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Carlos Alberto

How to upload

in what format I can upload molecules for studing their properties in the NUITNS toolkit? Thanks.

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  1. 0 Like 0 Dislike

    Baudilio Tejerina

    The Cartesian coordinates for the atoms of the molecule of

    1,3,5-Tris(4-carboxyphenyl)benzene

    follow. The structure given here is C1 (asymmetric) but it may easily be C3

    C 6.0 -0.035797 2.894943 0.013290
    C 6.0 -0.054214 5.716736 0.054900
    C 6.0 -0.961517 3.595535 0.798828
    C 6.0 0.019043 -1.390671 -0.000443
    C 6.0 -0.019302 1.410416 0.000458
    C 6.0 -1.211761 -0.721725 0.000824
    C 6.0 1.231445 -0.688843 0.000061
    C 6.0 -1.214417 0.679260 -0.000870
    C 6.0 1.194977 0.711548 -0.000092
    C 6.0 0.879929 3.631683 -0.753677
    C 6.0 -0.975784 4.991608 0.822128
    H 1.0 0.033691 -2.491608 0.003906
    C 6.0 -2.485886 -1.483871 0.012970
    H 1.0 -2.175613 1.216324 0.002914
    C 6.0 0.875809 5.026000 -0.734818
    C 6.0 -0.053970 7.202286 0.073685
    O 8.0 -0.865372 7.818924 0.754227
    O 8.0 0.822159 7.937210 -0.643265
    H 1.0 0.607574 8.865265 -0.453140
    C 6.0 2.526108 -1.415207 0.011017
    C 6.0 4.982605 -2.803940 0.045532
    C 6.0 3.597427 -0.960129 0.791824
    C 6.0 2.706100 -2.577698 -0.754684
    C 6.0 4.815628 -1.642502 0.811279
    C 6.0 3.917297 -3.268250 -0.739151
    C 6.0 6.270950 -3.543488 0.060638
    O 8.0 7.212753 -3.144547 0.735596
    O 8.0 6.468842 -4.671555 -0.653503
    H 1.0 7.381256 -4.947067 -0.466217
    C 6.0 -4.906479 -2.934052 0.041595
    C 6.0 -2.624466 -2.633377 0.801041
    C 6.0 -3.581711 -1.069809 -0.761765
    C 6.0 -3.820267 -3.356140 0.817841
    C 6.0 -4.779175 -1.782333 -0.749939
    C 6.0 -6.184586 -3.691284 0.051346
    O 8.0 -6.306976 -4.701126 0.734680
    O 8.0 -7.257248 -3.315857 -0.676727
    H 1.0 -7.947464 -3.973236 -0.489594
    H 1.0 -1.681183 3.052353 1.432327
    H 1.0 1.610245 3.117493 -1.399139
    H 1.0 -1.712646 5.507538 1.458374
    H 1.0 1.607376 5.571671 -1.352112
    H 1.0 2.140961 1.274887 0.005035
    H 1.0 3.487625 -0.064407 1.424210
    H 1.0 1.894333 -2.955734 -1.396942
    H 1.0 5.632492 -1.258774 1.443359
    H 1.0 4.024063 -4.175293 -1.355423
    H 1.0 -1.795120 -2.976868 1.440186
    H 1.0 -3.503983 -0.181320 -1.408981
    H 1.0 -3.893127 -4.251953 1.455154
    H 1.0 -5.616745 -1.432663 -1.374542

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  2. 0 Like 0 Dislike

    Baudilio Tejerina

    Hi Carlos.

    The atomic position must be expressed in Cartesian coordinates. The format of the file that contains the molecular geometry should read the coordinates in the following style:

    Atom_symbol Atomic_Number X Y Z


    For example: C 6.0 0.0456 -3.4355 1.0178 .etc. rest of the atoms follow, one per file record.


    With the exception of TEDViz (see examples), the tools in NUITNS take this common format so, you can upload the same file as input to various tools.

    Regards, Baudilio

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