Dear Sten

=0A

Good morning

= =0A

=0A

I am a ccl subscribers. Regularly I check the m= ails.

=0A

As suggusted by use I am able to sel= ect the point group and then I saved the coordinates of the selected s= ymmetry of the molecule using "file/save strucutre in xyz format". =0A

=0A

To check symmetry of the the saved geom,&nbs= p;I used gaussview program, to my surprise it have given same initial symme= try of the molecule not the chemcraft saved symmetry molecule.

= =0A

=0A

Please suggest how to save the symmetry in chem= craft.

=0A

Thanks in advance

=0A

&nbs= p;

=0A

Dr. Joshi Laxmikanth Rao

=0A

IICT, Hyderabad= . India

=0A

=0A= From: Sten Nilsson Lill ste= nil]*[chem.gu.se <owner-chemistry-*-ccl.net>
To: "Rao, J.laxmikanth " <lkjoshiji-*-yah= oo.com>
Sent: Wednesd= ay, 13 May, 2009 1:32:19 PM
Subject= : CCL: Generating symmetry from where it almost exists...

Sent to CCL by: "Sten Nilsson Lill" [stenil=3D-=3Dchem.gu.se]John,

> from my experience Chemcraft is very useful for symmetr= izing molecules.

You can download the program at http://www.chemcraftprog.com/ an= d it works
for Windows and Linux.

If you go to the Edit menu ther= e's an option called "Set Point Group". I
normally let the program sugge= st the symmetry by using the "Auto"
function. There you will get a few p= oint group options to select from. If
the program doesn't include your speci= fic symmetry you can directly define
it to set the point group you are s= earching for, just pick it in the menu.

Hope that helps,

Sten=

> Folks,
>
> I have a bunch of cartesian= geometries that have "almost" C2 symmetry.
> Graphical inspection sa= ys yhey should be C2 but the code I'm using won't
> generate C2, even= with large "out-of-symmetry" threshold values. Can
> anyone> point me to a simple utility that could be used to clean these struct= ures
> up?
>
> Thanks!
>
> John McKelvey
&= gt;

Ph. D. Sten Nilsson Lill
Dep. of Chemistry
University = of Gothenburg
Kemig=E5rden 4
S-412 96 G=F6teborg, Sweden
Phone: +4= 6-31-772 2873
Fax: +46-31-772 3840
E-mail: stenil{}chem.gu.se
Alte= rnative e-mail: stenil{}physto.se

-=3D This is automatically added to each message by the mailing script =3D-
To recov= er the email address of the author of the message, please change
the str= ange characters on the top line to the -*- sign. You can also
look up the = X-Original-From: line in the mail header.

E-mail to subscribers: CHEM= ISTRY-*-ccl.net or use:
http://www.ccl.net/cgi-b= in/ccl/send_ccl_message

E-mail to administrators: CHEMISTRY-REQUEST-*-ccl.net or use
http://www.c= cl.net/cgi-bin/ccl/send_ccl_message
&= nbsp; http://www.ccl.net/chemistry/sub_unsub.shtml

Be= fore posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.net/jobs
Conferences: http://server.ccl.net/chemistry/announcements/conferences/

Sear= ch Messages: http://www.ccl.net/chemistry/searchccl/index.shtml
= = http://= www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry= /aboutccl/instructions/

