9
$\begingroup$

I have got aggregate of 4 non-protein compounds I would submit for molecular dynamics simulation. The problem is I can't find software capable to do that. Amber, GROMACS, LAMMPS, all of them require structure to be built up from the aminoacids so the topology can be read. I've seen GROMACS has x2top that should be able to generate topology from non-protein structure. However, for my system it fails. What can I do?

What I need is to achieve most probable relative positions of each of four compounds belonging to the one aggregate compound.

Here are .xyz coordinates of the aggregate:

248
    Energy:    -128.8882289
N          2.94981        4.07926       -5.95549
C          1.55689        4.07222       -5.57866
H          0.95978        3.62638       -6.43298
C          0.93686        5.43505       -5.21651
C          0.87184        6.32909       -6.38603
C          1.67148        7.45272       -6.69880
N          1.24256        8.02487       -7.89049
C          0.19644        7.27018       -8.30869
N         -0.06225        6.22632       -7.42362
C          1.30522        3.12008       -4.38134
O          0.47546        2.19923       -4.49799
N          2.01969        3.35894       -3.21757
C          1.92802        2.65116       -2.01591
C          0.88945        1.74242       -1.73904
C          0.84547        1.06621       -0.51116
F         -0.18927        0.21946       -0.29679
C          1.82258        1.27431        0.49798
N          1.80287        0.69700        1.80611
N          1.39566       -0.45359        1.96381
C          1.34687       -1.02655        3.27192
C          1.52415       -2.43840        3.37979
F          1.81094       -3.17945        2.28364
C          1.42458       -3.09620        4.60909
C          1.13511       -2.37755        5.79381
N          1.02421       -3.08555        6.99322
C          1.04112       -2.55703        8.27589
O          1.18165       -1.33803        8.49824
C          0.83998       -3.56312        9.44452
H         -0.17494       -4.03912        9.27838
N          0.78281       -2.92516       10.73973
C          1.93934       -4.64304        9.37883
C          1.54272       -5.80248        8.55823
C          2.10713       -6.27545        7.34959
N          1.46038       -7.43692        6.94522
C          0.51317       -7.68025        7.88448
N          0.53075       -6.71251        8.88577
C          0.94035       -0.98628        5.70659
C          1.05359       -0.32782        4.47349
F          0.84082        1.00858        4.45349
C          2.86069        2.20697        0.20128
F          3.83578        2.45682        1.10659
C          2.91419        2.87552       -1.02517
H          3.47097        4.75474       -5.43025
H          3.04735        4.27405       -6.93267
H          1.54324        5.94078       -4.41699
H         -0.09332        5.25659       -4.80267
H          2.51022        7.85384       -6.12959
H         -0.39199        7.42945       -9.22115
H         -0.78097        5.54995       -7.49636
H          2.71437        4.07873       -3.24086
H          0.09023        1.54368       -2.47318
H          1.57350       -4.18887        4.63032
H          1.02086       -4.08511        6.91187
H          0.11162       -2.18010       10.73068
H          1.67727       -2.55447       10.99878
H          2.18617       -4.99839       10.41904
H          2.88063       -4.20359        8.95158
H          2.93228       -5.84292        6.78254
H         -0.19451       -8.51933        7.88727
H         -0.06349       -6.66413        9.67581
H          0.69461       -0.38655        6.59911
H          3.74390        3.58154       -1.20015
H        -15.18170       -5.74686       -4.99155
F         -7.02571       -5.08907       -3.98787
H          0.65534      -11.21141       -2.50902
H         -9.52391       -4.63234       -4.36237
N        -14.25254       -5.57136       -4.66445
H        -13.91637       -4.71222       -5.05351
C          1.18679      -11.63930       -1.65826
H          2.08113       -9.05540       -1.64176
C         -9.32902       -5.35310       -3.54994
C         -8.00147       -5.67502       -3.25496
H        -11.78293       -4.83581       -3.83134
N          1.11328      -12.99119       -1.34556
C          2.03505      -10.97543       -0.74023
C          2.44727       -9.55973       -0.70751
N        -11.70170       -5.56231       -3.14774
