ORCA as External Optimizer¶
Even though ORCA features a vast amount of electronic structure models, it cannot cover all available methods. Therefore, ORCA features an external optimization interface that allows you to use ORCA's optimization infrastructure with electronic structure methods and model potentials provided by external programs. This way you'll be able to utilize the lates MNDO based semi-empirical methods like PM7 or neural network potentials like AIMNet2 within the ORCA infrastructure, e.g. to optimize structures, search transition states with NEB-TS, or sample conformers with GOAT.
The external optimization infrastructure can be accessed via the ORCA simple input keyword !ExtOpt which can be combined with other common keywords
like !Opt or !GOAT. As every program typically provides output in different formatting and style, individual wrapper scripts are required to link ORCA and its external optimizer infrastructure. The full path to your wrapper script can be provided via the %method block:
! ExtOpt
%method
ProgExt "/full/path/to/wrapperscript"
Ext_Params "optional command line arguments"
end
Important
Some wrapper scripts and how to use them can be found in the official ORCA GitHub repository. The repository is open to the community and contributions are very welcome!
Note
Not that depending on your OS and infrastructure, you may need to do some modifications to the wrapper script!
Note
In case of methods that are imported via Python interfaces such as AIMNet2 and UMA, two different scripts can be used. One is a standalone which might slow down your calculation due to heavy imports. The other option is a server/client approach. Here, the server must be started beforehand with the respective script and then the respective client script can be used similar to the other scripts. More information are given in the following examples or in the respective README files on GitHub.
Example 1: Optimization of Disorazol Z1 with PM7 via MOPAC¶
In this example, we will optimize disorazol, a potential anti-cancer drug, within ORCA utilizing energies and gradients generated with the PM7 method in MOPAC. To do so, we simply add the !Opt simple input keyword and an additional --method PM7 argument for the mopac wrapper script:
!ExtOpt Opt PAL4
%method
ProgExt "/full/path/to/mopac.py"
Ext_Params "--method PM7"
end
*XYZFILE 0 1 structure.xyz
We can now run the ORCA input file via orca basename.inp as usual and the external optimizer infrastructure will generate two output files, the
normal ORCA output basename.out and the output of the external program, in this case MOPAC basename_EXT.out.
We can now check the ORCA output for convergence and will find the typical success message:
***********************HURRAY********************
*** THE OPTIMIZATION HAS CONVERGED ***
*************************************************
The MOPAC output also indicates normal execution for the last energy and gradient calculation:
** MOPAC v22.0.6 **
** **
*******************************************************************************
** Digital Object Identifier (DOI): 10.5281/zenodo.6511958 **
** Visit the DOI location for information on how to cite this program. **
*******************************************************************************
PM7 CALCULATION RESULTS
*******************************************************************************
[...]
**********************
* *
* JOB ENDED NORMALLY *
* *
**********************
TOTAL JOB TIME: 0.62 SECONDS
The PM7 optimized structure is stored in the basename.xyz file as usual alongside the optimization trajectory basename_trj.xyz. The full optimization
of disorazol is shown in the animation below.
