法，能够自动对接原子和分子结构，形成遭遇复合物和聚集体。
Note 注释
Note that the DOCKER algorithm is not fully parallelized at the moment, yet limiting the size of treatable
systems. Full parallelization will be added in a future ORCA version.
请注意，DOCKER 算法目前尚未完全并行化，因此限制了可处理系统的规模。完整的并行化将在未来的 ORCA 版本中加入。
The DOCKER in combination with Grimmes' efficient GFNn-xTB methods (GFN1-xTB, GFN2-xTB, GFN0-xTB, GFN-FF) can
easily be envoked via simple input:
DOCKER 结合 Grimmes 的高效 GFNn-xTB 方法（GFN1-xTB、GFN2-xTB、GFN0-xTB、GFN-FF）可通过简单的输入轻松调用：
!DOCKER(GFN2-XTB)
%DOCKER
GUEST "guest.xyz"
END
*XYZFILE 0 1 host.xyz
Detailed functionality of DOCKER can be controlled via the %DOCKER block, for more information see the ORCA manual.
DOCKER 的详细功能可通过 %DOCKER 块进行控制，更多信息请参阅 ORCA 手册。
Example 1: Dimerization of Uracil#
示例 1：尿嘧啶的二聚化
As a simple example, we can use DOCKER to create structure candidates for the uracil dimer.
The used sample input looks like:
作为一个简单的示例，我们可以使用 DOCKER 来生成尿嘧啶二聚体的结构候选物。所用的示例输入如下：
! XTB PAL4
%DOCKER
GUEST "uracil.xyz"
END
*XYZFILE 0 1 uracil.xyz
This calculation will dock two uracil monomers at the GFN2-xTB level in the gas-phase. The output of this
calculations looks like:
此计算将在气相中以 GFN2-xTB 水平对接两个尿嘧啶单体。该计算的输出结果如下：
***************
* ORCA Docker *
***************
Reading guests from file uracil.xyz
Number of structures read from file 1
Charge and multiplicity of guest from input
Docking approach independent
Docking level normal
Optimizing host .... -24.614947 Eh
Optimizing guest .... -24.614947 Eh
Starting Docker
---------------
Guest structure .... structure number 1
Guest charge and multiplicity .... (0 , 1)
Final charge and multiplicity .... (0 , 1)
PES used during evolution .... GFN2-XTB
Setting random seed .... done
Creating spatial grid
Grid Max Dimension 12.50 Angs
Angular Grid Step 14.40 degrees
Cartesian Grid Step 0.50 Angs
Points per Dimension 25 points
Initializing workers
Population Density 0.50 worker/Ang^2
Population Size 123
Evolving structures
Minimization Algorithm mutant particle swarm
Min, Max Iterations (3 , 10)
Iter Emin avDE stdDE Time
(Eh) (Eh) (ang) (min)
-------------------------------------------------------
1 -49.254341 9.888241 3.233712 0.62
2 -49.258510 10.477635 3.390259 0.65
3 -49.258510 9.521873 2.969795 0.65
4 -49.258510 8.793785 2.942822 0.65
No new minimum found after 3 (MinIter) steps.
Total time for evolution 2.57 minutes
Running final optimization
Maximum number of structures 11
Minimum energy difference 0.10 kcal/mol
Maximum RMSD 0.25 Angs
Optimization strategy regular
Coordinate system redundant 2022
Fixed host false
Struc Eopt Interaction Energy Time
(Eh) (kcal/mol) (min)
------------------------------------------------
1 -49.248577 -11.723427 0.07
2 -49.250442 -12.893751 0.07
3 -49.245624 -9.870339 0.04
4 -49.252991 -14.493130 0.06
5 -49.248470 -11.656256 0.05
6 -49.259335 -18.474228 0.05
7 -49.259264 -18.429538 0.08
8 -49.254913 -15.699019 0.04
9 -49.254927 -15.708244 0.04
10 -49.241672 -7.390198 0.03
11 -49.246534 -10.441269 0.04
Time for 11 geometry optimizations: 0.58 minutes
All optimized structures saved to : orca.docker.struc1.allopt.xyz
-------------------------------------
LOWEST INTERACTION ENERGY: -18.474228 kcal/mol (structure 6)
-------------------------------------
Total time for docking: 3.19 minutes
The lowest energy structure was 1, with energy -49.259335.
