From owner-chemistry@ccl.net Thu Oct 8 00:54:01 2009 From: "Babak Khalili khalili.babak()gmail.com" To: CCL Subject: CCL:G: TS optimization Message-Id: <-40435-091007002040-20773-a6J80qY9t0/CxAyrLbHK/g-*-server.ccl.net> X-Original-From: Babak Khalili Content-Type: multipart/alternative; boundary=000325559e2697c64f04754fd395 Date: Wed, 7 Oct 2009 06:50:19 +0330 MIME-Version: 1.0 Sent to CCL by: Babak Khalili [khalili.babak^gmail.com] --000325559e2697c64f04754fd395 Content-Type: text/plain; charset=UTF-8 Dear Abhishek Try to increase memory, more and more, by try and error way. If this problem occurs again, it means that your molecule is bigger than that Gaussian, was able to do calculation on it. Regards, Babak Khalili On Tue, Oct 6, 2009 at 17:34, Abhishek Dutta Chowdhury abhishekdc{=} chem.iitb.ac.in wrote: > > Sent to CCL by: "Abhishek Dutta Chowdhury" [abhishekdc|chem.iitb.ac.in] > Hello all, > I am facing problem during optimization of transition state. My job > automatically stops after 1st cycle but I did not find any error message in > output file. Can anybody tell me where the problem lies? > > Many thanks in advance. > > Abhishek> > > --000325559e2697c64f04754fd395 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Dear Abhishek
Try to increase memory, more and more, by try and error wa= y. If this problem occurs again, it means that your molecule is bigger than= that Gaussian, was able to do calculation on it.

Regards,
Babak= Khalili

On Tue, Oct 6, 2009 at 17:34, Abhishek Dutta= Chowdhury abhishekdc{=3D}chem.iitb.ac.i= n <owne= r-chemistry]=[ccl.net> wrote:

Sent to CCL by: "Abhishek =C2=A0Dutta Chowdhury" [abhishekdc|chem.iitb.ac.in]
Hello all,
=C2=A0I am facing problem during optimization of transition state. My job a= utomatically stops after 1st cycle but I did not find any error message in = output file. Can anybody tell me where the problem lies?

Many thanks in advance.

