Publication Examples
The following examples were discussed in the original CREST publication, Phys. Chem. Chem. Phys., 2020, 22, 7169-7192.
Table of contents
- Sampling of conformations at the transition-state
- Sampling of conformations for metal-organic systems
- Conformational sampling of tyrosine on a graphene surface
Sampling of conformations at the transition-state
At first, a transition-state (TS) has to be localized. Then, the TS mode has to be identified and reasonable constraints have to be applied to freeze this mode during the CREST run. Choosing suitable constraints is the responsibility of the user! For a detailed guide on how to add constraints see Example 4.
In this example, a methyl group is transferred onto the catechol molecule. To preserve the TS vibrational mode the atoms which are dominantly contributing to this mode are fixed. In this case, the carbon (atom #36) of the methyl group being transferred, the sulfur (atom #37) of the S-adenosyl-L-methionine (SAM) and the oxygen (atom #35) of the catechol group are constrained. For running the TS conformational search only these atoms have to be constrained. But to retain the surrounding enzyme environment additionally the distances of all ligands to the magnesium cation and the amide magnesium water angle were constrained. As stated before all atoms with constraints have to be removed from the list of atoms which are used in the metadynamics simulation.
crest input.tomlcrest coord --cinp constraints.inp --gbsa methanol
# This is a CREST input file
input = "coord"
runtype = "imtd-gc"
threads = 4
constraints = "constraints.inp"
subrmsd = true
[calculation]
[[calculation.level]]
method = "gfn2"
alpb = "methanol"
$coord
-2.57480197685137 -0.38573933229522 0.86228536590435 Mg
-5.87996595426622 -1.46598597135567 -1.00931632324148 O
-5.79755045954234 1.88737481602186 1.36486580018227 O
-6.93504356011937 0.41703174067196 -0.07677235660280 C
-9.68583177367761 0.93957235453071 -0.70260934507636 C
-9.88785370898918 2.90051382662291 -1.27585066001173 H
-10.31204304615949 -0.31693795001232 -2.19707799857187 H
-10.81224558069477 0.63532604630470 0.98871505743889 H
-1.35732893615725 2.84149984259631 3.74273757259152 O
-1.31788637685368 1.88478932440519 -1.80336662588251 O
-1.03506712269361 -3.09136305475668 -1.65209468828016 O
-3.01034174150676 3.35231258504990 4.30691490291278 H
-0.64007292100150 4.31049584542225 2.93186531615926 H
-3.02042382593105 -2.69109360436689 3.78441246580865 O
-0.67413309122153 -2.78784634989936 4.10013037720282 C
0.80704125300360 -1.59087682326574 2.72475235410942 O
0.37030033373577 -4.45667671167827 6.17913372417457 C
1.65729077111170 -3.36053569450090 7.34278701173010 H
-1.17079464125707 -5.18933342363882 7.31676317209597 H
1.41212360996512 -6.00880794547076 5.32805483610633 H
-0.04610218809699 0.99217247488345 -2.84947633284740 H
-0.58166801572397 4.35407649708453 -2.13719082516246 C
1.69930763718877 4.60968100984284 -3.53188509022323 C
-1.89895861199073 6.41295502711680 -1.26089925937752 C
2.61815567802848 7.04758861150735 -3.94211016089909 C
-0.94293511850593 8.82264113991643 -1.71734825726509 C
-3.65794447068903 6.13213826999732 -0.25859371242962 H
1.29133066638906 9.11831895867148 -3.04019344765619 C
4.35136261809131 7.29515670682662 -4.99253235854911 H
-1.96139641783255 10.45433175989920 -1.03894063047482 H
2.01793975704253 10.99527109251927 -3.38477251662235 H
5.63677744964081 -0.19526366812337 -3.54734464996746 H
3.55857435122244 0.44545364581733 -0.79647639427433 H
6.02794370271953 2.75567866080431 -1.74563412676399 H
2.74773927853638 2.50310064429053 -4.32763740793204 O
5.16232303152189 0.93488296527549 -1.93713143185301 C
7.77908129622702 -0.95480533027442 0.60724611364076 S
6.20470140355368 -3.99408071134196 0.68137239550646 C
7.00770708640275 -5.10883646299712 2.20213746286551 H
4.19551348270129 -3.68373090740626 0.97362752914345 H
6.54643468112530 -4.90904155689111 -1.11917138292065 H