H          3.57245       -9.50454       -0.72587
C        -10.39538       -5.93575       -2.82231
C        -14.21157       -5.56054       -3.22256
C         -7.67004       -6.60441       -2.22389
C          1.90085      -13.16305       -0.25528
N         -6.28334       -6.81223       -1.93951
H        -15.66861       -1.98691       -4.18721
H        -15.00747       -6.26815       -2.83416
C        -16.24979       -2.62698       -3.52327
C        -12.87527       -6.14638       -2.69589
N          2.48240      -11.96293        0.14523
N        -17.62237       -2.47886       -3.36451
C         -4.49640       -8.10162       -1.25030
N         -5.88501       -7.91808       -1.55368
C         -3.87925       -9.32440       -1.64388
H          3.17318       -7.23677        0.36085
F         -4.56957      -10.23766       -2.36676
C         -3.70257       -7.19528       -0.49914
C         -2.55065       -9.60942       -1.31470
O          0.35611       -6.94553        0.32760
C         -2.37455       -7.48350       -0.15432
C         -1.77678       -8.68949       -0.56764
F         -4.23242       -6.02796       -0.06245
C          0.53834       -8.17137        0.18934
C        -10.08912       -6.84769       -1.79487
H          2.07812      -14.10928        0.27181
C        -15.78188       -3.69142       -2.71834
C          1.90838       -8.82060        0.53509
N         -0.46010       -9.03051       -0.24672
C         -8.75617       -7.18141       -1.51305
C        -17.99820       -3.43334       -2.47759
H         -2.12268      -10.56741       -1.65501
C        -14.40721       -4.19212       -2.54285
H         -1.81598       -6.74527        0.44577
H         -0.19493       -9.97937       -0.43360
N          2.86803       -7.88077        1.06569
H        -13.69657       -3.43595       -2.97421
H          3.09956      -11.82715        0.90716
N        -16.90981       -4.19498       -2.05957
H        -19.01808       -3.61296       -2.11480
O        -12.90229       -7.09102       -1.88528
H        -10.88203       -7.32042       -1.19068
H        -16.92146       -4.93886       -1.40693
F         -8.52681       -8.05466       -0.50489
H          1.69989       -9.56622        1.36285
H          2.46898       -7.36611        1.82784
H        -14.16857       -4.30034       -1.44929
H         18.09012        9.42357       -1.81836
F         16.48163        1.39387       -2.87539
H          7.96220       -4.06105       -3.51819
H         17.60268        3.68354       -2.56623
N         17.92323        8.43985       -1.73935
H         18.68774        7.93896       -2.14905
C          7.37441       -4.57902       -2.75953
H          9.42815       -6.32849       -3.18884
C         16.75252        3.51753       -1.88275
C         16.06761        2.30160       -1.96011
H         17.92140        5.71877       -1.46626
N          6.15726       -4.08817       -2.30354
C          7.67815       -5.80012       -2.11118
C          8.83234       -6.69634       -2.31074
N         17.09147        5.70197       -0.90756
H          8.45585       -7.72472       -2.57522
C         16.36409        4.50931       -0.94985
C         17.71875        8.06851       -0.35999
C         14.95253        2.01848       -1.11633
C          5.71401       -4.98725       -1.39019
N         14.35655        0.72269       -1.21801
H         21.61587        8.58107       -0.75362
H         17.19055        8.92234        0.16625
C         21.09462        9.17140        0.00018
C         16.74102        6.87002       -0.24821
N          6.60605       -6.04649       -1.24540
N         21.60136       10.37175        0.48346
C         12.54069       -0.70153       -1.10751
N         13.14748        0.58850       -1.03360
C         11.16073       -0.75363       -1.47075
H         10.79779       -8.38500       -1.72194
F         10.49608        0.37743       -1.80507
C         13.15822       -1.93853       -0.78035
C         10.45825       -1.96102       -1.50679
O         12.02403       -5.92934       -1.08952
C         12.45238       -3.15052       -0.80187
C         11.09434       -3.18059       -1.17037
F         14.45681       -1.97792       -0.40174
C         10.80784       -5.65638       -1.12525
C         15.27807        4.24224       -0.09560
H          4.78194       -4.91884       -0.81412
C         19.85964        8.88077        0.62505
C          9.73569       -6.78130       -1.06352
