From owner-chemistry@ccl.net Mon Jan 9 19:45:00 2012 From: "tim hockswender timhockswender .. gmail.com" To: CCL Subject: CCL: What is the format of this file containing Cartesian coordinates? Message-Id: <-46127-120109181554-31425-x/MfsrppDozGCbGMEPqcTQ.:.server.ccl.net> X-Original-From: tim hockswender Content-Type: multipart/alternative; boundary=f46d040169711373d504b62094fb Date: Mon, 9 Jan 2012 18:15:46 -0500 MIME-Version: 1.0 Sent to CCL by: tim hockswender [timhockswender]=[gmail.com] --f46d040169711373d504b62094fb Content-Type: text/plain; charset=ISO-8859-1 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 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 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> > > --f46d040169711373d504b62094fb Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Andrew, I pasted the coordinates into Avogadro and the resultant molec= ule looks very strange.
You should try to re-build.
=A0=
One suggestion is to use Symyx Draw to redo the desired structur= e. Save it as a mol file. SD will not display in 3D but Avogadro (in my exp= erience) will convert any standard drawing into a space-filling molecule. =A0
=A0
Save it then use the Extensions in Avogadro to optimiz= e geometry. Do this repeatedly until the structure seems stable. Then you c= an generate an inp(ut) file which will need more editing to fit your needs.=
=A0
Tom Hockswender
On Mon, Jan 9, 2= 012 at 2:08 PM, Andrew DeYoung andrewdaviddeyoung=3D-=3Dgmail.com <owner-chemistry*ccl.net> wrote:

Sent to CCL by: Andrew DeYoung [andrewdaviddeyoung.*.gmail.com]
Dear Professor Holland,

Thank you. =A0I have downloaded and installed Avogadro. =A0Unfortunately, Avogadro will not open the below text containing the coordinates (if I
save this text in an extensionless file called "mytest"); it give= s 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 Av= ogadro
> (Main Page - Avogadro - Free cross-platform molecule editor) You can t= hen
> 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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