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Topology Check |
Utility Tools |
Examples and Guides |
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Checking the molecular topology with CREST. |
/page/examples/utilities/utils_3.html |
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The molecular topology used by CREST, and in particular used for the structure sorting in CREGEN,
can be printed with the command --testtopo <FILE>.
Taking the caffeine molecule as an example
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crest --testtopo caffeine.xyz{% include image.html file="caffeine.png" alt="caffeine" max-width=400 %}
will provide the output
{% capture crest_output %} ============================================== | | | C R E S T | | | | Conformer-Rotamer Ensemble Sampling Tool | | based on the GFN methods | | P.Pracht, S.Grimme | | Universitaet Bonn, MCTC | ============================================== Version 2.12, Thu 19. Mai 16:32:32 CEST 2022 Using the xTB program. Compatible with xTB version 6.4.0
Cite work conducted with this code as
• P.Pracht, F.Bohle, S.Grimme, PCCP, 2020, 22, 7169-7192. • S.Grimme, JCTC, 2019, 15, 2847-2862.
and for works involving QCG as
• S.Spicher, C.Plett, P.Pracht, A.Hansen, S.Grimme, JCTC, 2022, 18 (5), 3174-3189.
with help from: C.Bannwarth, F.Bohle, S.Ehlert, S.Grimme, C.Plett, P.Pracht, S.Spicher
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
Command line input:
crest --testtopo caffeine.xyz
Coordinates (Bohr): 0.888171196170 4.854328018555 0.001133835570 O -5.909362016047 -0.838282431108 -0.000566917785 O -1.830388554489 -2.480265308453 0.000000000000 N 4.191790100731 0.266829304041 -0.000566917785 N -2.546783661868 2.040337107456 -0.000188972595 N 2.668104067813 -3.660777108979 0.000377945190 N 1.621195891902 0.489816966058 -0.001511780759 C 0.736426202441 -1.939614714359 -0.000755890380 C 0.058014586643 2.687190299901 -0.001133835570 C -3.602006631955 -0.471486624350 -0.000755890380 C 4.730361996281 -2.267293193967 0.000566917785 C -2.697772765217 -5.094701159305 0.001511780759 C 6.033139065726 2.279198467447 0.000566917785 C -4.340511532941 4.134909349657 0.001322808165 C 6.644843355514 -2.983310356156 0.001511780759 H -1.974952589611 -6.042020777688 -1.688848080887 H -4.759463775900 -5.214887729681 0.002078698544 H -1.974196699231 -6.040131051739 1.692627532786 H 7.935337206289 1.474175213047 0.000377945190 H 5.757617022319 3.418892187469 -1.699241573608 H 5.757239077129 3.417191434114 1.701509244747 H -3.417947324494 5.981171602121 -0.000566917785 H -5.541054428529 3.973526753587 1.678265615571 H -5.545589770808 3.972392918018 -1.672218492533 H
CN neighbours
O (1) 1.0619 9 O (2) 1.0561 10 N (3) 3.1322 8 10 12 N (4) 3.2817 7 11 13 N (5) 3.1440 9 10 14 N (6) 2.2107 8 11 C (7) 3.4651 4 8 9 C (8) 3.6067 3 6 7 C (9) 3.1545 1 5 7 C (10) 3.1799 2 3 5 C (11) 3.5116 4 6 15 C (12) 4.0689 3 16 17 18 C (13) 4.0547 4 19 20 21 C (14) 4.0789 5 22 23 24 H (15) 1.0011 11 H (16) 0.9979 12 H (17) 0.9981 12 H (18) 0.9979 12 H (19) 0.9982 13 H (20) 0.9985 13 H (21) 0.9985 13 H (22) 0.9981 14 H (23) 0.9980 14 H (24) 0.9980 14
Number of fragments in the system: 1
Total number of rings in the system: 2
ring size: 6 3 5 7 8 9 10 ring size: 5 4 6 7 8 11
Total number of rings in the system: 2 {% endcapture %} {% include codecell.html content=crest_output style="font-size:10px" %}