Docked structures saved to orca.docker.xyz
****ORCA-DOCKER TERMINATED NORMALLY****
We see that DOCKER generated 11 candidate structures and identified structure 6 as the energetically lowest one
which is stored in orca.docker.xyz. All other structures after optimization can be found in orca.docker.struc1.allopt.xyz.
我们观察到 DOCKER 生成了 11 个候选结构，并识别出结构 6 为能量最低的结构，该结构存储在 orca.docker.xyz 中。所有经过优化的其他结构可在 orca.docker.struc1.allopt.xyz 中找到。
Fig. 1: Uracil dimer structures generated by DOCKER (duplicates removed) with relative energies in kcal/mol.
图 1：DOCKER 生成的尿嘧啶二聚体结构（重复项已去除），附有相对能量（单位：千卡/摩尔）。
Structures Example 1# 结构示例 1
Uracil 尿嘧啶
12
N -0.2707028 0.7632994 1.0276159
H -0.5957915 1.3097757 1.8163465
C -0.3386212 1.3810817 -0.2276640
O -0.7270425 2.5346295 -0.3329857
N 0.3638189 -1.2896563 0.1949192
H 0.0796815 0.9143946 -2.3190044
C 0.3781329 -0.7736192 -1.0714063
H 0.6499130 -1.4675080 -1.8526542
C 0.0669084 0.5154897 -1.3194961
H 0.4818502 -2.2779688 0.3498201
C -0.0016589 -0.5616540 1.3117092
O -0.0864879 -1.0482643 2.4227999
Example 2: Generation of (MeCp)Mn(CO)3#
示例 2：(MeCp)Mn(CO) 3 #的生成
In our second example, we will automatically generate (MeCp)Mn(CO)3, also known as MCMT, a prominent antiknock reagent. To do so, we will start from a Mn+ ion
and use DOCKER to coordinate MeCp- and three CO ligands. For the initial coordination of MeCp-, the input file looks like the following:
在我们的第二个示例中，我们将自动生成（MeCp）Mn(CO) 3 ，即 MCMT，一种重要的抗爆剂。为此，我们将从 Mn + 离子开始，并使用 DOCKER 来配位 MeCp - 和三个 CO 配体。对于 MeCp - 的初始配位，输入文件如下所示：
! XTB
%DOCKER
GUEST "mecp.xyz"
GuestCharge -1
END
*XYZ 1 1
Mn 0 0 0
*
In this case, we assume that Mn+ has a closed-shell 3d6 configuration and the charge of the MeCp- is set to -1. After the successful coordination of MeCp-,
we want to add three CO ligands to the (MeCp)Mn complex. To do so, we use the NRepeatGuest option in the %DOCKER block.