=0A=0A=0A =

Now surf faster and smarter ! Check out the new= Firefox 3 - Yahoo! Edition * Clic= k here! --0-1428823028-1242294417=:66482-- From owner-chemistry@ccl.net Fri May 15 08:55:00 2009 From: "Stephan Irle sirle(0)iar.nagoya-u.ac.jp" To: CCL Subject: CCL: Announcement: International CREST and Morokuma 75th Birthday Symposia Message-Id: <-39329-090515041649-12251-qvNPBSE1TmpeMbMkm9ygZQ/a\server.ccl.net> X-Original-From: "Stephan Irle" Date: Fri, 15 May 2009 04:16:44 -0400 Sent to CCL by: "Stephan Irle" [sirle(a)iar.nagoya-u.ac.jp] We invite you to participate in the joint International Symposia: "CREST International Symposium on Theory and Simulations of ComplexMolecular Systems" & "International Symposium on Theory of MolecularStructure, Function and Reactivity, Celebrating Prof. Morokuma 's 75th Birthday ", to be held at Kyoto University's Fukui Institute for Fundamental Research, Tuesday, July 21 from Sunday, July 19, 2009, to Tuesday, July 21 in Kyoto, Japan. For a list of invited talks and more details of the symposia, please find more information athttp://kmweb.fukui.kyoto- u.ac.jp/symposia09/ Incidentally, Gion Festival, one of the most important and gorgeous festivals in Japan, will take place in Kyoto on July 17. We invite participants to submit a poster presentation. The application deadline for online poster submission via the symposia webpage is Sunday, May 31. We will provide poster awards as follows to encourage young participants: Student award: For undergraduate or graduate students. Young investigator award: For temporary/tenure-track postdoctoral researchers or temporary/tenure-track assistant professor, who obtained a doctor degree 2004 or later. Details on registration fees and optional banquet participation can be found at the Birthday Symposium website. We sincerely hope to see you at the meeting. Organizing Committees: International Symposium on Theory of Molecular Structure, Function and Reactivity, Celebrating Prof. Morokumas 75th Birthday Stephan Irle (Nagoya University), Co-chair Seiji Mori (Ibaraki University), Co-chair Masanori Tachikawa (Yokohama City University), Co-chair Shigeki Kato (Kyoto University) Nobuaki Koga (Nagoya University) Shigeyoshi Sakaki (Director, Fukui Institute for Fundamental Chemistry, Kyoto University) CREST International Symposium on Theory and Simulations of Complex Molecular Systems Keiji Morokuma (Kyoto University) Stephan Irle (Nagoya University) Contact email address:morokumasymp,,fukui.kyoto-u.ac.jp From owner-chemistry@ccl.net Fri May 15 09:29:01 2009 From: "John McKelvey jmmckel_+_gmail.com" To: CCL Subject: CCL: Generating symmetry from where it almost exists... Message-Id: <-39330-090515092104-14140-o2DZuQcbvSpEAgwV5k6flQ-,-server.ccl.net> X-Original-From: John McKelvey Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 15 May 2009 09:20:50 -0400 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel]^[gmail.com] Hello! One advantage that SYMMOL has is that once the threshholds are set it tells you what point group you have. If you want to see if there are possibly higher symmetries possible, whether it makes sense or not, one can increase the magnitudes of the threshholds. The source for SYMMOL is readily downloaded and modified to suit input and output requirements. John McKelvey On 5/14/09, laxmikanth rao lkjoshiji*|*yahoo.com wrote: > Dear Sten > > Good morning > > I am a ccl subscribers. Regularly I check the mails. > > As suggusted by use I am able to select the point group and then I saved = the > coordinates of the=A0selected symmetry of the molecule using "file/save > strucutre in xyz format". > > To check symmetry of the the saved geom,=A0I used gaussview program, to m= y > surprise it have given same initial symmetry=A0of the molecule not the > chemcraft saved symmetry molecule. > > Please suggest how to save the symmetry in chemcraft. > > Thanks in advance > > Dr. Joshi Laxmikanth Rao > IICT, Hyderabad. India > > > > > ________________________________ > From: Sten Nilsson Lill stenil]*[chem.gu.se > To: "Rao, J.laxmikanth " > Sent: Wednesday, 13 May, 2009 1:32:19 PM > Subject: CCL: Generating symmetry from where it almost exists... > > > Sent to CCL by: "Sten Nilsson Lill" [stenil=3D-=3Dchem.gu.se] > John, > >> from my experience Chemcraft is very useful for symmetrizing molecules. > > You can download the program at http://www.chemcraftprog.com/ and it work= s > for Windows and Linux. > > If you go to the Edit menu there's an option called "Set Point Group". I > normally let the program suggest the symmetry by using the "Auto" > function. There you will get a few point group options to select from. If > the program doesn't include your specific symmetry you can directly defin= e > it to set the point group you are searching for, just pick it in the menu= . > > Hope that helps, > > Sten > > > > >> Folks, >> >> I have a bunch of cartesian geometries that have "almost" C2 symmetry. >> Graphical inspection says yhey should be C2 but the code I'm using won't >> generate C2, even with large "out-of-symmetry" threshold values.