Abhishek



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--000325559e2697c64f04754fd395-- From owner-chemistry@ccl.net Thu Oct 8 08:50:01 2009 From: "Tim Cheeseright tim . cresset-bmd.com" To: CCL Subject: CCL: Release of FieldScreen 2.5.0 Message-Id: <-40436-091008084922-1435-/qjuxz438JHSL5SdDog6YQ:+:server.ccl.net> X-Original-From: "Tim Cheeseright" Date: Thu, 8 Oct 2009 08:49:18 -0400 Sent to CCL by: "Tim Cheeseright" [tim*cresset-bmd.com] Cresset specializes in the use of molecular Fields to help identify novel active chemistry across any target family. We have an impressive track record of discovering and optimizing novel active leads for customers built over 8 years. We are pleased to announce the release of V2.5.0 of our FieldScreen package. FieldScreen is a ligand based virtual screening system designed to find bioisosteres to your lead molecule amongst millions of other structures. The starting structure could come from a ligand in a proteinligand X-ray structure, a docked solution, a FieldTemplater (www.cresset-bnd.com/fieldtemplater.shtml) solution, or your favoured conformation. FieldScreen allows you to screen against compounds from corporate screening collections, commercially available compounds, virtual libraries and specialist collections such as Derwent World Patent Index. The new version 2.5.0 of FieldScreen has some significant enhancements: - Faster searching due to new FieldPrint format - Significantly reduced disk space requirements using new compression tools - New, easy to use web based interface for FieldScreen system settings - More powerful results visualization with all new FieldView application - New physicochemical data such as TPSA, wcLogP and 'Rule of 5' (RO5) violations for all results To find out more about FieldScreen 2.5.0 see www.cresset-md.com/fieldscreen.shtml. To see our track record with FieldScreen see www.cresset-bmd.com/casestudy.shtml For more specific information please email me at tim],[cresset-bmd.com Tim Cheeseright Cresset BMD From owner-chemistry@ccl.net Thu Oct 8 09:25:01 2009 From: "Silvio a Beccara s.abeccara=-=gmail.com" To: CCL Subject: CCL:G: Third derivative of energy in Gaussian Message-Id: <-40437-091008033258-13778-amBZuDHNuvcRrpdRNoUf0Q ~~ server.ccl.net> X-Original-From: Silvio a Beccara Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 8 Oct 2009 08:53:02 +0200 MIME-Version: 1.0 Sent to CCL by: Silvio a Beccara [s.abeccara_+_gmail.com] Dear friends, I'd need to know whether it is possible, with Gaussian 03, to obtain the (possibly analytic) third derivatives of molecular total energy with respect to atomic positions. I've already tried the Freq and Polar keywords, but I don't seem to be able to find the information I need. Kind regards Silvio a Beccara University of Trento - Italy From owner-chemistry@ccl.net Thu Oct 8 11:39:01 2009 From: "Diana O Rourke orourke(_)tripos.com" To: CCL Subject: CCL: Announcing Benchware Pantheon, new software for chemists Message-Id: <-40438-091008100806-21532-FL6ms6n2RLY2/aHYctg5Ug^-^server.ccl.net> X-Original-From: "Diana O Rourke" Date: Thu, 8 Oct 2009 10:08:01 -0400 Sent to CCL by: "Diana O Rourke" [orourke . tripos.com] Benchware Pantheon is a new Windows program from Tripos that enables discovery scientists to rapidly and accurately merge data from multiple sources, and analyze and visualize that data for faster and better decision making. You can merge disparate data sources like Excel spreadsheets, .cvs and .sdf files in just seconds using drag-and-drop features. Biological data can be merged with chemical structures, and you can sort, analyze and visualize the combined data in 2D and 3D. Pantheon provides a unique combination of a chemically aware spreadsheet and grid view with powerful 3D molecular visualization. Using Pantheon's simple but powerful communication capability, you can share your findings with colleagues by e-mail, and take advantage of Pantheons integration with standard productivity tools, such as Microsofts Excel and PowerPoint. Learn more at a free webinar: New Productivity Tool for Chemists - Introducing Benchware Pantheon. This webinar will be offered twice on Oct 13: 10am European Summer Time (Paris, Berlin)and 11am EDT (Boston, Philadelphia. Info and registration is at www.tripos.com/index.php?family=modules,SimplePage,,,&page=trade_shows#webinars More information about Benchware Pantheon is available from the Tripos website, at www.tripos.com/index.php?family=modules,SimplePage,BW_Pantheon and a free 30-day trial is available for download as well (registration is needed). Diana O'Rourke Dir. of Marketing, Tripos orourke(-at-)tripos.com From owner-chemistry@ccl.net Thu Oct 8 12:15:01 2009 From: "Simon J Grimshaw sgrimshaw[-]chemcomp.com" To: CCL Subject: CCL: CCG announces MOE2009 demonstration session Message-Id: <-40439-091008101327-24334-6zhaOP6jbg/PL3KtBdsqUg++server.ccl.net> X-Original-From: "Simon J Grimshaw" Date: Thu, 8 Oct 2009 