From owner-chemistry@ccl.net Mon Jan  9 12:47:00 2012
From: "jacqueline cawthray jcawth01,,gmail.com" <owner-chemistry!=!server.ccl.net>
To: CCL
Subject: CCL: Clarification for restricted/unrestricted spin in TDDFT
Message-Id: <-46124-120109124606-22212-/vR4robuXdGjEygBcI0W0Q!=!server.ccl.net>
X-Original-From: "jacqueline  cawthray" <jcawth01()gmail.com>
Date: Mon, 9 Jan 2012 12:46:04 -0500


Sent to CCL by: "jacqueline  cawthray" [jcawth01_+_gmail.com]
Hi

I'm trying to calculate the UV spectra of some transition metal complexes 
involving Cu2+, Fe3+ and Zn2+. I have successfully been able to calculate Zn2+ 
complexes which show good agreement with experimental results. However I am 
not having much luck with Cu2+ or Fe3+. I understand I may need to change 
basis sets (I have been using B3LYP/6-31+g(d,p) and am currently trying with 
LanL2Dz on the metal) but have read about using unrestricted B3LYP. Can 
someone possibly explain (in laymans terms) what the difference between 
restricted and unrestricted is so I can decide which to use?

Thanks
Jacquie


From owner-chemistry@ccl.net Mon Jan  9 15:32:00 2012
From: "Andrew DeYoung andrewdaviddeyoung=-=gmail.com" <owner-chemistry^-^server.ccl.net>
To: CCL
Subject: CCL: What is the format of this file containing Cartesian coordinates?
Message-Id: <-46125-120109140812-14353-+4gZDyeX03a93fLVFd5IAQ^-^server.ccl.net>
X-Original-From: Andrew DeYoung <andrewdaviddeyoung,gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Date: Mon, 9 Jan 2012 14:08:06 -0500
MIME-Version: 1.0


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
>
>


From owner-chemistry@ccl.net Mon Jan  9 16:23:00 2012
From: "Geoffrey Hutchison geoffh---pitt.edu" <owner-chemistry!A!server.ccl.net>
To: CCL
Subject: CCL: What is the format of this file containing Cartesian coordinates?
Message-Id: <-46126-120109162114-10796-qpCFFO4+pPwQSr7c/eeRQg!A!server.ccl.net>
X-Original-From: Geoffrey Hutchison <geoffh{}pitt.edu>
Content-Transfer-Encoding: 8bit
Content-type: text/plain; charset=iso-8859-1
Date: Mon, 09 Jan 2012 16:21:07 -0500
MIME-version: 1.0 (Apple Message framework v1251.1)


Sent to CCL by: Geoffrey Hutchison [geoffh]|[pitt.edu]
> 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:


No, he literally means "copy the text from the paper", launch Avogadro, and pick the "Paste" command. I'd send a screenshot, but I think that's ruled out by CCL conventions.

Suffice to say, there's code in Avogadro to "guess" the format of XYZ-like data. I don't know the exact format, but the code finds the "C" and "H" atoms, decides the coordinates are X, Y, Z, (something) element, (something) and generates the system.

Hope that helps,
-Geoff

---
Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geoffh-,-pitt.edu
web: http://hutchison.chem.pitt.edu/


From owner-chemistry@ccl.net Mon Jan  9 19:45:00 2012
From: "tim hockswender timhockswender .. gmail.com" <owner-chemistry.:.server.ccl.net>
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 <timhockswender__gmail.com>
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 <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>
>
>

--f46d040169711373d504b62094fb
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable

<div>Andrew, I pasted the coordinates into Avogadro and the resultant molec=
ule looks very strange.</div><div>You should try to re-build.</div><div>=A0=
</div><div>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.<b=
r>
=A0<br>=A0</div><div>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.=
<br>
=A0<br>Tom Hockswender<br></div><div class=3D"gmail_quote">On Mon, Jan 9, 2=
012 at 2:08 PM, Andrew DeYoung andrewdaviddeyoung=3D-=3D<a href=3D"http://g=
mail.com" target=3D"_blank">gmail.com</a> <span dir=3D"ltr">&lt;<a href=3D"=
mailto:owner-chemistry*ccl.net" target=3D"_blank">owner-chemistry*ccl.net</=
a>&gt;</span> wrote:<br>


