Docking
Another feature of the xtb program is the aISS docking tool. This efficient tool is designed for docking two or more molecules. It can be used with:
xtb dock mol1.xyz mol2.xyz
The best structure found is saved to best.xyz. Additionally, by default, the 15 best structures are written to the final_structures.xyz file. Both files can be visualized by opening them with a graphical program like Molden.
The best_after_gen.xyz file contains the best structure found before GFN optimization.
Charges and the number of unpaired electrons for both molecules can be defined individually using the --chrg1 <INT>, --chrg2 <INT>, --uhf1 <INT>, and --uhf2 <INT> flags.
Many standard xtb flags like the use of solvation as well as choosing different methods can be applied.
Further, thresholds for the docking can be adjusted with an additional input file. Also, the generation of a whole ensemble with the --ensemble flag can be requested. Further details are available at the documentation and the publication.
As an example, dock the following molecules in THF solvent. Molecule 1 has a charge of +1, while molecule 2 has a charge of -1.
--fast flag.
26
energy: -48.614767811026 gnorm: 0.000258649455 xtb: 6.4.1 (afa7bdf)
C 4.91530661517725 6.70283245094063 7.93716475951803
C 4.70274443502525 6.57377729590493 9.29524339877115
H 4.09102174399250 7.26033628697812 9.85619438676986
C 5.30083332347772 5.50886296651214 9.95148435215316
H 5.14950194396918 5.39341270236785 11.01271420108665
C 6.07968625421465 4.60874288641406 9.24518865717228
H 6.54677504050510 3.78278315133684 9.75767540823253
C 6.25703022783366 4.75482454682128 7.88004220926858
H 6.86007029320169 4.04168399010195 7.34301476032045
C 5.66602589617880 5.80800301477451 7.18908033030661
C 5.86757693738733 6.01057612526783 5.69193856008651
C 7.08202831053878 6.91791330345741 5.48228665306979
H 7.24115049352935 7.07340643740184 4.41937035609539
H 7.97015992903950 6.46898272395727 5.91528468405366
H 6.90905459937370 7.88538694516834 5.94891470399975
C 6.00723529207749 4.69862546864148 4.92713759447965
H 5.21841097621933 3.99954166143467 5.19740910959166
H 6.96848369282735 4.23481873803338 5.12168284991214
H 5.95419366234075 4.90262716196177 3.86004767791694
C 3.64840129849507 9.67356063984810 8.63166910176501
O 4.73243266730302 6.72691667725402 5.16545009366973
H 4.06891690953035 6.10561213656021 4.82852948175645
F 4.75466800938595 9.73439880907246 9.35215456436095
F 2.67459899148865 9.19239065754443 9.38100275774183
F 3.32953186458964 10.86751693409879 8.19537197705647
I 4.01066059229276 8.37336628814393 6.88654737084331
15
energy: -58.627917250038 gnorm: 0.000569925187 xtb: 6.4.1 (afa7bdf)
C 1.69917908436396 3.16419000234708 5.71715609389680
C 2.60797179763240 5.77666501630793 1.55859710223873
N 3.04393410713759 4.87876887895570 4.08766375461315
O 1.71709471089772 5.74460140297995 5.99119818311252
O 0.49329287309353 4.87672637525144 4.06446686790556
O 2.06112121487995 3.28932161619064 2.35293444108821
O 4.39145876797790 4.00283070449141 2.20140862554339
F 2.78451881723356 3.06550089656539 6.49714305953822
F 0.63418103893843 3.02555503292592 6.52249893622828
F 1.70857427523024 2.10779486104579 4.90543392667151
F 1.42635733996611 6.33666447079787 1.81496418774220
F 3.53272631929243 6.73443277485248 1.71239388025687
F 2.60933613238697 5.44729166600378 0.25762027938529
S 1.67585920791859 4.85884119332730 4.86637940756559
S 3.05359431305024 4.27861510795718 2.63234125421372