N         10.33617       -4.35316       -1.19072
C         14.58375        3.02684       -0.18691
C         20.69763       10.81665        1.39124
H          9.39657       -1.93873       -1.80486
C         18.98066        7.71141        0.44765
H         12.98913       -4.07196       -0.51983
H          9.35005       -4.23241       -1.32787
N         10.30574       -8.09865       -0.89693
H         19.56647        6.90777       -0.07566
H          6.50934       -6.82415       -0.64051
N         19.62080        9.94087        1.50745
H         20.77041       11.74227        1.97621
O         15.70174        6.99012        0.42661
H         14.94922        4.97548        0.66030
H         18.84443       10.03273        2.11405
F         13.55602        2.82368        0.67020
H          9.12052       -6.57875       -0.13351
H         10.94041       -8.10690       -0.12051
H         18.66052        7.30605        1.44630
H        -13.76816       14.18822        0.15446
F         -7.80049        8.53951       -1.12529
H         -7.63542       -1.62444       -0.88481
H         -9.18708       10.67465       -0.82679
N        -13.17375       13.38157        0.17397
H        -12.40898       13.52486       -0.45771
C         -7.26280       -2.38041       -0.19256
H         -4.92758       -1.46248       -1.31115
C         -9.45404        9.87889       -0.11042
C         -8.75922        8.66874       -0.17804
H        -10.77948       11.98996        0.22485
N         -8.11638       -3.21139        0.52310
C         -5.91608       -2.69441        0.10809
C         -4.67369       -2.10453       -0.42557
N        -11.12066       11.31524        0.88069
H         -4.00416       -2.93001       -0.79885
C        -10.47282       10.07761        0.85340
C        -12.71357       13.14074        1.52107
C         -9.04883        7.58895        0.71076
C         -7.31478       -4.02595        1.25291
N         -8.22918        6.42421        0.60687
H        -10.97501       16.64039        0.56276
H        -13.61494       13.20121        2.20653
C        -11.72035       16.60868        1.35758
C        -12.18298       11.69437        1.68630
N         -5.96893       -3.74749        1.02909
N        -12.42268       17.73783        1.76153
C         -7.84670        4.15808        0.85037
N         -8.66644        5.32269        0.93868
C         -8.51924        2.89889        0.78641
H         -2.17063       -1.22446       -0.39021
F         -9.87124        2.84337        0.74802
C         -6.42644        4.11547        0.87959
C         -7.81553        1.69236        0.74875
O         -3.58659        1.12673        0.30641
C         -5.71718        2.90526        0.84970
C         -6.40005        1.67698        0.77865
F         -5.70416        5.25640        0.96629
C         -4.39806        0.21018        0.54285
C        -10.77381        9.02711        1.73940
H         -7.64584       -4.80706        1.94962
C        -12.12509       15.48849        2.12004
C         -3.92767       -1.26917        0.63595
N         -5.74810        0.44199        0.76341
C        -10.07810        7.81061        1.66405
C        -13.24784       17.32506        2.75528
H         -8.39188        0.75356        0.69354
C        -11.63630       14.09952        2.06136
H         -4.61552        2.94570        0.88616
H         -6.33787       -0.36423        0.85277
N         -2.49355       -1.41802        0.53990
H        -10.72396       14.07694        1.40613
H         -5.19146       -4.22413        1.41527
N        -13.09845       15.96346        3.00678
H        -13.95622       17.95292        3.31041
O        -12.70838       10.94446        2.52936
H        -11.55643        9.13140        2.50996
H        -13.58224       15.42900        3.68464
F        -10.40171        6.84946        2.56012
H         -4.21459       -1.62930        1.67173
H         -2.03679       -0.78457        1.17047
H        -11.33159       13.74988        3.08562
$\endgroup$
  • $\begingroup$ +1. Welcome to the site and thanks for asking your question here! We hope to see much more of you !!! Also: beautiful that you are our 1234th user! $\endgroup$ – Nike Dattani Aug 20 at 15:45
  • 1
    $\begingroup$ This was posted on chemistry. While I think this is a better site for this question, why the duplicate? $\endgroup$ – Cody Aldaz Aug 20 at 16:27
4
$\begingroup$