Figure: PM7 optimization of Disorazol Z1 using MOPAC via ORCA's external optimization feature.¶
Structures Example 1¶
Disorazol Z1 unoptimized
100
N 4.9056000000 9.4983000000 7.3808000000
N 3.7927000000 9.5666000000 2.0870000000
O 2.5573000000 8.0061000000 9.6644000000
O 3.3918000000 10.1213000000 9.7156000000
O 5.2191000000 7.4378000000 6.5692000000
O 8.0703000000 5.7271000000 -3.3425000000
H 8.4793000000 6.2292000000 -3.8777000000
O 3.8441000000 5.1815000000 -1.7983000000
O 4.1962000000 7.2585000000 -2.5227000000
O 5.7494000000 7.3570000000 0.0202000000
O 5.2928000000 9.5498000000 -0.3412000000
O 3.6351000000 7.8654000000 3.5190000000
O 0.1414000000 7.9363000000 13.2750000000
H -0.0323000000 8.6062000000 13.7510000000
O 4.0052000000 5.9237000000 11.4984000000
O 4.1148000000 8.0439000000 12.1910000000
C 3.3498000000 8.9937000000 9.2481000000
C 4.1739000000 8.5676000000 8.1215000000
C 4.3556000000 7.3413000000 7.6276000000
H 3.9560000000 6.5429000000 7.9526000000
C 5.5061000000 8.8068000000 6.4792000000
C 6.3252000000 9.2591000000 5.4169000000
H 6.5409000000 10.1837000000 5.4085000000
C 6.8332000000 8.5052000000 4.4092000000
H 6.6774000000 7.5688000000 4.4252000000
C 7.5931000000 9.0500000000 3.3203000000
H 7.8827000000 9.9519000000 3.3933000000
C 7.9255000000 8.3786000000 2.2042000000
H 7.7777000000 7.4397000000 2.1753000000
C 8.5004000000 9.0299000000 1.0416000000
H 8.8888000000 9.8850000000 1.1815000000
C 8.5398000000 8.5555000000 -0.1902000000
H 8.9178000000 9.1235000000 -0.8513000000
C 8.0489000000 7.2107000000 -0.6584000000
H 8.1052000000 6.5656000000 0.0899000000
H 8.6358000000 6.8860000000 -1.3861000000
C 6.6079000000 7.2710000000 -1.1634000000
H 6.4818000000 8.0841000000 -1.7324000000
C 5.2131000000 8.5454000000 0.3262000000
C 4.4832000000 8.4751000000 1.5970000000
C 4.3950000000 7.4418000000 2.4632000000
H 4.7866000000 6.5835000000 2.3585000000
C 3.3035000000 9.1646000000 3.2191000000
C 2.4956000000 9.8742000000 4.1681000000
H 2.2882000000 10.7844000000 3.9959000000
C 2.0219000000 9.3133000000 5.2824000000
H 2.2487000000 8.4039000000 5.4406000000
C 1.2003000000 9.9627000000 6.2618000000
H 0.9438000000 10.8630000000 6.1060000000
C 0.7753000000 9.3696000000 7.3810000000
H 0.9868000000 8.4509000000 7.4986000000
C 0.0240000000 10.0149000000 8.4197000000
H -0.3403000000 10.8681000000 8.2161000000
C -0.2125000000 9.5385000000 9.6375000000
H -0.7177000000 10.0976000000 10.2172000000
C 0.2270000000 8.2198000000 10.1989000000
H 0.1913000000 7.5389000000 9.4817000000
H -0.4077000000 7.9461000000 10.9073000000
C 1.6423000000 8.2499000000 10.7851000000
H 1.8236000000 9.1522000000 11.1746000000
C 6.1247000000 6.0246000000 -1.9217000000
C 6.6730000000 6.0246000000 -3.3852000000
H 6.5642000000 6.9461000000 -3.7573000000
C 5.9542000000 5.0738000000 -4.2858000000
H 5.9810000000 4.1520000000 -4.0589000000
C 5.2885000000 5.4115000000 -5.3651000000
H 5.2418000000 6.3378000000 -5.5673000000