在这种情况下，我们假设 Mn + 具有闭壳层 3d 6 构型，并且 MeCp - 的电荷设为-1。在成功配位 MeCp - 后，我们希望向(MeCp)Mn 配合物中添加三个 CO 配体。为此，我们在 %DOCKER 块中使用 NRepeatGuest 选项。
! XTB
%DOCKER
GUEST "co.xyz"
NRepeatGuest 3
END
*XYZFILE 0 1 mecpmn.xyz
DOCKER now successively adds three CO ligands. The lowest energy structures obtained from the docking tasks are visualized in the following:
DOCKER 现依次添加三个 CO 配体。以下展示了对接任务中获得的最低能量结构：
Structures Example 2# 结构示例 2
MeCp-
13
C -3.64427622132568 3.09316683643494 0.01091629612016
C -3.87999219107613 2.51600304373552 1.25660734396560
C -2.65274176334490 2.12553705874125 1.78901754813097
C -1.65193000677097 2.45920643455840 0.87321354895126
C -2.27129809643429 3.05878854146220 -0.22576830966736
H -4.39748886822314 3.49586021999700 -0.66020373614263
H -4.84980591903549 2.38868239855723 1.72914527345892
H -2.49667408630002 1.64042064054602 2.74824348877019
H 0.32165777036830 2.14198139178304 0.08049985624744
H -1.76541215415890 3.42885463317223 -1.11296797433561
H 0.30624914501611 3.06684333388484 1.58428181364891
C -0.17765723116959 2.23720831134323 1.04896114415727
H 0.01898370151214 1.32580055067847 1.62184463601315
CO 一氧化碳
2
C 0.17457487970377 0.17457487970377 0.17457487970377
O 0.82542512029623 0.82542512029623 0.82542512029623
(MeCp)Mn(CO)3
20
Mn 0.10772025158918877019 0.81212587335336905436 -1.92171687668995194720
C 0.43167555634988569180 2.93675983488815095512 -1.83871863568744564610
C -0.63752834317906326156 2.66571247544714085009 -2.71909965291139421595
C -0.13396552236281986104 1.87780830368776330275 -3.78868516508951946875
C 1.25981510310186650692 1.69221580813308847269 -3.59264603016447070516
C 1.59750708039633160240 2.31699309621178395346 -2.36361211321316444511
H 0.40657825604932584795 3.62569053823126674629 -1.00455233931485121701
H -1.62297332911990621618 3.11079681509173155973 -2.67506328708324714327
H -0.66985357831151026708 1.64130628469667350089 -4.69871163430750549139
H 2.55690064213908341273 1.95515857280974292287 -5.25054887769718092727
H 2.60580860691424787134 2.47173017653485782574 -2.00214023348514480460
H 3.10260418224006251364 0.71975088588299618308 -4.11234615985394214022
C 2.22543258111944686206 1.14467797515485525395 -4.59710627144102712549
H 1.76131130861969520396 0.37866263578440867432 -5.21584341734327683326
C 0.83920336042927801135 -0.76204682118684241576 -2.33671046519168701394
O 1.34461847467276229828 -1.74307886048269322643 -2.65547492857369826780
C 0.43423449309114875438 0.64416016169359235910 -0.17566096895699659375
O 0.66488528228962273658 0.59271701978585245030 0.94801502974767526410
C -1.54261490113692767423 0.14793316793256136576 -1.78391727528337851183
O -2.62372995624129723424 -0.23489302928064861864 -1.72713471935651186051
Example 3: Docking of cyclooctanol to
示例 3：环辛醇与
In this example, we will dock cyclooctanol to
在此示例中，我们将环辛醇对接至
! XTBFF
%DOCKER
GUEST "cyclooctanol.xyz"
END
*XYZFILE 0 1 cyclodextrin.xyz
DOCKER yields the host-guest complex with cyclooctanol being located in the center of the cyclodextrin as the energetically most favorable structure. Other interaction motifs
with the alcohol being located at the outer rim of the cyclodextrin are also included in the orca.docker.struc1.allopt.xyz file.
DOCKER 生成了宿主-客体复合物，其中环辛醇位于环糊精中心，这是能量上最有利的结构。 orca.docker.struc1.allopt.xyz 文件中还包含了酒精位于环糊精外缘的其他相互作用模式。
Structures Example 3# 结构示例 3
Cyclooctanol 环辛醇
25
C -0.630732270324 0.540222793603 1.600761414434
C -1.432371159469 0.384302216526 -0.908462854692
C 1.671939879560 0.611757364766 -0.383488862093
C 1.551063510269 -0.552164900142 0.625485448688
C -0.346477476064 -0.353247209406 -1.713695099990