6.61325357496481 0.34737209228094 3.55003016825311 C
7.52593267335208 -0.62757026577676 5.10500275305939 H
7.10342021330197 2.33658535430792 3.58672294810726 H
4.57513571292400 0.10172782556556 3.62256009227771 H
-1.61022171124489 -5.31411191371024 -2.02789529853598 C
-3.17527947979499 -6.57718946281529 -0.51674594958634 N
-3.77763814894346 -8.33207207055257 -0.93763600526181 H
-4.05833804986482 -5.57635320116590 0.85099090510650 H
-0.47266612030322 -6.78426594278943 -4.18601622917577 C
0.51805850799787 -8.43374379675092 -3.46937160488911 H
-1.96305386150678 -7.41025810365247 -5.45278966275112 H
0.83013814067146 -5.58152886274452 -5.21822759129119 H
$end
$constrain
atoms: 35-37
force constant=0.5
reference=coord.ref
distance: 10, 1, auto
distance: 2, 1, auto
distance: 11, 1, auto
distance: 14, 1, auto
distance: 9, 1, auto
angle: 9, 1, 11, 180
$metadyn
atoms: 3-8,12-13,15-34,38-53
$end
The TS conformer search yields 141 conformers within 6 kcal/mol. For each of these conformers, Hessians have to be calculated to ensure that the transition-state mode is preserved. Those conformers with preserved mode can be optimized into the TS and the true TSs have to be confirmed by again a Hessian calculation (only one imaginary mode). During the optimization, some conformers can become identical or rotamers of each other. To this end, all optimized geometries are appended and sorted with the cregen sorting routine.
cat TSconf*.xyz >> allts.xyz
crest coord -cregen allts.xyz -ewin 30
After sorting only 91 unique TS conformers are obtained within an energy window of 6.1 kcal/mol. This procedure can in principle be refined at DFT level.
Sampling of conformations for metal-organic systems
In CREST’s original publication two examples for sampling of metal-organic systems were provided: trans-Cu(II)(L-valine)2 and [Pt(COMe)2(2-py)3COH].
Calculation of trans-Cu(II)(L-valine)2 conformers in the gas phase
crest input.tomlcrest coord --nci
# This is a CREST input file
input = "coord"
runtype = "nci-mtd"
threads = 4
[calculation]
[[calculation.level]]
method = "gfn2"
$coord
-0.002022192318 -0.000684522852 1.349121896005 CU
2.028671941135 2.818125977315 1.174767316951 O
4.406562542342 2.529552834523 0.838287117696 C
5.900488893190 4.242544277537 0.591753944418 O
5.382406579092 -0.254197829091 0.699650595616 C
3.456927714843 -1.958681435237 1.737975874213 N
3.442953703137 -3.661542617496 0.846227450863 H
3.710547158869 -2.249430796311 3.618554595139 H
7.133224715719 -0.349791899055 1.804782999185 H
6.007018333138 -0.877714812490 -2.069473442827 C
7.266213509953 -3.466799912264 -2.312238367182 C
8.881995597301 -3.618089140164 -1.050454618739 H
7.930334466002 -3.738254167109 -4.236839656939 H
5.952357752542 -4.994107920656 -1.890594175637 H
3.663534173447 -0.712885768717 -3.746419767180 C
4.156219468360 -1.164942859389 -5.689573088070 H
2.890265219159 1.189883399588 -3.704912704715 H
2.203522204085 -2.025873622846 -3.126878925482 H
7.355957431563 0.567207315613 -2.680683804317 H
-2.033163868813 -2.819780021566 1.179505209377 O
-4.409877555278 -2.530551975348 0.835068556898 C
-5.903043316660 -4.243023566156 0.580387940800 O
-5.384798675016 0.253509426488 0.697143335052 C
-3.461334991004 1.955672873602 1.742931448447 N
-3.448757571238 3.662158486139 0.858135081470 H
-3.716247763220 2.238184300034 3.624611253622 H
-7.138671974341 0.348502264395 1.797538738740 H
-6.001307995929 0.880859137312 -2.072901114603 C
-7.255902292489 3.472119634743 -2.316426880308 C
-7.917767124579 3.744910887179 -4.241612390481 H
-5.939710712311 4.997073845686 -1.893506102537 H
-8.872648523224 3.626011270865 -1.056195385178 H
-3.653380600330 0.714736239795 -3.743504646086 C
-2.884657484645 -1.189944325855 -3.704494974332 H
-2.192229886598 2.022965931298 -3.116395721134 H
-4.139423979729 1.172691111744 -5.686934420106 H
-7.350580840264 -0.561585906341 -2.689213500551 H
$end
Results in 52 conformers within an energy window of 6 kcal/mol.
