CCL: What is the format of this file containing Cartesian coordinates?
- From: tim hockswender <timhockswender__gmail.com>
- Subject: CCL: What is the format of this file containing Cartesian
coordinates?
- Date: Mon, 9 Jan 2012 18:15:46 -0500
Andrew, I pasted the coordinates into Avogadro and the resultant molecule
looks very strange.
You should try to
re-build.
One suggestion is to use Symyx Draw to redo
the desired structure. Save it as a mol file. SD will not display in 3D but
Avogadro (in my experience) will convert any standard drawing into a
space-filling molecule.
Save it then use the Extensions in Avogadro to
optimize geometry. Do this repeatedly until the structure seems stable. Then you
can generate an inp(ut) file which will need more editing to fit your needs.
Tom Hockswender
On Mon, Jan 9, 2012
at 2:08 PM, Andrew DeYoung andrewdaviddeyoung=-=
gmail.com <owner-chemistry*ccl.net> wrote:
Sent to CCL by: Andrew DeYoung [andrewdaviddeyoung.*.gmail.com]
Dear Professor Holland,
Thank you. I have downloaded and installed Avogadro.
Unfortunately,
Avogadro will not open the below text containing the coordinates (if I
save this text in an extensionless file called "mytest"); it gives
me
an error message:
"Reading molecular file failed"
Do you have any other ideas?
Thank you so much for your time.
Andrew DeYoung
Carnegie Mellon University
On Sun, Jan 8, 2012 at 5:10 PM, Edward Holland
hollandej~~Cardiff.ac.uk <owner-chemistry : ccl.net> wrote:
> Hi,
> Handy tip: You can copy and paste many common formats directly into
Avogadro
> (Main Page - Avogadro - Free cross-platform molecule editor) You can
then
> visualise it here or save into a format you are more familiar with.
>
> Yours
>
> Ed Holland
>
> On 8 Jan 2012, at 19:50, Andrew DeYoung andrewdaviddeyoung- -gmail.com
> wrote:
>
> -0.02689401 0.05432733 1.07516282 3 H 1
> 0.03282702 -0.01179385 0.68330051 2 O 2
> 0.60586594 -0.05478650 -1.06215854 3 H 3
> 0.54625340 0.01126245 -0.67028541 2 O 4
> -0.00037430 0.00545262 0.11451905 1 C 5
> -0.87007097 0.50375034 -0.04749619 1 C 6
> -0.86607388 -0.50142967 -0.04692549 1 C 7
> 0.87536552 0.51049597 0.02025204 1 C 8
> 0.87795979 -0.51877321 0.02366501 1 C 9
> -0.00283324 1.00386837 -0.01257709 1 C 10
> 0.00039748 -1.00136092 -0.01066833 1 C 11
> -1.73307292 0.00197123 -0.03871588 1 C 12
> -0.86683173 1.50543512 -0.02856670 1 C 13
> -0.86909689 -1.50476823 -0.02691608 1 C 14
> 1.73809709 0.00167020 0.06437659 1 C 15
> 0.86891453 1.50286912 0.03907748 1 C 16
> 0.87181125 -1.50614862 0.04060303 1 C 17
> -1.73625671 1.00707540 -0.04218536 1 C 18
> -1.73743458 -1.00321958 -0.04099753 1 C 19
> 1.73948240 1.00519036 0.06254294 1 C 20
> 1.73748379 -1.00684011 0.06397068 1 C 21
> -0.00097315 2.00519687 -0.00474136 1 C 22
> -0.00025493 -2.00481803 -0.00256281 1 C 23
> -2.60679486 0.50744858 -0.05730558 1 C 24
> -2.60244033 -0.49997860 -0.05660149 1 C 25
> -1.73600183 2.00826255 -0.03828653 1 C 26
> -1.73589004 -2.00632024 -0.03581581 1 C 27
> -0.86809971 2.50743539 -0.01969374 1 C 28
> -0.86743107 -2.50800945 -0.01663035 1 C 29
> 1.73739025 -2.00803386 0.03602309 1 C 30
> 0.86918912 -2.50605556 0.01898868 1 C 31
> -2.60674237 1.50998962 -0.06149746 1 C 32
> -2.60337977 -1.50359739 -0.05952099 1 C 33
> -0.00151756 3.01254125 0.00026303 1 C 34
> -1.73833995 3.01353076 -0.04134158 1 C 35
> 1.73896850 -3.01089377 0.04144619 1 C 36
> -2.60747482 2.51319434 -0.06379837 1 C 37
> 0.87160242 -3.51651549 0.01963025 1 C 38
> -2.60959081 3.52137327 -0.06444686 1 C 39
> 1.74167046 -4.01903762 0.03732286 1 C 40
> 0.57935253 -0.00591929 -0.10150666 1 C 41
> -0.29895259 0.51824224 -0.01065610 1 C 42
> -0.29637000 -0.51095564 -0.00724144 1 C 43
> -1.15911004 -0.00215128 -0.05137018 1 C 44
> 0.57861451 1.00085598 0.02367761 1 C 45
> 0.58190077 -1.00453933 0.02559150 1 C 46
> -1.15848220 1.00634128 -0.05096692 1 C 47
> -1.16048708 -1.00566650 -0.04953595 1 C 48
> 1.44505788 0.50095217 0.05994684 1 C 49
> 1.44905447 -0.50423433 0.06052232 1 C 50
> -0.29287191 1.50575663 -0.02758935 1 C 51
> -0.28990959 -1.50337425 -0.02606221 1 C 52
> -2.02697593 0.50391544 -0.04217217 1 C 53
> -2.02491349 -0.50419505 -0.04152028 1 C 54
> 1.44809109 1.50425324 0.03991273 1 C 55
> 1.44587383 -1.50598582 0.04156281 1 C 56
> 0.57921418 2.00435850 0.01557045 1 C 57
> 0.58001551 -2.00575731 0.01775155 1 C 58
> -1.15838843 2.00756158 -0.02302302 1 C 59
> -1.15757535 -2.00795444 -0.02057379 1 C 60
> 2.31207394 -0.00245438 0.05172946 1 C 61
> -2.02776434 1.50719055 -0.04446594 1 C 62
> -2.02602610 -1.50572182 -0.04269775 1 C 63
> 2.31642963 1.00271453 0.05400912 1 C 64
> 2.31524228 -1.00755964 0.05519446 1 C 65
> -0.29021505 2.50557497 -0.00598370 1 C 66
> -0.28747789 -2.51054533 -0.00287556 1 C 67
> 1.44708230 -2.50791413 0.03270193 1 C 68
> 2.31499473 -2.00876451 0.05130262 1 C 69
> 0.58051995 -3.01303700 0.01275161 1 C 70
> -2.02771967 2.50972812 -0.04865231 1 C 71
> -1.15998355 3.01040245 -0.02842868 1 C 72
> 2.31732484 -3.01400623 0.05435683 1 C 73
> 1.45151430 -3.51897104 0.03339008 1 C 74
> -2.03208004 3.51717648 -0.04935652 1 C 75
> 2.31999134 -4.02068999 0.05257440 1 C 76
>
>
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