1
$\begingroup$

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?

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
$\endgroup$
3
  • 1
    $\begingroup$ The MD software you mentioned were developed for biochemical problems. Other software, eg NAMD, DL-POLY, Desmond are able to perform calculations on other kind of systems, too. First I would figure out what kind of forcefield you need for your model and then check where they are implemented. (Maybe you want to briefly describe your problem. Most contributors here will not have time to download and visualize the xyz file just to figure out what you are talking about) $\endgroup$ – Greg Aug 20 '20 at 11:51
  • $\begingroup$ I told what I need - to achieve most probable relative positions of each of four compounds belonging to the one aggregate compound. $\endgroup$ – user98045 Aug 20 '20 at 12:28
  • 3
    $\begingroup$ I personally think this question is on topic here, however, you might want to try a more specialist community to ask it: Matter Modeling. (Since you have already gotten an answer, I can't recommend asking it there again and deleting it here. We generally discourage cross-postings though. But maybe you can browse their questions to find some more relevant information for you.) $\endgroup$ – Martin - マーチン Aug 20 '20 at 13:31
2
$\begingroup$

In this case, the problem is not the software really, it's the topology of your molecules. This is a hairy problems, but there are some tools that you can use.

To generate topologies, look into acpype for Amber-based topologies and LigParGen for OPLS-AA-based topologies. However, note that the performances might vary, since these tools are very generic and do not guarantee solid results for all types of molecules. Nevertheless, these will allow you to run simulations (these tools offer topologies in formats for different softwares; GROMACS is free and relatively easy to use, so I would try that.)

If you want something a bit more solid and you have computational resources available (or a good desktop), try xtb, which is a semi-empirical tight-binding software. Its accuracy is somewhere between DFT and older semi-empirical methods, and it is fast. You can run molecular dynamic simulations or use their tool for conformational sampling called CREST.

$\endgroup$
2
$\begingroup$

There is at least one well-known third-party topology generation service for Gromacs and that is the PRODRG server maintained by the van Aalten group at the University of Dundee.

The Gromacs site though states a caveat:

The charges and charge groups generated by PRODRG are typically not consistent with functional groups that were derived more rigorously for the force field of interest. It is therefore the task of the user to validate any parameters obtained, and to modify them, if necessary, since the artifacts of not doing so are now published. A thorough understanding of the underlying force field theory is recommended. See the parameterization page for more details.

$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.