[Pt(COMe)2(2-py)3COH] conformers in methanol
![[Pt(COMe)<sub>2</sub>(2-py)<sub>3</sub>COH]](/crest-docs/assets/images/pub-example-2-2.png)
crest input.tomlcrest coord --gbsa methanol --ewin 10
# This is a CREST input file
input = "coord"
runtype = "imtd-gc"
threads = 4
ewin = 10.0
[calculation]
[[calculation.level]]
method = "gfn2"
alpb = "methanol"
$coord
1.48235976014562 0.32575477023909 0.83983586742930 pt
4.37233116325056 -2.04701937728251 0.66066526359202 c
5.11582123352082 -2.89977152283009 -1.35531347223172 o
5.60331010456907 -2.97886601012202 3.10440618630801 c
5.11582123352082 -1.79782119213888 4.71363082065877 h
4.96457322302306 -4.90914755554552 3.43123243126445 h
7.64542186308448 -3.03767428737742 2.85382472163511 h
3.90413261656682 3.15849014823120 0.32067896584616 c
3.77547628198769 4.50973504009881 -1.55263489557537 o
5.78086877201500 3.82467530185737 2.40255812110202 c
6.44902868945004 5.75938447561023 2.16769917785472 h
4.93481948506077 3.56859662386391 4.26032709535443 h
7.38167845589603 2.54234683232997 2.24297074917982 h
-1.45880054444693 -2.37015120764916 1.99982157738756 n
-1.37380633216814 -3.71993156176379 4.12084829921227 c
-3.47313332880892 -4.91477704969539 5.12088380983082 c
-5.76730431783315 -4.67836853101913 3.87619679514437 c
-5.86160354159028 -3.26072055256804 1.67926544374004 c
-3.65812239940936 -2.14869231241016 0.79621720883004 c
-3.66283159693252 -0.54983471562441 -1.60480456492594 c
-1.36490194262998 -1.28858913220566 -3.20027766220770 c
-1.32606807059918 -3.74293708770554 -3.74494019740640 n
0.45445456851927 -4.60152659727760 -5.28248940926294 c
2.25936790283487 -3.06404352583571 -6.38168829870466 c
2.17878809080250 -0.49502320914006 -5.86813254537940 c
0.32467195716495 0.43733364975533 -4.26146660021256 c
0.14833216307473 2.45190076015779 -3.96574713712955 h
3.52744783732032 0.78490530819858 -6.70693851206628 h
3.68438581320421 -3.84772429150018 -7.60737222739882 h
0.39857914622211 -6.61487483432435 -5.63264243360372 h
-5.86517134452916 -0.98949461824931 -3.04219073283502 o
-5.69660399402350 -2.62769064394335 -3.83817172589844 h
-3.63492223167593 2.20020246734036 -0.78356738209650 c
-1.79344269668899 2.91320936536104 0.78584828153889 n
-1.75920841806563 5.28509912105245 1.61658700736449 c
-3.54797404257573 7.05739011313605 0.91252418313075 c
-5.45207721188036 6.32967358689699 -0.73330822586627 c
-5.50553000527517 3.85501674464698 -1.58299523562631 c
-6.94955289136293 3.18275045232518 -2.84989409127871 h
-6.87435123990475 7.65734792470912 -1.34159783995923 h
-3.43966438926938 8.95769115346132 1.63587922145511 h
-0.24274666012596 5.76489302728759 2.90140613593504 h
-7.59878342212486 -2.99720202278941 0.64743151148342 h
-7.44966324325272 -5.57429713925087 4.59918333687282 h
-3.30863455866736 -5.99888080678762 6.83682316863177 h
0.45096235462570 -3.84321729467325 5.03295296314152 h
$end
The search for the Pt-complex conformers results in 43 conformers within an energy window of 10 kcal/mol.