=A0 Can >> anyone >> point me to a simple utility that could be used to clean these structure= s >> up? >> >> Thanks! >> >> John McKelvey >> > > > Ph. D. Sten Nilsson Lill > Dep. of Chemistry > University of Gothenburg > Kemig=E5rden 4 > S-412 96 G=F6teborg, Sweden > Phone: +46-31-772 2873 > Fax: +46-31-772 3840 > E-mail: stenil{}chem.gu.se > Alternative e-mail: stenil{}physto.se > > > > -=3D This is automatically added to each message by the mailing script = =3D-> the strange characters on the top line to the . sign. You can also> > > =A0 =A0 =A0> > E-mail to administrators: CHEMISTRY-REQUEST . ccl.net or use > =A0 =A0 =A0> > > =A0 =A0 =A0> =A0 =A0 =A0> > > > > Explore and discover exciting holidays and getaways with Yahoo! Ind= ia > Travel http://in.travel.yahoo.com/ From owner-chemistry@ccl.net Fri May 15 14:10:01 2009 From: "Michel Petitjean petitjean.chiral[*]gmail.com" To: CCL Subject: CCL: Almost symmetric structures (was: Generating symmetry from where it almost exists...) Message-Id: <-39331-090515134746-17835-1GTRAUkkOwXQryg0rSty+Q*server.ccl.net> X-Original-From: Michel Petitjean Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 15 May 2009 19:47:34 +0200 MIME-Version: 1.0 Sent to CCL by: Michel Petitjean [petitjean.chiral||gmail.com] Hi CCLers and Symmetrists, I would be glad to know the algorithm restoring symmetry from a distorted symmetric structure, particularly when it is "far from symmetry". But what means "far from symmetry" ? Here, we need a symmetry measure. There are dozens of symmetry measures in the literature (see the pdf of my review published in 2003, available from my web page), and I have built my own one. For this latter, it can be shown that Br-CHF-Cl, assumed to be a regular tetrahedron with the carbon lying at his center, is a maximal chiral object (can be checked with the freeware QCM, http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html) . How can it be symmetrized to become achiral ? If existing, is the resulting symmetrized molecule unique ? If a "not too much chiral" Br-CHF-Cl geometry is needed, what conditions should satisfy the five points in order to enable the symmetrization process working ? It is an exciting topic. Maybe crystallographers or computational chemists can enlight us. Best wishes. Michel Petitjean, DSV/iBiTec-S/SB2SM (CNRS URA 2096), CEA Saclay, bat. 528, 91191 Gif-sur-Yvette Cedex, France. Phone: +331 6908 4006 / Fax: +331 6908 4007 E-mail: michel.petitjean%%cea.fr, petitjean.chiral%%gmail.com >> I have a bunch of cartesian geometries that have "almost" C2 symmetry. >> Graphical inspection says yhey should be C2 but the code I'm using won't >> generate C2, even with large "out-of-symmetry" threshold values. Can >> anyone >> point me to a simple utility that could be used to clean these structures >> up? From owner-chemistry@ccl.net Fri May 15 14:45:00 2009 From: "Roland Lindh roland.lindh(_)gmail.com" To: CCL Subject: CCL:G: Problem with CASSCF Message-Id: <-39332-090512174402-27844-KPPi6HPLg9IjMnTD0WXSQQ() server.ccl.net> X-Original-From: Roland Lindh Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-2022-JP Date: Tue, 12 May 2009 23:42:31 +0200 MIME-Version: 1.0 Sent to CCL by: Roland Lindh [roland.lindh===gmail.com] tang_shi_ya tang_shi_ya!=!126.com wrote: > Dear CCLers$B!$(B > I'm doing a CASSCF calculation and I need some suggestion or tips to > get appropriate active space. > BTW,in my Gaussian output files, there are all "(A)" ,not "(A'')" or > "(A')") at "Orbital Symmetries" part(on a Guess=Only job), especially > a small molecule "acrolein", therefore, I'm in a puzzle as to how to > ensure the active space. > Thanks in advance. > ------------------------------------------------------------------------ > tang_shi_ya > 2009-05-08 Dear Shi Ya, I have some experience from doing this with MOLCAS. For me to help you I need to know what you will do with the calculation. If you are just doing electronic spectroscopy or if you also would like to dissociate some bond. The latter will require a somewhat larger active space. Symmetry is trivial in MOLCAS what is going on in Gaussian I do not have a clue on. Take care, -roland From owner-chemistry@ccl.net Fri May 15 21:14:00 2009 From: "David Close closed-x-etsu.edu" To: CCL Subject: CCL:G: Density Keyword Message-Id: <-39333-090515211155-9668-6bMS+wX9iVwceDkLuyeMvw*o*server.ccl.net> X-Original-From: "David Close" Date: Fri, 15 May 2009 21:11:52 -0400 Sent to CCL by: "David Close" [closed++etsu.edu] I want to look at spin densities calculated with Gaussian. I am interested in using QCISD. The manual says to use the keyword density=QCI. That seems to work. But then to generate the spin densities I need the formchk and cubegen utilitles. With cubegen I typed cubegen 0 spin=qci file.fchk file.cube I get the error message "TOTAL QCI DENSITY not found in .fchk file". What's wrong? This technique works just fine if I use density=MP2. Then I can generate spin densities using spin=MP2.