The question is how to build a simulation model rather than the choice of software. You can build a box and then put your four molecules into the box. I have used the supported coordinates to build a structure file [xxx.vasp] (You can use VESTA software to open it and view it). The key point is how to set the position of these molecules. If the position is set down, you can use VASP or any other software to perform molecular dynamics. XXX.vasp can be read by VASP software.

struct
1.0
   80.0000000000         0.0000000000         0.0000000000
    0.0000000000        80.0000000000         0.0000000000
    0.0000000000         0.0000000000        80.0000000000
C    H    F    N    O
96   88   16   40    8
Cartesian
77.964949608        69.024572372        79.259772301
77.552728653        70.440268517        79.292488098
10.395380259        74.064249992        77.177691460
14.211570024        74.439458847        76.777439117
 7.670040131        73.395590782        77.776107788
78.099150658        66.836948395        79.744720459
16.249790192        77.373018265        76.476731300
12.875269651        73.853621483        77.304110527
 4.496399760        71.898379326        78.749699593
 3.879249990        70.675601959        78.356118202
 3.702569902        72.804718018        79.500861168
 2.550649941        70.390582085        78.685297966
 2.374550104        72.516498566        79.845681190
 1.776780039        71.310510635        79.432358742
79.461660385        71.828632355         0.189340003
10.089119673        73.152308464        78.205127716
15.781880617        76.308579445        77.281661034
78.091621399        71.179399490         0.535090044
 8.756170273        72.818589211        78.486948013
17.998199463        76.566658020        77.522411346
14.407210350        75.807881355        77.457151413
72.625589371        75.420980453        77.240471840
63.247480392         3.517529964        78.117251396
63.932390213         2.301599979        78.039889336
72.321848869        74.199881554        77.888817787
71.167659760        73.303661346        77.689261436
63.635911942         4.509309828        79.050149918
62.281250954         8.068510294        79.640011787
65.047469139         2.018480003        78.883671761
74.285988808        75.012750626        78.609809875
58.905382156         9.171400070         0.000180000
63.258981705         6.870020032        79.751791954
67.459306717        79.298467636        78.892488480
68.839268684        79.246368408        78.529248238
66.841778755        78.061470985        79.219651222
69.541749954        78.038978577        78.493208885
67.547616959        76.849479675        79.198131561
68.905658722        76.819410324        78.829631805
69.192161560        74.343619347        78.874750137
64.721927643         4.242239892        79.904398918
10.472819805        10.077610016         0.853400007
60.140361786         8.880769610         0.625049993
70.264310837        73.218698502        78.936481476
65.416250229         3.026840091        79.813089371
59.302368164        10.816650391         1.391240060
61.019339561         7.711409926         0.447649993
 7.262800336        77.619590759        79.807438850
 9.454039335         9.878889918        79.889578819
 8.759220243         8.668740392        79.821958542
 5.916079879        77.305588722         0.108089997
 4.673689902        77.895469666        79.574432373
12.713569403        13.140740395         1.521070004
 9.048830271         7.588950396         0.710759982
 7.314780354        75.974049568         1.252910048
11.720349789        16.608680487         1.357579976
12.182979584        11.694370508         1.686300039
 7.846699953         4.158080220         0.850370005
 8.519240618         2.898890078         0.786409974
 6.426439881         4.115470052         0.879589990
 7.815529704         1.692360044         0.748749971
 5.717179775         2.905260026         0.849699974
 6.400049925         1.676979959         0.778649971
 4.398059845         0.210180003         0.542850010
10.773810148         9.027110338         1.739400029
12.125089169        15.488489866         2.120039910
 3.927670121        78.730831146         0.635950044
10.078099966         7.810609937         1.664049923
13.247840405        17.325060368         2.755280137
11.636300087        14.099519253         2.061359882
 9.329019785        74.646902084        76.450061798
 8.001469374        74.324979782        76.745038033
77.085809708         2.875519991        78.974828720
78.813209534        68.360700607        78.341741562
77.139310837         2.206970006         0.201280005
79.059648514        79.013719559         5.706590414
78.946409225        79.672179222         4.473490119
79.160017967        76.436882019         9.444519877
78.443107605         4.072219729        74.421339035
79.486827850        72.319750786         7.884479761
79.063138962         5.435050130        74.783492088
79.128160477         6.329089999        73.613967896