Conformational sampling of tyrosine on a graphene surface
To sample a tyrosine molecule at a graphene surface, the graphene sheet has to be constrained. All atoms in the graphene layer are constrained and removed from the metadynamics list. For a detailed guide on how to fix substructure parts see Example 4.
In order for the caluculation to be stable, some of the MD settings have to be adjusted. The SHAKE constraint is turned off (--shake 0), the timestep is reduced to 1 fs (--tstep 1), and only the unconstrained atoms are included in the metadynamics bias and structure comparisons in CREGEN (--subrmsd).
crest input.tomlcrest coord --subrmsd --shake 0 --tstep 1 --cinp constraints.inp
# This is a CREST input file
input = "coord"
runtype = "imtd-gc"
threads = 4
constraints = "constraints.inp"
subrmsd = true
[dynamics]
tstep = 1.0
shake = 0
[calculation]
[[calculation.level]]
method = "gfn2"
$coord
25.57030991921202 -1.29059115296523 -0.00598160501741 C
25.57044241258889 1.28341269512943 -0.00397025649369 C
23.26056590790795 2.70217665940709 -0.00029100251731 C
23.24029402398585 5.32779404644931 0.00100734191172 C
20.94157103860908 6.71653777403401 0.00350095166658 C
20.91152361664611 9.36664222799565 0.00390218154564 C
18.62125921494789 10.73533662251798 0.00644642379287 C
18.58134086796354 13.40310199790359 0.00577252431633 C
16.30144187186615 14.75441822463413 0.00911453357094 C
16.24838174294015 17.43954219647988 0.00645557179198 C
13.98481323267349 18.77014376357869 0.00996412506652 C
13.91132086532623 21.47993962309619 0.00398308521361 C
11.68223395792687 22.76705405593083 0.00667868517840 C
23.23975279130400 -5.33474095446540 -0.00731302769541 C
23.26029458648507 -2.70912180306862 -0.00467349937707 C
20.93174016704535 -1.33727196043975 -0.00133108922934 C
20.93188342707722 1.33055529046503 0.00081585427198 C
18.61221093462830 2.68271748197896 0.00282646704916 C
18.60800793365893 5.36022077189572 0.00464910445605 C
16.29058723267624 6.70694827919018 0.00657403025646 C
16.28436011426403 9.38628406493185 0.00875170443409 C
13.96723583506467 10.73158318782874 0.01208246556117 C
13.95992943220878 13.41187709257133 0.01391081920492 C
11.64338138388279 14.75451471117306 0.01811199832376 C
11.63248103339880 17.43948496412882 0.01741770073639 C
9.32215273401024 18.77351998648383 0.02061202665840 C
9.29861569072829 21.47602775444658 0.01579094470882 C
7.01463133268908 22.77127484019967 0.01713945360400 C
20.91057452024432 -9.37335860619177 -0.00926090528278 C
20.94088299656363 -6.72324817926078 -0.00658702044546 C
18.60745075594095 -5.36670680488450 -0.00374295822885 C
18.61193643260484 -2.68920008796749 -0.00153341601501 C
16.28742192884590 -1.34235637938395 -0.00078002692156 C
16.28757499289433 1.33609346344897 0.00147976178734 C
13.96434116375503 2.68237236768262 0.00076404228717 C
13.96287174466134 5.36168711625019 0.00444321914007 C
11.64121337713845 6.70589478724923 0.00506279531532 C
11.63822495880011 9.38856356746231 0.01140806380708 C
9.31876144361668 10.72973740054357 0.01538062834809 C
9.31472052037413 13.41484574971875 0.02046267069700 C
6.99521035114103 14.75419616780989 0.02462006312471 C
6.99130768004798 17.44070137881147 0.02532754092530 C
4.67042012951467 18.77581140475820 0.02736696446206 C
4.66258399962784 21.47489924179938 0.02293852266839 C
2.35249685077769 22.77391798267787 0.02212621551956 C
18.57998109654765 -13.40958568048023 -0.01028264322867 C