C 4.6049000000 4.4908000000 -6.2970000000
H 5.0371000000 4.5342000000 -7.1759000000
H 3.6641000000 4.7510000000 -6.3828000000
H 4.6600000000 3.5747000000 -5.9519000000
C 6.4819000000 4.7200000000 -1.1795000000
H 6.0961000000 3.9561000000 -1.6578000000
H 6.1195000000 4.7517000000 -0.2694000000
H 7.4560000000 4.6222000000 -1.1401000000
C 4.6014000000 6.0628000000 -2.0557000000
C 2.7629000000 7.3715000000 -2.6880000000
H 2.4485000000 6.6708000000 -3.2971000000
H 2.5461000000 8.2509000000 -3.0626000000
H 2.3245000000 7.2694000000 -1.8182000000
C 1.9499000000 7.1463000000 11.8547000000
C 1.5515000000 7.7172000000 13.2595000000
H 2.0156000000 8.5920000000 13.3965000000
C 1.9293000000 6.7865000000 14.3766000000
H 1.4671000000 5.9586000000 14.4302000000
C 2.8297000000 7.0217000000 15.2686000000
H 3.3353000000 7.8210000000 15.1781000000
C 3.1467000000 6.1272000000 16.4504000000
H 2.6361000000 5.2941000000 16.3758000000
H 2.9036000000 6.5858000000 17.2819000000
H 4.1052000000 5.9236000000 16.4580000000
C 1.2577000000 5.8417000000 11.5618000000
H 0.2911000000 5.9489000000 11.6841000000
H 1.5894000000 5.1510000000 12.1728000000
H 1.4415000000 5.5743000000 10.6365000000
C 3.4517000000 6.9453000000 11.8293000000
C 5.5498000000 7.9725000000 12.1232000000
H 5.8177000000 7.5826000000 11.2654000000
H 5.8841000000 7.4133000000 12.8554000000
H 5.9258000000 8.8744000000 12.2038000000
Example 2: NEB-TS with PM6-D3H4X via MOPAC¶
In this example, we will run a NEB-TS transition state search of the dihydrogen activation by Erker's frustrated Lewis pair (FLP) within ORCA utilizing energies and gradients generated with the PM6-D3H4X method in MOPAC. PM6-D3H4X is the default method chosen in the wrapper script. Therefore, no further method definition is required.
Figure: Dihydrogen activation by Erker's frustrated Lewis pair.¶
The corresponding ORCA input includes the full path to the MOPAC wrapper mopac.py and the usual NEB-TS input:
!ExtOpt NEB-TS PAL8
%method
ProgExt "/full/path/to/mopac.py"
end
%NEB
NEB_END_XYZFILE "products.xyz"
PreOpt true
NImages 15
END
*XYZFILE 0 1 reactants.xyz
To link ORCA and MOPAC, we will use the mopac.py wrapper script that is available at https://github.com/ORCAQuantumChemistry/orca-external-tools/. The full path to that script must be defined via the progext keyword in the %method block.
We can now run the ORCA input file as usual via orca basename.inp > basename.out and if everything is set up properly, ORCA will call MOPAC via the wrapper script to calculate energies and gradients and reformat them to be readable by ORCA. The ORCA output will look the same as if the chosen task, in this case
NEB-TS was done with any method native to ORCA.
After the successful NEB-TS run, the generated minimum energy pathway is stored as basename_MEP_trj.xyz and can be visualized using one of various
graphical user interfaces and the relative energies can be plotted.