78.328518867         7.452720404        73.301200867
79.803562164         7.270179987        71.691308022
78.694782257         3.120079935        75.618658066
78.071980476         2.651160061        77.984089851
79.110550880         1.742419899        78.260960579
79.154529572         1.066210046        79.488840103
78.177418709         1.274310052         0.497980006
78.653130531        78.973450661         3.271920085
78.475852013        77.561597824         3.379790187
78.575420380        76.903800964         4.609089792
78.864889145        77.622451782         5.793809891
78.958878517        77.442970276         8.275890350
78.060660362        75.356960297         9.378830194
78.457279205        74.197521210         8.558230400
77.892870903        73.724551201         7.349590063
 0.174940005        75.960879326         9.278380275
79.344658852        68.788590431        77.490978241
 9.523909688        75.367660522        75.637631416
13.916370869        75.287780762        74.946489334
77.918868065        70.944600105        78.358240128
11.782929897        75.164189339        76.168661118
76.427550316        70.495457649        79.274129868
15.668609142        78.013091087        75.812788010
15.007469654        73.731851578        77.165842056
76.826820374        72.763228416         0.360850021
10.882029533        72.679581642        78.809318542
16.921459436        75.061140060        78.593068123
78.300108910        70.433778763         1.362849921
77.531018257        72.633891106         1.827839911
14.168570042        75.699658394        78.550710678
61.909880638         9.423569441        78.181638718
72.037801743        75.938949585        76.481809616
77.921881676        65.890722275         0.271809995
 2.122679949        69.432592392        78.344988823
 1.815979928        73.254728317         0.445769988
 0.194930006        70.020627975        79.566397667
13.696570396        76.564049721        77.025790215
76.900439262        68.172850609         0.907159969
19.018080235        76.387038231        77.885198593
62.397317886         3.683540225        77.433772087
61.312260628         7.938960195        77.850952148
62.078599930         5.718770027        78.533740044
70.571851730        73.671512604        76.811161041
71.544151306        72.275280952        77.424778938
58.384132385         8.581069708        79.246377945
62.809448242         8.922340274         0.166250002
69.202213287        71.614999771        78.278059959
60.433530807         6.907770038        79.924340248
73.490657806        73.175849915        79.359488487
59.229588509        11.742269993         1.976210028
65.050783157         4.975480139         0.660300031
61.155567169        10.032730103         2.114049941
70.879478455        73.421249390        79.866490364
69.059591293        71.893100739        79.879488945
76.529030800         4.754740298        74.569749832
76.952648163         4.274050295        73.067331314
78.456759453         5.940780044        75.583009720
 0.093319993         5.256589651        75.197329521
77.489781380         7.853839993        73.870410919
 0.391990021         7.429450154        70.778851509
 0.780970007         5.549950004        72.503638268
77.285628319         4.078730047        76.759138107
79.909768105         1.543679982        77.526822090
78.426499367        75.811128616         4.630320072
78.979139328        75.914888382         6.911870241
79.888381958        77.819900513        10.730680227
78.322730064        77.445530891        10.998780727
77.813830376        75.001611710        10.419039726
77.119369507        75.796408653         8.951579928
77.067718506        74.157080650         6.782540083
 0.194509998        71.480669975         7.887269855
 0.063490001        73.335871696         9.675809741
79.305391312        79.613451958         6.599110365
76.256098747         3.581539989        78.799848557
15.181699991        74.253139496        75.008449554
61.339478493         7.306050062         1.446300000
13.768160343        14.188220501         0.154459998
 7.635419965        78.375558853        79.115190506
 9.187080264        10.674650669        79.173212051
11.556429863         9.131399989         2.509959936
13.582240343        15.428999662         3.684639931
 4.214590192        78.370699883         1.671729982
 2.036789954        79.215431213         1.170469970
11.331589222        13.749879599         3.085619807
79.040222168         3.626379967        73.567018509
12.408980131        13.524860144        79.542288780
 4.927579761        78.537521362        78.688850403
10.779479742        11.989959478         0.224849992
 4.004159868        77.069988251        79.201149940
10.975010395        16.640390158         0.562760010
13.614939451        13.201210499         2.206530124
 2.170629948        78.775539398        79.609789848
 7.645840049        75.192937851         1.949619949
 8.391879797         0.753559992         0.693539977
 4.615519941         2.945699990         0.886159986