18.62015473984217 -10.74181472085148 -0.00815563904508 C
16.28339497432454 -9.39252741923171 -0.00521520823422 C
16.28988963380622 -6.71318737538808 -0.00404056626572 C
13.96230713311354 -5.36770826591533 -0.00442097129394 C
13.96405926362842 -2.68839552363364 -0.00377125200632 C
11.63966160646814 -1.34407984382584 -0.00904818073003 C
11.63980125609782 1.33828860894632 -0.00694514984261 C
9.31718204611965 2.68076977770467 -0.01577395709023 C
9.31651311270946 5.36383477266664 -0.00518866604770 C
6.99345645543046 6.70626536261829 -0.00580602080543 C
6.99238975005242 9.38889650419404 0.01018123529597 C
4.66942445816832 10.73022469984729 0.01596892428477 C
4.66767523754332 13.41536689488851 0.02498093342981 C
2.34659451442003 14.75374729750557 0.02932151339149 C
2.34541319267838 17.44224899252958 0.03052836779358 C
0.02192747834666 18.77650769724976 0.03128547441315 C
0.02204581702233 21.47485010389652 0.02595882570531 C
-2.30827777761409 22.77415959011223 0.02256838460730 C
16.24661075554111 -17.44578823181741 -0.01013734215265 C
16.29993060120758 -14.76066846818401 -0.00812704005076 C
13.95855696550417 -13.41788125850394 -0.00444039516866 C
13.96612442985704 -10.73758744438051 -0.00414530231920 C
11.63725550740641 -9.39433325364823 -0.00401359135821 C
11.64051700131476 -6.71165587242432 -0.00602746222362 C
9.31595899918277 -5.36940309841218 -0.01310009453262 C
9.31693993550326 -2.68633606543353 -0.01891241488459 C
6.99250858337540 -1.34364841298911 -0.04053087185396 C
6.99262614528279 1.33843607842166 -0.04039634224145 C
4.66829807447026 2.68060255606494 -0.05849331187865 C
4.66838077810071 5.36444295219266 -0.02946711255395 C
2.34546795808210 6.70546777798594 -0.02011056812930 C
2.34548672067421 9.39005944206936 0.00792927448916 C
0.02151160692621 10.73096229461900 0.01836028425584 C
0.02166355850542 13.41525943333584 0.02919214654642 C
-2.30314738868724 14.75399842979222 0.03371873327606 C
-2.30170671357899 17.44247566484074 0.03391819200193 C
-4.62657873721502 18.77628435247385 0.03298595758151 C
-4.61848784408495 21.47537522910175 0.02560169171120 C
-6.97041113719043 22.77198785523224 0.01911534529519 C
13.90914113254730 -21.48594598108393 -0.01033584558689 C
13.98290020369888 -18.77616131023010 -0.00756967293109 C
11.63069926259142 -17.44525404116543 -0.00301796684893 C
11.64186594877656 -14.76028958926714 -0.00225240122053 C
9.31334018064636 -13.42037835388799 -0.00050064690806 C
9.31765144447383 -10.73527777129347 -0.00273906743608 C
6.99141240533732 -9.39419601810598 -0.00610150867183 C
6.99273536257410 -6.71153949160536 -0.01572184076338 C
4.66777019559512 -5.36946863827436 -0.03472958133329 C
4.66784980463537 -2.68568430403884 -0.05767595376480 C
2.34451914565195 -1.34413003433670 -0.08972846459708 C
2.34456672574876 1.33936603534043 -0.08992506624553 C
0.02090811162037 2.68094549890774 -0.08525730399650 C
0.02111281557256 5.36367785785738 -0.04218166058112 C
-2.30319003521588 6.70557418244421 -0.01593859385830 C
-2.30260481415700 9.39011489524983 0.01310861544943 C
-4.62640274973063 10.73069866586899 0.02658914458233 C
-4.62436575510021 13.41584995240830 0.03462561586354 C
-6.95176077190229 14.75491657239231 0.03775667851738 C
-6.94759324240958 17.44141219089441 0.03541282761784 C
-9.27832130444150 18.77446705578989 0.03155385525560 C
-9.25452218190166 21.47696510552652 0.02154959462713 C
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