<blockquote style=3D"margin:0px 0px 0px 0.8ex;padding-left:1ex;border-left-=
color:rgb(204,204,204);border-left-width:1px;border-left-style:solid" class=
=3D"gmail_quote"><br>
Sent to CCL by: Andrew DeYoung [andrewdaviddeyoung.*.<a href=3D"http://gmai=
l.com" target=3D"_blank">gmail.com</a>]<br>
Dear Professor Holland,<br>
<br>
Thank you. =A0I have downloaded and installed Avogadro. =A0Unfortunately,<b=
r>
Avogadro will not open the below text containing the coordinates (if I<br>
save this text in an extensionless file called &quot;mytest&quot;); it give=
s me<br>
an error message:<br>
<br>
&quot;Reading molecular file failed&quot;<br>
<br>
Do you have any other ideas?<br>
<br>
Thank you so much for your time.<br>
<br>
Andrew DeYoung<br>
Carnegie Mellon University<br>
<br>
On Sun, Jan 8, 2012 at 5:10 PM, Edward Holland<br>
hollandej~~<a href=3D"http://Cardiff.ac.uk" target=3D"_blank">Cardiff.ac.uk=
</a> &lt;owner-chemistry : <a href=3D"http://ccl.net" target=3D"_blank">ccl=
.net</a>&gt; wrote:<br>
&gt; Hi,<br>
&gt; Handy tip: You can copy and paste many common formats directly into Av=
ogadro<br>
&gt; (Main Page - Avogadro - Free cross-platform molecule editor) You can t=
hen<br>
&gt; visualise it here or save into a format you are more familiar with.<br=
>
&gt;<br>
&gt; Yours<br>
&gt;<br>
&gt; Ed Holland<br>
&gt;<br>
&gt; On 8 Jan 2012, at 19:50, Andrew DeYoung andrewdaviddeyoung- -<a href=
=3D"http://gmail.com" target=3D"_blank">gmail.com</a><br>
&gt; wrote:<br>
&gt;<br>
&gt; -0.02689401 0.05432733 1.07516282 3 H 1<br>
&gt; 0.03282702 -0.01179385 0.68330051 2 O 2<br>
&gt; 0.60586594 -0.05478650 -1.06215854 3 H 3<br>
&gt; 0.54625340 0.01126245 -0.67028541 2 O 4<br>
&gt; -0.00037430 0.00545262 0.11451905 1 C 5<br>
&gt; -0.87007097 0.50375034 -0.04749619 1 C 6<br>
&gt; -0.86607388 -0.50142967 -0.04692549 1 C 7<br>
&gt; 0.87536552 0.51049597 0.02025204 1 C 8<br>
&gt; 0.87795979 -0.51877321 0.02366501 1 C 9<br>
&gt; -0.00283324 1.00386837 -0.01257709 1 C 10<br>
&gt; 0.00039748 -1.00136092 -0.01066833 1 C 11<br>
&gt; -1.73307292 0.00197123 -0.03871588 1 C 12<br>
&gt; -0.86683173 1.50543512 -0.02856670 1 C 13<br>
&gt; -0.86909689 -1.50476823 -0.02691608 1 C 14<br>
&gt; 1.73809709 0.00167020 0.06437659 1 C 15<br>
&gt; 0.86891453 1.50286912 0.03907748 1 C 16<br>
&gt; 0.87181125 -1.50614862 0.04060303 1 C 17<br>
&gt; -1.73625671 1.00707540 -0.04218536 1 C 18<br>
&gt; -1.73743458 -1.00321958 -0.04099753 1 C 19<br>
&gt; 1.73948240 1.00519036 0.06254294 1 C 20<br>
&gt; 1.73748379 -1.00684011 0.06397068 1 C 21<br>
&gt; -0.00097315 2.00519687 -0.00474136 1 C 22<br>
&gt; -0.00025493 -2.00481803 -0.00256281 1 C 23<br>
&gt; -2.60679486 0.50744858 -0.05730558 1 C 24<br>
&gt; -2.60244033 -0.49997860 -0.05660149 1 C 25<br>
&gt; -1.73600183 2.00826255 -0.03828653 1 C 26<br>
&gt; -1.73589004 -2.00632024 -0.03581581 1 C 27<br>
&gt; -0.86809971 2.50743539 -0.01969374 1 C 28<br>
&gt; -0.86743107 -2.50800945 -0.01663035 1 C 29<br>
&gt; 1.73739025 -2.00803386 0.03602309 1 C 30<br>
&gt; 0.86918912 -2.50605556 0.01898868 1 C 31<br>
&gt; -2.60674237 1.50998962 -0.06149746 1 C 32<br>
&gt; -2.60337977 -1.50359739 -0.05952099 1 C 33<br>
&gt; -0.00151756 3.01254125 0.00026303 1 C 34<br>
&gt; -1.73833995 3.01353076 -0.04134158 1 C 35<br>
&gt; 1.73896850 -3.01089377 0.04144619 1 C 36<br>
&gt; -2.60747482 2.51319434 -0.06379837 1 C 37<br>
&gt; 0.87160242 -3.51651549 0.01963025 1 C 38<br>
&gt; -2.60959081 3.52137327 -0.06444686 1 C 39<br>
&gt; 1.74167046 -4.01903762 0.03732286 1 C 40<br>