 5.191460252        75.775871277         1.415269971
 6.337870359        79.635767937         0.852769986
10.723960400        14.076939821         1.406129897
13.956220150        17.952921391         3.310410082
75.218057632        75.081157684        79.185881615
70.603427887        78.061270714        78.195137978
67.010869980        75.928039551        79.480171204
70.649948120        75.767588615        78.672127724
14.252539873        74.428639412        75.335550308
11.701700687        74.437689781        76.852259636
 6.283339858        73.187770844        78.060488701
77.517600060        68.037071228         0.145229995
17.622369528        77.521138191        76.635489464
 5.885009766        72.081918716        78.446321487
78.886718750        67.008810043        78.654441833
65.643448830         0.722690001        78.781991005
73.393950462        73.953509331        78.754601479
58.398637772        10.371749401         0.483460017
66.852521896         0.588500015        78.966398239
69.694261551        71.901350021        79.103069305
78.757438660         8.024870157        72.109508514
77.050189972         4.079259932        74.044508934
73.842740059        75.911831856        77.696461678
62.908530235         5.701969862        79.092440605
69.663829803        75.646839142        78.809280396
 0.062250001         6.226319671        72.576379776
77.980308533         3.358939886        76.782431602
60.379199982         9.940870404         1.507450044
13.173749447        13.381569386         0.173969995
 8.116379976        76.788611412         0.523100011
11.120660305        11.315239668         0.880689994
 8.229180574         6.424210072         0.606869981
 5.968929529        76.252508163         1.029090062
12.422679663        17.737829685         1.761530042
 8.666440248         5.322690010         0.938680023
 5.748099685         0.441989973         0.763409957
 2.493550032        78.581981659         0.539899990
13.098449707        15.963460207         3.006779850
78.197131157         0.697000027         1.806109995
78.604340553        79.546408653         1.963810027
78.975791931        76.914448738         6.993219852
 0.460099988        70.969491005        79.753279686
77.131967545        72.119231224         1.065690070
16.909809113        75.805020332        77.940430641
62.076768875         8.439849615        78.260650635
79.217190742        77.074842453        10.739729404
78.539619446        72.563080788         6.945220232
79.469251633        73.287491798         8.885769844
 7.025710344        74.910931587        76.012129784
 4.569570124        69.762339592        77.633237839
 8.526809812        71.945338249        79.495110512
63.518371582         1.393869966        77.124609947
 9.871239662         2.843369842         0.748019964
10.401709080         6.849460006         2.560120225
 5.704160333         5.256400108         0.966290012
78.189058304        76.820549965         2.283639908
 0.189270005         0.219459999        79.703211784
79.159178734         1.008579955         4.453489780
76.164221764         2.456820011         1.106590033
66.443977356         2.823680043         0.670199990
 7.800489664         8.539509773        78.874711990
69.503917694         0.377429985        78.194928169
65.543189049        78.022079468        79.598259926
 4.232420027        73.972039223        79.937548637
64.298257828         6.990119815         0.426610000
 3.586589992         1.126729995         0.306410007
79.524540901         2.199229896        75.502009392
12.708380222        10.944459438         2.529360056
67.975969315        74.070658684        78.910479546
12.902290821        72.908978462        78.114719391
78.818349838        78.661971092         8.498240709
79.643888474        73.054471016         0.327600017
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1
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There are two issues here:

  1. How to build A model for simulations?
  2. How to create the input files from the model from step 1 to my molecular dynamic software?

For the first step I would try to use any specific software for design/build/draw structures to manually create the system. Also, it is possible to use software like Packmol.

For the second step, and as each molecular dynamic have its own input structure, you need the "conversion" tool that come with it to use as input the structure from step 1. I rather prefer to use a recommended graphical user interface for the molecular dynamics software. For example, the software DESMOND came with the MAESTRO graphical interface where you setup the inputs and also analyses the outputs.

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  • $\begingroup$ To add to this, there will be force-fields that can simulate a collection of molecules using just atomic positions too (There are similar ML ones for systems like water eg. n2p2) $\endgroup$ – fireball.1 Aug 24 at 15:44

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