From owner-chemistry@ccl.net Wed Mar 15 03:22:00 2006 From: "Frank Neese neese#%#mpi-muelheim.mpg.de" To: CCL Subject: CCL: Calculation of ESR/ EPR spectra Message-Id: <-31201-060314082602-19775-QB42uEgMSeBpRNGmPa3poQ-*-server.ccl.net> X-Original-From: Frank Neese Content-Type: text/plain; charset="us-ascii"; format=flowed Date: Tue, 14 Mar 2006 14:25:55 +0100 Mime-Version: 1.0 Sent to CCL by: Frank Neese [neese]![mpi-muelheim.mpg.de] Dear Jim, the ORCA program is somewhat specialized in EPR/ESR and is efficient and easy to use. It doesn't interface to Gamess but it is free. You can get it from http://ewww.mpi-muelheim.mpg.de/bac/index_en.php simply go to the "download area" and follow the instructions how to download the code. You will have to agree to the license conditions. You will then receive a password via e-mail which lets you login into the download area where you will find the various manuals and executables. We have also installed a mailing list. To subscribe send an e-mail to: majordomo^mpi-muelheim.mpg.de subject (leave empty) message text: subscribe orca^mpi-muelheim.mpg.de to unscubscribe yourself do the same by replacing 'subscribe' by 'unsubscribe' To post a message to the mailing list send an e-mail to orca^mpi-muelheim.mpg.de all the best, Frank From owner-chemistry@ccl.net Wed Mar 15 06:53:00 2006 From: "me00109:-:cc.uoi.gr" To: CCL Subject: CCL: DFT for pi-pi Interaction? Message-Id: <-31202-060314040749-465-pG/wg72Q4FUhQjbX1MDuhg:server.ccl.net> X-Original-From: me00109(a)cc.uoi.gr Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-7 Date: Tue, 14 Mar 2006 10:18:46 +0200 MIME-Version: 1.0 Sent to CCL by: me00109]=[cc.uoi.gr Dear Sue, Study the article: Tsuzuki, S.; Luthi, H. P. J. Chem. Phys. 2001, 114 3949. See if it covers your demands. In any case you can also perform an initial assessment for your system employing some functionals and compare your results with a higher level of theory. I hope I helped George Papamokos > Sent to CCL by: "Sue L" [chsue2004 .. yahoo.com] > Hi, > > Do you know any DFT method that describes well the pi-pi interaction of the > aromatic system? > > Thank you very much. > > Sue> > > From owner-chemistry@ccl.net Wed Mar 15 07:27:01 2006 From: "Shireen Al Falah shireenfalah[A]hotmail.com" To: CCL Subject: CCL: Transition State Search Message-Id: <-31203-060315032513-6152-Mg8pfjGiQCzjNpv+Rkdt/g%server.ccl.net> X-Original-From: "Shireen Al Falah" Content-Type: text/html; format=flowed Date: Wed, 15 Mar 2006 08:37:54 +0100 Mime-Version: 1.0 Sent to CCL by: "Shireen Al Falah" [shireenfalah{:}hotmail.com]

Hi,

third structure could be an intial guess for the transition state structure, it does not need to be optimized.