C 1.045411187360 0.298908175121 -1.752711207143
C -1.632861731037 -0.010632183198 0.575203191529
C 0.671032349882 -0.242300057237 1.849176839651
O -1.681185499105 -1.442691736454 0.751432117782
H -2.389914109012 -1.787025754614 0.185107018296
H -2.612389568993 0.409188132726 0.855678146000
H 1.144022454617 -1.433333371366 0.119148972672
H 1.197707493752 1.509427283252 0.030890091794
H -0.273875953996 -1.377678481706 -1.331024077317
H -1.149974959929 0.598772588999 2.565183251253
H -0.408068891048 1.576204730682 1.316751264090
H 0.421705955622 -1.184910127026 2.347531382837
H -2.397293252906 0.197426701475 -1.400917694821
H -0.691153740113 -0.445480421749 -2.750924529479
H 1.253716468584 0.348058633354 2.569678229592
H 1.712922614019 -0.377640668532 -2.303755614568
H -1.282960754333 1.472215430141 -0.954991499672
H 2.544099431570 -0.844333451745 0.985769664918
H 2.723584454521 0.879434706570 -0.537218529100
H 0.992053566569 1.225519605958 -2.340607064660
147
C -4.768156171798 1.055174471214 0.258034264598
C -5.404850114264 1.008927566532 -1.141456596734
C -5.701190428586 -0.444101356553 -1.500230499929
C -6.566922945568 -1.095132901509 -0.429444412072
C -5.944023234260 -0.909251015627 0.961874923878
O -5.723964169934 0.476062234654 1.190451853191
O -4.520893809964 1.495163779082 -2.156645399046
C -4.781180905736 2.785495817758 -2.701659708858
C -4.543203871423 2.694075892578 -4.215557614729
C -3.048268225489 2.523562281817 -4.505432294779
C -2.230087502276 3.551813448387 -3.716578005833
C -2.551561939665 3.489720490885 -2.222581311833
O -3.970183112270 3.772408736447 -2.088185165969
O -0.848972448174 3.220229881563 -3.972823367252
C -0.001236389272 4.252226558610 -4.406596252093
C 0.953480063919 3.686915101775 -5.462648372618
C 1.895893231101 2.678328559883 -4.825584398224
C 2.584582025984 3.292442363130 -3.610610243467
C 1.526609026582 3.791826443334 -2.621742016042
O 0.757976222371 4.801830284254 -3.328933192582
O 3.409605715924 2.243002608721 -3.069704656552
C 4.746389478908 2.564762741477 -2.768795904040
C 5.633800571134 1.389101419939 -3.201888064843
C 5.371252224410 0.166533483837 -2.332566235151
C 5.483102357163 0.525703331709 -0.853546498191
C 4.528748012529 1.693242161953 -0.551414423438
O 4.936742216352 2.814573101106 -1.385557869816
O 5.134487817667 -0.660049995090 -0.132449801880
C 5.952539099900 -1.031425707446 0.972739342125
C 6.131861164318 -2.555161365862 0.904908926769
C 4.802834265041 -3.244913503190 1.224388280876
C 4.198888590255 -2.665644970437 2.507493746443
C 4.045312029032 -1.146922608325 2.407433464451
O 5.379466587217 -0.610254575144 2.197707095291
O 2.926922822507 -3.330309928538 2.662232421037
C 2.630614066727 -3.881534426611 3.920907223146
C 1.922547167522 -5.227229696810 3.707421634115
C 0.551817638463 -5.016989699782 3.077313634888
C -0.260694697751 -4.007511809678 3.882617549830
C 0.547907479789 -2.706101601676 4.010196667646
O 1.790366838513 -3.033364246600 4.693387531977
O -1.483830121378 -3.815303255694 3.163900076592
C -2.699240328740 -3.847465365950 3.904850349300
O -3.139021281548 -2.539100508899 4.225857386154
C -3.342939889016 -1.709857330277 3.049597486344
C -4.474962771158 -2.359636494283 2.252037024700
C -4.105225680377 -3.784509478111 1.828894172820
C -3.722943770703 -4.615912753874 3.056643749726
C -3.594154377510 -0.279783175830 3.552142962223
O -2.589818816694 0.642920709410 3.117530044015
O -3.236397762468 -5.912242398683 2.749749090131
O -5.212042601529 -4.397233960459 1.174118957866
O -4.752209880113 -1.653261576766 1.024102271225
O -0.184550696744 -6.244343275918 3.034831446110
O 2.663959772304 -6.099272502801 2.828050722313