&gt; 0.57935253 -0.00591929 -0.10150666 1 C 41<br>
&gt; -0.29895259 0.51824224 -0.01065610 1 C 42<br>
&gt; -0.29637000 -0.51095564 -0.00724144 1 C 43<br>
&gt; -1.15911004 -0.00215128 -0.05137018 1 C 44<br>
&gt; 0.57861451 1.00085598 0.02367761 1 C 45<br>
&gt; 0.58190077 -1.00453933 0.02559150 1 C 46<br>
&gt; -1.15848220 1.00634128 -0.05096692 1 C 47<br>
&gt; -1.16048708 -1.00566650 -0.04953595 1 C 48<br>
&gt; 1.44505788 0.50095217 0.05994684 1 C 49<br>
&gt; 1.44905447 -0.50423433 0.06052232 1 C 50<br>
&gt; -0.29287191 1.50575663 -0.02758935 1 C 51<br>
&gt; -0.28990959 -1.50337425 -0.02606221 1 C 52<br>
&gt; -2.02697593 0.50391544 -0.04217217 1 C 53<br>
&gt; -2.02491349 -0.50419505 -0.04152028 1 C 54<br>
&gt; 1.44809109 1.50425324 0.03991273 1 C 55<br>
&gt; 1.44587383 -1.50598582 0.04156281 1 C 56<br>
&gt; 0.57921418 2.00435850 0.01557045 1 C 57<br>
&gt; 0.58001551 -2.00575731 0.01775155 1 C 58<br>
&gt; -1.15838843 2.00756158 -0.02302302 1 C 59<br>
&gt; -1.15757535 -2.00795444 -0.02057379 1 C 60<br>
&gt; 2.31207394 -0.00245438 0.05172946 1 C 61<br>
&gt; -2.02776434 1.50719055 -0.04446594 1 C 62<br>
&gt; -2.02602610 -1.50572182 -0.04269775 1 C 63<br>
&gt; 2.31642963 1.00271453 0.05400912 1 C 64<br>
&gt; 2.31524228 -1.00755964 0.05519446 1 C 65<br>
&gt; -0.29021505 2.50557497 -0.00598370 1 C 66<br>
&gt; -0.28747789 -2.51054533 -0.00287556 1 C 67<br>
&gt; 1.44708230 -2.50791413 0.03270193 1 C 68<br>
&gt; 2.31499473 -2.00876451 0.05130262 1 C 69<br>
&gt; 0.58051995 -3.01303700 0.01275161 1 C 70<br>
&gt; -2.02771967 2.50972812 -0.04865231 1 C 71<br>
&gt; -1.15998355 3.01040245 -0.02842868 1 C 72<br>
&gt; 2.31732484 -3.01400623 0.05435683 1 C 73<br>
&gt; 1.45151430 -3.51897104 0.03339008 1 C 74<br>
&gt; -2.03208004 3.51717648 -0.04935652 1 C 75<br>
&gt; 2.31999134 -4.02068999 0.05257440 1 C 76<br>
&gt;<br>
&gt;<br>
<br>
<br>
<br>
-=3D This is automatically added to each message by the mailing script =3D-=
<br<br=<br<br>
<br>
E-mail to subscribers: <a href=3D"mailto:CHEMISTRY*ccl.net" target=3D"_blan=
k">CHEMISTRY*ccl.net</a> or use:<br>
 =A0 =A0 =A0<a href=3D"http://www.ccl.net/cgi-bin/ccl/send_ccl_message" tar=
get=3D"_blank">http://www.ccl.net/cgi-bin/ccl/send_ccl_message</a><br>
<br>
E-mail to administrators: <a href=3D"mailto:CHEMISTRY-REQUEST*ccl.net" targ=
et=3D"_blank">CHEMISTRY-REQUEST*ccl.net</a> or use<br>
 =A0 =A0 =A0<a href=3D"http://www.ccl.net/cgi-bin/ccl/send_ccl_message" tar=
get=3D"_blank">http://www.ccl.net/cgi-bin/ccl/send_ccl_message</a><br>
<br>
Subscribe/Unsubscribe:<br>
 =A0 =A0 =A0<a href=3D"http://www.ccl.net/chemistry/sub_unsub.shtml" target=
=3D"_blank">http://www.ccl.net/chemistry/sub_unsub.shtml</a><br>
<br>
Before posting, check wait time at: <a href=3D"http://www.ccl.net" target=
=3D"_blank">http://www.ccl.net</a><br>
<br>
Job: <a href=3D"http://www.ccl.net/jobs" target=3D"_blank">http://www.ccl.n=
et/jobs</a><br>
Conferences: <a href=3D"http://server.ccl.net/chemistry/announcements/confe=
rences/" target=3D"_blank">http://server.ccl.net/chemistry/announcements/co=
nferences/</a><br>
<br>
Search Messages: <a href=3D"http://www.ccl.net/chemistry/searchccl/index.sh=
tml" target=3D"_blank">http://www.ccl.net/chemistry/searchccl/index.shtml</=
a><br>
<br<br>
 =A0 =A0 =A0<a href=3D"http://www.ccl.net/spammers.txt" target=3D"_blank">h=
ttp://www.ccl.net/spammers.txt</a><br>
<br>
RTFI: <a href=3D"http://www.ccl.net/chemistry/aboutccl/instructions/" targe=
t=3D"_blank">http://www.ccl.net/chemistry/aboutccl/instructions/</a><br>
<br>
<br>
</blockquote></div><br>