hope this  will help

From:  "Christopher David Thompson cdth:-:unimelb.edu.au" <owner-chemistry.%.ccl.net>
Reply-To:  "CCL Subscribers" <chemistry.%.ccl.net>
To:  "Alfalah, Sherin " <shireenfalah.%.hotmail.com>
Subject:  CCL: Transition State Search
Date:  Tue, 14 Mar 2006 20:22:26 -0500
>Sent to CCL by: "Christopher David Thompson" [cdth===unimelb.edu.au]
>Gday,
>
>I'm attempting a transition state search using the following route line;
>
>  opt=qst2 mp2 geom=connectivity aug-cc-pvdz
>
>The two starting geometries are local minima on the surface. The job is quickly terminating at this
>point;
>
>New curvilinear step not converged.
>  ***** Convergence failure in GTrans *****
>  Try using 3 structures as input for
>  QST transition state search
>
>Thoughts? What 3rd structure would be suitable here?
>
>Cheers,
>Chris
>
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From owner-chemistry@ccl.net Wed Mar 15 08:02:00 2006 From: "Judith Bandy jbandy++inforsense.com" To: CCL Subject: CCL: Free Webcast: Bridging Chemistry with Integrative Analytics Message-Id: <-31204-060314135615-8975-TEM+QCqOohK9HgpMIymT9Q_-_server.ccl.net> X-Original-From: "Judith Bandy" Date: Tue, 14 Mar 2006 13:56:11 -0500 Sent to CCL by: "Judith Bandy" [jbandy()inforsense.com] Webcast: Bridging Chemistry with Integrative Analytics: Introducing InforSense ChemSense Date and time: Wednesday, March 29, 2006, 3:00pm(GMT)/ 10:00am(EST)/ 7:00am(PST) 6:00pm(GMT)/ 1:00pm(EST)/ 10:00am(PST) Presenter(s) Info: Stephen Whiteley, Product Manager InforSense ChemSense Anthony Rowe, Product Manager - InforSense KDE Register Here to Join the Live Webcast (https://inforsense.webex.com/inforsense/onstage/tool/program/upcomingprograms.php) Description: Bridging Chemistry with Integrative Analytics InforSense ChemSense enables companies to exploit chemistry information and software assets to identify new drug leads based on relationships found in complex heterogeneous data. 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Register Here to Join the Live Webcast (https://inforsense.webex.com/inforsense/onstage/tool/program/upcomingprograms.php) 2006 InforSense Ltd. All rights reserved. InforSense, the InforSense logo and TextSense are registered trade-marks of InforSense Ltd. Open Discovery Workflow is a trademark of InforSense Ltd. All other brands or product names are trademarks of their respective holders. If you would like to be added to our mailing list or receive further information about our Webcasts please email information%a%inforsense.com www.inforsense.com From owner-chemistry@ccl.net Wed Mar 15 08:37:00 2006 From: "sv0037!A!unt.edu" To: CCL Subject: CCL: Transition State Search Message-Id: <-31205-060314210948-24506-kSWujfcLvggAhShPOq37wQ,+,server.ccl.net> X-Original-From: sv0037[-]unt.edu Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format="flowed" Date: Tue, 14 Mar 2006 19:27:45 -0600 MIME-Version: 1.0 Sent to CCL by: sv0037!=!unt.edu construct a guesstimate with slightly longer bond measurements of the reaction transition coordinate where the bond making/breaking happening(which you think possible) but y dont u work using opt=(ts,calcfc/calcall) on the gustimate ts!!! From owner-chemistry@ccl.net Wed Mar 15 15:55:01 2006 From: "Jianxi Xiao jianxix ~~ eden.rutgers.edu" To: CCL Subject: CCL: How to choose a docking program? Message-Id: <-31207-060315103736-12085-SDmXg4waXONCGSOANS/uoQ|,|server.ccl.net> X-Original-From: "Jianxi Xiao" Date: Wed, 15 Mar 2006 10:37:34 -0500 Sent to CCL by: "Jianxi Xiao" [jianxix[-]eden.rutgers.edu] Hi, CCLers, I am trying to dock a small DNA (~22nt) to a large protein (~ 770 residues) based on the known structures. I have no experience about docking, and there are so many docking proprams like autoDock, Dock, Sybyl, MONTY. Which one should I choose? Thanks a lot! Jianxi Xiao Rutgers University Department of Chemistry 610 Taylor Rd Piscataway, NJ 08854 jianxix]_[eden.rutgers.edu From owner-chemistry@ccl.net Wed Mar 15 16:30:00 2006 From: "Alfred Gil agil]-[cesca.es" To: CCL Subject: CCL:G: "SVD failed for GenInv" error in G03.C02 Message-Id: <-31208-060315082756-22363-HIOaYbZi9IJJuSIi5l60qQ ~~ server.ccl.net> X-Original-From: Alfred Gil Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Wed, 15 Mar 2006 13:47:13 +0100 MIME-Version: 1.0 Sent to CCL by: Alfred Gil [agil * cesca.es] Hello, I am running a pcm solvent calculation in g03 (rev c02) with the following parameters opt(modredundant,maxcycle=100) ub3lyp/6-31g(d,p) scrf=(solvent=water,pcm) . . [geometry] . . B 4 8 S 30 -0.1 [scan in the bond length between atoms 4 and 8] After 17 steps of geometry optimization (within first scan step) I get the following error, Berny optimization. SDV returned info= 42 to GenInv. SVD failed for GenInv. Does anybody know where the problem is? Thanks in advance. -- ...................................................................... __ / / Alfred Gil i Arranz C E / S / C A Departament de Sistemes /_/ Centre de Supercomputació de Catalunya Gran Capitŕ, 2-4 (Edifici Nexus) • 08034 Barcelona T. 93 205 6464 • F. 93 205 6979 • agil=-=cesca.es ...................................................................... From owner-chemistry@ccl.net Wed Mar 15 17:05:01 2006 From: "zborowsk_+_chemia.uj.edu.pl" To: CCL Subject: CCL:G: Transition State Search Message-Id: <-31209-060315163644-17863-rsHEOiLM8Kroy5ID8Dt9Uw]^[server.ccl.net> X-Original-From: zborowsk||chemia.uj.edu.pl Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-2 Date: Wed, 15 Mar 2006 22:36:41 +0100 (CET) MIME-Version: 1.0 Sent to CCL by: zborowsk/a\chemia.uj.edu.pl Hi I haven´t seen such a message anytime What software did you use?? Gaussian?? Probably your program "think" that the QST3 method will be better. And the 3rd structure is something similar to the TS you want to obtain > Sent to CCL by: "Christopher David Thompson" [cdth===unimelb.edu.au] > Gday, > > I'm attempting a transition state search using the following route line; > > opt=qst2 mp2 geom=connectivity aug-cc-pvdz > > The two starting geometries are local minima on the surface. The job is > quickly terminating at this > point; > > New curvilinear step not converged. > ***** Convergence failure in GTrans ***** > Try using 3 structures as input for > QST transition state search > > Thoughts? What 3rd structure would be suitable here? > > Cheers, > Chris> > > > -- Krzysztof Zborowski Faculty of Chemistry Jagiellonian University 3 Ingardena Street 30-060 Krakow Poland phone: +48(12)632-4888 ext. 2064 or 2067 fax: +48(12)634-05-15 email: zborowsk%%chemia.uj.edu.pl ICQ 158385743 gg 3817259 skype kzys70