Figure: NEB-TS minimum energy path and TS guess at the PM6-D3H4X level.¶
Structures Example 2¶
Reactants
72
P -0.3662186668 -0.4096435953 2.4180808260
H -2.3885845963 2.9955626038 5.4479529454
C 3.5664000355 -1.2461611941 0.0460721904
C 4.0345311647 -2.4799363070 -0.4218846155
C 0.5906956936 0.2741158964 0.9024119146
C 3.5926063693 -0.9405728379 1.4305609924
C 4.5295774292 -3.4308472274 0.4683424173
C 4.5577094567 -3.1556020395 1.8335312075
C 4.0922904559 -1.9282805675 2.3166260030
F 3.1102486338 -0.3601181140 -0.8720376588
F 4.0021101028 -2.7560478584 -1.7496868199
F 4.9741403016 -4.6268853216 0.0074899162
F 1.6609927682 2.4069841606 3.8673812046
C -0.7759877333 0.8592881293 5.2072930505
C -1.4939909110 1.0603727091 2.7564911367
C -2.3065451624 1.7164461694 1.7700735919
C -3.0879214210 2.8224332432 2.1412495307
C -3.1135208398 3.2836385061 3.4572948761
C -2.3445997439 2.6407919742 4.4247654087
C -1.5404447670 1.5392172532 4.0953319641
C -2.4846728629 1.2620308898 0.3401290842
H -3.7127028087 3.3080989098 1.3989223051
C -3.9915180710 4.4386702859 3.8472359970
C -3.7015934076 -0.9976824375 2.7817835838
C -1.4544914791 -1.7959121031 1.7030713575
C -0.8119512656 -2.8653235985 0.9961802904
C -1.5662737058 -3.8866609251 0.4051153805
C -2.9470678924 -3.9294813072 0.5367618161
C -3.5865139050 -2.9635810366 1.3034699798
C -2.8773777715 -1.9059311104 1.9015453922
C 0.6819036932 -3.0332378272 0.8715721201
H -1.0640870808 -4.6743923886 -0.1457984450
C -3.7492527548 -5.0276088777 -0.0971420363
H -4.6599624638 -3.0451075440 1.4349647467
B 3.0131350631 0.4514405801 2.0128430573
C 5.5998693277 1.5036915913 4.7858506455
F 5.0250895074 -4.0897589233 2.6989572953
C 3.6623672934 1.1516096769 3.3212470857
C 1.7990587780 1.1803087417 1.2101586227
C 3.5424989674 2.6717065465 5.2406955397
C 2.9450043758 2.0748303851 4.1243326081
F 5.8097090173 0.0955408361 2.9136274998
C 4.8629985399 2.3837814910 5.5735623559
C 5.0154824347 0.8944206734 3.6702979916
F 6.8964470055 1.2469203924 5.0950886633
F 5.4364357513 2.9702372312 6.6536309660
F 2.8327779615 3.5384554667 6.0062750205
F 4.0918640768 -1.7367717031 3.6606716382
H 0.9522007858 -0.5586335520 0.2878715846
H -0.0387216445 0.8519353506 0.2211678560
H 1.4521972827 2.1118638057 1.6812212976
H 2.2187472490 1.5065174227 0.2373150753
H 1.2597087595 -2.3232278677 1.4806724365
H 0.9682076828 -4.0312044561 1.2673758660
H 0.9898144936 -2.9734141085 -0.1934005127
H -4.7345601984 -1.3813207626 2.9216722406
H -3.2485998390 -0.9334458836 3.7925050715
H -3.8598668324 -0.0135626474 2.3409536060
H -3.1033972147 -5.7316587228 -0.6633823322
H -4.2901809290 -5.5978503546 0.6870174798
H -4.4867829971 -4.5870722156 -0.8009478600
H -2.0262115947 0.2848534207 0.1168859802
H -3.5663902937 1.1076816015 0.1403115110
H -2.1084885857 2.0393134711 -0.3581158096
H -4.5580195499 4.8362082252 2.9777413749
H -4.7247988658 4.1041275923 4.6121757931
H -3.3732792824 5.2572015006 4.2701561221
H -0.9351373579 1.3585919087 6.1869438451
H -1.1222854849 -0.1908963403 5.3037483428
H 0.3093227895 0.8512713219 5.0034519911
H 0.7540838587 -2.8519089197 4.2554242046
H 1.2874419057 -3.0099218389 4.6931723926
Product
72
P -0.5141474859 -0.6146687557 1.7732495131