C -0.112067000745 -1.564788975500 4.798952693676
O -0.210337828193 -0.357681537935 4.036867304899
O 5.024881064493 -4.643095422996 1.382102424732
O 6.693911888860 -2.929159911725 -0.342283720488
C 3.466751479823 -0.434295482702 3.639050836220
O 2.329967007163 0.377175167644 3.324885499243
O 6.319709114461 -0.869819169395 -2.610127765329
O 5.385640514138 1.004133738539 -4.573485145543
C 4.504476233469 2.200136754824 0.898687559110
O 3.187722254955 2.200260420892 1.457696214264
O 2.843223282204 2.284149776002 -5.822911591096
O 0.175552532942 3.105298227672 -6.513301615039
C 2.045082050159 4.430729003200 -1.323104337841
O 1.602228075858 3.730031019422 -0.157179893914
O -2.828995557128 2.690563243358 -5.900312531915
O -5.361450625896 1.680849636558 -4.779032660480
C -1.808966539678 4.489684938930 -1.324427633829
O -1.121808041149 3.853924846599 -0.239077114847
O -6.363062932305 -0.461043290926 -2.769609870138
O -6.703112476703 -2.487830136598 -0.783945322535
C -4.405296214070 2.446534033100 0.798324514728
O -3.036824005234 2.539767647551 1.207129840321
H 3.282501152588 -6.623909218484 3.359804141215
H 0.359424928163 -6.877011821849 2.535528733781
H 6.285133583584 -2.369784363194 -1.033697694396
H 4.159944176031 -5.032762720855 1.619510868186
H 6.002521048463 1.486428693729 -5.145449345243
H 6.231259710207 -1.083463969856 -3.554365563580
H 0.788936658496 2.578163223515 -7.053446392765
H 3.480027836996 1.681959070868 -5.386839981618
H -5.371711197912 0.926347937718 -4.156101861598
H -1.863174074103 2.642813978645 -6.050615131415
H -7.559959726253 -2.808110299869 -0.461672686413
H -6.559462720613 -1.392607814634 -2.967083790286
H -2.274321366049 -5.839797958636 2.584878018179
H -5.449368934143 -3.809702710273 0.429090106313
H 3.544535229553 -3.999963094651 4.515228014857
H 1.789435496147 -5.704650688585 4.686084074183
H 0.684231199152 -4.618953148417 2.061116063118
H -0.477334697318 -4.413151186556 4.880893070069
H 0.780290402417 -2.338204097570 3.004421399265
H 6.922099169647 -0.526333128082 0.908982542462
H 6.858743114297 -2.846678771786 1.672090333889
H 4.095892583914 -3.054803281312 0.401743920374
H 4.843960636187 -2.917231928777 3.360985179551
H 3.419404232095 -0.906236088796 1.540367590235
H 5.041055251106 3.492832524909 -3.273354732515
H 6.682707475842 1.685617035325 -3.081304207251
H 4.349752102781 -0.193625552349 -2.520990208976
H 6.516596724781 0.814582460618 -0.615593368930
H 3.511213703141 1.395402704469 -0.828449405358
H -0.580626904781 5.089842049911 -4.808574818070
H 1.548764530724 4.524212430570 -5.855902194422
H 1.313210430051 1.809166344325 -4.486677451142
H 3.221643628606 4.131434935990 -3.923499381229
H 0.865393985329 2.959655760072 -2.354212277638
H -5.815383070098 3.078710183869 -2.492099247336
H -4.867013043957 3.639165160245 -4.666897323435
H -2.733411744973 1.520642301791 -4.175131113253
H -2.439368794773 4.559483474931 -4.101317728275
H -2.349902692928 2.476756832706 -1.855119427994
H -6.635347699959 -1.224463131275 1.752736462948
H -7.550382137333 -0.609081575538 -0.432016396941
H -4.745497378323 -0.984004916786 -1.563167159056
H -6.335870851237 1.593233867389 -1.149400157337
H -3.860506681274 0.440773406235 0.249985210931
H -2.540473527584 -4.349942718201 4.864862396316
H -4.625940538336 -4.758336220626 3.662070147545
H -3.238012752047 -3.725511536294 1.152880872379
H -5.386954103015 -2.387565486897 2.865063760371
H -2.428692056632 -1.711378877744 2.444669062802
H 5.102012255112 1.556471784745 1.545395233591
H 4.930258611752 3.211773749331 0.909875095609
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