--f46d040169711373d504b62094fb--


From owner-chemistry@ccl.net Mon Jan  9 20:20:01 2012
From: "Jussi Lehtola jussi.lehtola : helsinki.fi" <owner-chemistry(~)server.ccl.net>
To: CCL
Subject: CCL: What is the format of this file containing Cartesian coordinates?
Message-Id: <-46128-120109170018-12913-HhwaYd9ZzIZ7kyP2+1oKZg(~)server.ccl.net>
X-Original-From: Jussi Lehtola <jussi.lehtola~!~helsinki.fi>
Content-Transfer-Encoding: 8bit
Content-Type: text/plain; charset=UTF-8
Date: Tue, 10 Jan 2012 00:00:06 +0200
Mime-Version: 1.0


Sent to CCL by: Jussi Lehtola [jussi.lehtola%%helsinki.fi]
On Sun, 8 Jan 2012 14:50:02 -0500
"Andrew DeYoung andrewdaviddeyoung- -gmail.com"
<owner-chemistry[*]ccl.net> wrote:
> Sent to CCL by: Andrew DeYoung [andrewdaviddeyoung*|*gmail.com]
> Hi,
> 
> I have been reading the paper "Modeling of Graphite Oxide,"
> Boukhvalov, D. W.; Katsnelson, M. I., J. Am. Chem. Soc. 2008, 130,
> 10697-10701.  This paper has Supporting Information associated with
> it, located here: http://pubs.acs.org/doi/suppl/10.1021/ja8021686 .
> This Supporting Information contains the Cartesian coordinates for
> various chemical species discussed in the paper (obtained by ab initio
> calculations).  For example, one of the series of coordinates that
> this Supporting Information provides is the following:
> 
> -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

(clip)

Not having had a look at the paper, I'd guess this is some sort of
molecular dynamics input file. The first three columns are x, y and z
followed by an atom type number in the 4th column, the symbol of the
element in the 5th column, and a running atom index in the 7th column.

If you are running *nix, you can easily convert this to xyz format with
the following shell script:

wc -l atoms.dat | awk '{print $1}' > atoms.xyz
echo "Converted xyz file" >> atoms.xyz
cat atoms.dat | awk '{printf("%s % f % f % f\n",$5,$1,$2,$3)}' >>atoms.xyz

However, there seems to be something severely wrong with the file: for
instance, atoms 6 and 7, atoms 8 and 9, and so on seem to be on top of
each other.
-- 
--------------------------------------------------------
Mr. Jussi Lehtola, M. Sc.         Doctoral Student
jussi.lehtola[*]helsinki.fi         Department of Physics
http://www.helsinki.fi/~jzlehtol  University of Helsinki
Office phone: +358 9 191 50 632   Finland
--------------------------------------------------------
Jussi Lehtola, FM                 Tohtorikoulutettava
jussi.lehtola[*]helsinki.fi         Fysiikan laitos
http://www.helsinki.fi/~jzlehtol  Helsingin Yliopisto
Työpuhelin: (0)9 191 50 632
--------------------------------------------------------


From owner-chemistry@ccl.net Mon Jan  9 20:54:01 2012
From: "Edmanuel Torres torresam[-]ualberta.ca" <owner-chemistry!=!server.ccl.net>
To: CCL
Subject: CCL: What is the format of this file containing Cartesian coordinates?
Message-Id: <-46129-120109135327-25309-lL7vcbgCHmBj2GbKmqlb9g!=!server.ccl.net>
X-Original-From: Edmanuel Torres <torresam|a|ualberta.ca>
Content-Type: text/plain; charset=ISO-8859-1
Date: Mon, 9 Jan 2012 11:53:20 -0700
MIME-Version: 1.0


Sent to CCL by: Edmanuel Torres [torresam++ualberta.ca]
My guess is:

X Y Z Fragment Symbol #

Cheers, ET

On Sun, Jan 8, 2012 at 3:10 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
>
>