H -2.3073527307 2.5415227122 5.2483856969
C 3.8976464054 -0.7736830433 0.6748291330
C 4.5247100662 -1.8426146794 0.0226708706
C 0.7960404084 0.5055582004 1.0062180750
C 3.4852219019 -0.9019184371 2.0229276441
C 4.7715428862 -3.0366122778 0.7012890616
C 4.3956596054 -3.1689505522 2.0378517298
C 3.7562694931 -2.1149435235 2.6966389400
F 3.7084071929 0.3775089920 -0.0174764085
F 4.9014355568 -1.7168802815 -1.2745115723
F 5.3877541089 -4.0650705258 0.0663580708
F 1.9047854228 2.1938758994 4.8731094145
C -0.8427860787 0.3354249557 4.7853059771
C -1.5308898507 0.8388913102 2.3740198414
C -2.2590127333 1.6544577280 1.4587108400
C -2.9713968215 2.7670210580 1.9330673660
C -2.9841209658 3.0889912371 3.2918457138
C -2.2844527789 2.2872147662 4.1946961177
C -1.5588624833 1.1681184778 3.7562781608
C -2.3425715705 1.3777010917 -0.0222948677
H -3.5255341394 3.3828669768 1.2340679650
C -3.7470530146 4.2814694178 3.7931113692
C -3.8558392207 -0.9993416846 2.6178364960
C -1.7438745807 -2.0168792915 1.4681251655
C -1.2013404525 -3.1504470909 0.7739207164
C -2.0139939380 -4.2447116719 0.4577087755
C -3.3567024222 -4.2709212780 0.8086780201
C -3.9001692448 -3.1972478291 1.5078030549
C -3.1289717182 -2.0686592584 1.8469557506
C 0.2403947588 -3.2805834797 0.3178390294
H -1.5914867403 -5.0883136780 -0.0793534987
C -4.2188629803 -5.4446818188 0.4453839376
H -4.9485595045 -3.2468255157 1.7801953312
B 2.7567394502 0.2837013655 2.8476373452
C 6.0177199541 1.8502977606 4.4413803101
F 4.6541406446 -4.3233386945 2.7015593213
C 3.7762991086 1.1673199976 3.7398485466
C 1.7418275425 1.2332396443 1.9746652311
C 4.0864550469 2.8327398877 5.5034165123
C 3.2433615125 2.0637578055 4.6968703954
F 5.7852925983 0.2434250342 2.7363841220
C 5.4699451414 2.7266087992 5.3767201544
C 5.1875367204 1.0730681512 3.6253815578
F 7.3653983211 1.7491256408 4.3236838833
F 6.2823210744 3.4726519303 6.1657947726
F 3.5558807405 3.6825160121 6.4180585237
F 3.4137698580 -2.2805742554 4.0010234345
H 1.3905441557 -0.1307651185 0.3307470817
H 0.3053046121 1.2541114761 0.3556310926
H 1.1294752714 1.8711165172 2.6397637822
H 2.3805453331 1.9199621863 1.3802760347
H 0.9033881401 -2.4347594800 0.5565380917
H 0.6932355562 -4.1780305532 0.7913133181
H 0.2691623290 -3.4079172290 -0.7846856501
H -4.9025534621 -1.2872244579 2.8533990521
H -3.3562237151 -0.8243962839 3.5890394907
H -3.9449201055 -0.0828962455 2.0185058970
H -3.6461985220 -6.2183222471 -0.1091328387
H -4.6347687204 -5.9073257277 1.3660122938
H -5.0549875324 -5.1032784554 -0.2011287679
H -1.8025143116 0.4663469530 -0.3375470978
H -3.4070932679 1.2362719138 -0.3068286369
H -1.9328360358 2.2409662666 -0.5876555927
H -4.2561256215 4.8200797514 2.9652184492
H -4.5167210280 3.9535666366 4.5231508839
H -3.0505409799 4.9872577739 4.2928544539
H -0.9872448071 0.7306319616 5.8138247919
H -1.2220341262 -0.7066181096 4.7622904255
H 0.2361316733 0.3321254109 4.5832569326
H 0.3630550367 -1.4428985924 2.5800866384
H 2.0804831254 -0.2794083001 3.6378813047
Example 3: GOAT with AIMNet2¶
In this example, we will use GOAT to generate a conformer ensemble for the anti-inflammatory drug Ibuprofen. For this, we want to use AIMNet2.
It will be installed first when any of the respective scripts are used.
