Avogadro2 loading a .inp or .xyz file Inquiry?

General Discussion
1

Hello Avogadro Forum:),

I have generated a .inp file via ffTK exhibiting 3-D Coordinates of a ligand, I also transformed this same file to a .xyz file, however, can not load either into Avogadro2 via its File → Import
option (no selection to choose from since ffTK generated and it is in my Laptop) nor via dragging each into its screen i.e.:

Error while reading file ‘/Users/joelsubach/Desktop/3-chargeOpt/14C-ACC-C7/14C-ACC-C7.inp’:

OpenBabel error: conversion failed.

or

Error while reading file ‘/Users/joelsubach/Desktop/3-chargeOpt/14C-ACC-C7/14C-ACC-C7.xyz’:

Error parsing number of atoms.

are generated respectively (attached is .xyz file and below the .inp file is pasted):

! HF 6-31G* TightSCF opt
%maxcore 1000

%geom
ConnectFragments
{ 1 2 O 9 64 }
end
Constraints
{ B 9 64 C }
{ D * 65 9 * C }
end
invertConstraints true
end

%coords
CTyp xyz
Charge -2
Mult 1
Units Angs
coords

O(1) 101.70700073242188 104.2490005493164 71.82099914550781
C(1) 102.41699981689453 105.29000091552734 71.82499694824219
O(1) 103.53500366210938 105.50299835205078 72.3949966430664
C(1) 101.86699676513672 106.48200225830078 71.01599884033203
C(1) 100.74600219726562 106.33200073242188 70.18900299072266
C(1) 100.26799774169922 107.40299987792969 69.4280014038086
C(1) 100.88099670410156 108.66200256347656 69.48999786376953
C(1) 100.37699890136719 109.81500244140625 68.64700317382812
N(1) 101.49400329589844 110.63099670410156 68.16500091552734
C(1) 102.59200286865234 110.06900024414062 67.56900024414062
C(1) 102.73999786376953 108.7979965209961 66.99700164794922
C(1) 103.99800109863281 108.43900299072266 66.53099822998047
C(1) 105.0790023803711 109.35199737548828 66.63500213623047
C(1) 104.9280014038086 110.63600158691406 67.16100311279297
C(1) 103.64800262451172 111.03800201416016 67.58399963378906
C(1) 103.11799621582031 112.1989974975586 68.20500183105469
C(1) 101.8030014038086 111.93299865722656 68.56700134277344
C(1) 100.8219985961914 112.93099975585938 69.2020034790039
O(1) 101.35600280761719 114.03500366210938 69.48899841308594
O(1) 99.62200164794922 112.54399871826172 69.33200073242188
S(1) 106.7020034790039 108.69599914550781 66.46199798583984
O(1) 107.6719970703125 109.8030014038086 66.50199890136719
O(1) 106.73400115966797 107.72000122070312 65.36199951171875
N(1) 106.96399688720703 107.80400085449219 67.88200378417969
C(1) 106.86599731445312 108.61100006103516 69.11900329589844
C(1) 108.00900268554688 108.28900146484375 70.04900360107422
C(1) 109.3239974975586 108.43599700927734 69.58399963378906
C(1) 110.4010009765625 108.1500015258789 70.4229965209961
C(1) 110.17500305175781 107.72699737548828 71.73799896240234
C(1) 108.86599731445312 107.58899688720703 72.20500183105469
C(1) 107.78500366210938 107.88099670410156 71.36799621582031
C(1) 106.19499969482422 106.54199981689453 67.97000122070312
C(1) 106.6760025024414 105.71299743652344 69.13099670410156
C(1) 105.81400299072266 105.43000030517578 70.19599914550781
C(1) 106.25299835205078 104.6719970703125 71.28800201416016
C(1) 107.56500244140625 104.19499969482422 71.30999755859375
C(1) 108.43499755859375 104.4739990234375 70.24700164794922
C(1) 107.99099731445312 105.22200012207031 69.15699768066406
C(1) 101.98600006103516 108.822998046875 70.34100341796875
C(1) 102.4749984741211 107.74600219726562 71.08200073242188
H(1) 100.27799987792969 105.35099792480469 70.15299987792969
H(1) 99.41200256347656 107.26000213623047 68.76599884033203
H(1) 99.81600189208984 109.43199920654297 67.78099822998047
H(1) 99.7300033569336 110.51599884033203 69.18499755859375
H(1) 101.91699981689453 108.08799743652344 66.9729995727539
H(1) 104.15799713134766 107.4729995727539 66.05899810791016
H(1) 105.78700256347656 111.3010025024414 67.21900177001953
H(1) 103.5989990234375 113.1510009765625 68.38700103759766
H(1) 105.8949966430664 108.44200134277344 69.60900115966797
H(1) 106.91400146484375 109.6709976196289 68.8489990234375
H(1) 109.4800033569336 108.7509994506836 68.55400085449219
H(1) 111.41999816894531 108.26300048828125 70.05400085449219
H(1) 111.01599884033203 107.49199676513672 72.38899993896484
H(1) 108.68000030517578 107.24700164794922 73.22200012207031
H(1) 106.76699829101562 107.74199676513672 71.72599792480469
H(1) 106.33599853515625 106.01300048828125 67.02300262451172
H(1) 105.12200164794922 106.7490005493164 68.10199737548828
H(1) 104.79499816894531 105.81199645996094 70.22200012207031
H(1) 105.53500366210938 104.49099731445312 72.08599853515625
H(1) 107.91799926757812 103.60900115966797 72.15799713134766
H(1) 109.46099853515625 104.10900115966797 70.2699966430664
H(1) 108.66699981689453 105.46399688720703 68.33799743652344
H(1) 102.47200012207031 109.7979965209961 70.40299987792969
H(1) 103.33899688720703 107.85199737548828 71.73400115966797
H(2) 103.2030029296875 109.35800170898438 69.33599853515625
O(2) 103.49500274658203 109.01799774169922 70.18199920654297
H(2) 102.8270034790039 109.31099700927734 70.802001953125
end
end

14C-ACC-C7.xyz (4.3 KB)

If you have resolve towards this topic feel free to update me accordingly and I need Avogadro2 for this application, thanks:)

2

Well, the xyz file you posted in the other thread worked perfectly fine for me. The one you’ve just posted here isn’t working because it isn’t an xyz file, it has the exact same contents as you’ve posted in this post. Putting .xyz on the end doesn’t make it an XYZ file, it’s the format of the contents that determines that.

Why the .inp file isn’t working I don’t know though.

3

The problem is the O(1), C(1), etc. – Avogadro and Open Babel generally expect elements, not some sort of atom label with it.

4

Hello matterhorn103 and ghutchis thank you for your kind and prompt update:).

Yes I must of made an adjustment error during processing, accordingly the new .xyz file of the .inp coordinates created without the (1) etc. is functioning i.e. was dragged and entered into Avogadro2 satisfactorily, thanks again:)

1 Like
5

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