For the calculation, we will start the AIMNet2 server by executing the aimnet2server.sh script:
aimnet2server.sh
Then we can provide the aiment2client.py client via ORCA input:
! EXTOPT GOAT PAL8
%method
ProgExt "/full/path/to/aiment2client.py"
end
*XYZfile 0 1 ibuprofen.xyz
After the successful GOAT run, the final conformer ensemble is stored in basename.finalensemble.xyz that can be visualized with graphical user interfaces
like Avogadro 2 or ChimeraX.
Figure: Conformer ensemble of Ibuprofen generated with GOAT using PM6-D3H4X via MOPAC.¶
Structures Example 3¶
Ibuprofen Input
33
O 4.77890 0.19700 -0.13590
C 3.44760 0.36080 -0.18720
O 2.98080 1.45980 -0.37180
C 2.53530 -0.82620 -0.01460
C 2.77710 -1.46020 1.35670
C 1.10060 -0.37560 -0.11370
C 0.27900 -0.89600 -1.09610
C -1.03690 -0.48270 -1.18710
C -1.53140 0.45070 -0.29540
C -2.96590 0.90160 -0.39490
C -3.84720 -0.00780 0.46370
C -5.28200 0.52340 0.46260
C -3.82800 -1.42600 -0.11010
C -0.71030 0.97010 0.68790
C 0.60460 0.55380 0.78130
H 5.36430 0.95870 -0.24670
H 2.74070 -1.55890 -0.79500
H 2.57160 -0.72740 2.13710
H 2.11720 -2.31870 1.48160
H 3.81480 -1.78610 1.42840
H 0.66540 -1.62530 -1.79280
H -1.67860 -0.88870 -1.95510
H -3.04930 1.92880 -0.03990
H -3.29230 0.84860 -1.43350
H -3.46650 -0.02390 1.48490
H -5.66270 0.53950 -0.55860
H -5.90980 -0.12450 1.07430
H -5.29560 1.53380 0.87140
H -4.20870 -1.41000 -1.13130
H -2.80580 -1.80450 -0.10930
H -4.45580 -2.07400 0.50160
H -1.09670 1.69900 1.38480
H 1.24620 0.95960 1.54940
Lowest Conformer (AIMNet2)
33
O 1.89452635 2.74670433 1.65572355
C 2.46303606 1.53295140 1.81204838
O 2.81273687 1.12664895 2.88780233
C 2.56653560 0.78194831 0.50376922
C 3.67292032 -0.2677785 0.58211167
C 1.21043688 0.17850005 0.18521759
C 0.58967299 0.43999279 -1.0301631
C -0.6381833 -0.1240209 -1.3336595
C -1.2811642 -0.9653700 -0.4309326
C -2.6219811 -1.5635546 -0.7724310
C -3.7803819 -0.5563511 -0.7566304
C -5.0633632 -1.2101279 -1.2514248
C -3.9762248 0.04151965 0.63159179
C -0.6572722 -1.2227643 0.78438489
C 0.57074353 -0.6587236 1.09158276
H 1.84341759 3.13327885 2.53789267
H 2.80120095 1.50308672 -0.2766971
H 4.63561284 0.19127026 0.79559752
H 3.45485252 -0.9812724 1.37145269
H 3.73685105 -0.8010212 -0.3632347
H 1.07240053 1.09458246 -1.7441201
H -1.1056964 0.08912162 -2.2866663
H -2.5624071 -2.0075727 -1.7680116
H -2.8439965 -2.3743134 -0.0758410
H -3.5241062 0.25577994 -1.4393043
H -5.3598696 -2.0216935 -0.5853775
H -5.8800866 -0.4903223 -1.2828498
H -4.9362753 -1.6233665 -2.2511528
H -4.2296101 -0.7416544 1.34806325
H -3.0700625 0.53470069 0.97775697
H -4.7862335 0.77030765 0.63151268
H -1.1397547 -1.8767264 1.50038281
H 1.03232592 -0.8650591 2.04830637