10:13:23 -0400 Sent to CCL by: "Simon J Grimshaw" [sgrimshaw{:}chemcomp.com] Dear colleagues, CCG will be offering a session to introduce the new features of the 2009 release of the Molecular Operating Environment (MOE) on the occasion of the 5th German Conference on Chemoinformatics in Goslar, Germany. The "marketplace" session will take place on Sunday 8th of November at the conference venue Hotel Der Achtermann between 2 and 5 pm. If you would like to attend, please contact: Tracey Nixon Office Manager Chemical Computing Group St John's Innovation Centre Cowley Road Cambridge CB4 0WS UK Phone: +44 1223 422319 Fax: +44 1223 422318 email: tnixon:+:chemcomp.com Please note that attendance is limited to a maximum of 30 people. First come, first served! From owner-chemistry@ccl.net Thu Oct 8 12:48:00 2009 From: "Chris Swain swain##mac.com" To: CCL Subject: CCL: Release of FieldScreen 2.5.0 Message-Id: <-40440-091008122146-1267-bHKOgb5KkySlL43BIev/Cw===server.ccl.net> X-Original-From: Chris Swain Content-transfer-encoding: 7BIT Content-type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Date: Thu, 08 Oct 2009 17:21:25 +0100 MIME-version: 1.0 Sent to CCL by: Chris Swain [swain::mac.com] Tim, You have series of typos in the URLs. This link leads to all http://www.cresset-bmd.com/fieldstere.shtml Chris Dr Chris Swain BA MA (Cantab) PhD CChem FRSC Cambridge MedChem Consulting, 8 Mangers Lane, Duxford, Cambs, United Kingdom CB22 4RN. swain++mac.com http://www.cambridgemedchemconsulting.com On 8 Oct 2009, at 13:49, Tim Cheeseright tim . cresset-bmd.com wrote: > > Sent to CCL by: "Tim Cheeseright" [tim*cresset-bmd.com] > > Cresset specializes in the use of molecular Fields to help identify > novel active chemistry across any target family. We have an > impressive track record of discovering and optimizing novel active > leads for customers built over 8 years. We are pleased to announce > the release of V2.5.0 of our FieldScreen package. > > FieldScreen is a ligand based virtual screening system designed to > find bioisosteres to your lead molecule amongst millions of other > structures. The starting structure could come from a ligand in a > proteinligand X-ray structure, a docked solution, a FieldTemplater (www.cresset-bnd.com/fieldtemplater.shtml) > solution, or your favoured conformation. > > FieldScreen allows you to screen against compounds from corporate > screening collections, commercially available compounds, virtual > libraries and specialist collections such as Derwent World Patent > Index. > > The new version 2.5.0 of FieldScreen has some significant > enhancements: > - Faster searching due to new FieldPrint format > - Significantly reduced disk space requirements using new > compression tools > - New, easy to use web based interface for FieldScreen system settings > - More powerful results visualization with all new FieldView > application > - New physicochemical data such as TPSA, wcLogP and 'Rule of > 5' (RO5) violations for all results > > To find out more about FieldScreen 2.5.0 see www.cresset-md.com/fieldscreen.shtml > . > > To see our track record with FieldScreen see www.cresset-bmd.com/casestudy.shtml > > For more specific information please email me at tim###cresset-bmd.com > > Tim Cheeseright > Cresset BMD > > > > -= This is automatically added to each message by the mailing script > =- > To recover the email address of the author of the message, please > change> Conferences: http://server.ccl.net/chemistry/announcements/ > conferences/> > From owner-chemistry@ccl.net Thu Oct 8 14:54:01 2009 From: "Jean-Christophe Poully poully:+:galilee.univ-paris13.fr" To: CCL Subject: CCL:G: activation energy Message-Id: <-40441-091008142446-6275-cQGx0Fwwm8GSjhWGszuO0g%x%server.ccl.net> X-Original-From: Jean-Christophe Poully Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1"; format=flowed Date: Thu, 08 Oct 2009 20:24:32 +0200 Mime-Version: 1.0 Sent to CCL by: Jean-Christophe Poully [poully#galilee.univ-paris13.fr] Dear CCL members, I want to share a very useful trick I have=20 discovered recently : if you want to visualize=20 the frequencies from a Gaussian 09 calculation=20 with Gaussview 3, you need to replace each=20 "Atom AN" in the .out file by "Atom AN". It=20 looks like the same but there are TWO spaces=20 between "Atom" and "AN" in the first and ONE in=20 the second. It is the only thing to do and you=20 will be able to still use your old Gaussview 3,=20 at least if you only need to assign vibrational frequencies, as I do... Hope it will help, Jean-Christophe Poully Doctorant dans l'=E9quipe AMIBES Laboratoire de Physique des Lasers Institut Galil=E9e 99, avenue JB Cl=E9ment 93430 VILLETANEUSE Bureau B002 0149403853=20 From owner-chemistry@ccl.net Thu Oct 8 17:12:01 2009 From: "Daniel Glossman-Mitnik dglossman .. gmail.com" To: CCL Subject: CCL: Quantum Chemistry Literature Database Message-Id: <-40442-091008170923-13192-oV/HMGKZ5WJ4WuqSfBbeFw^server.ccl.net> X-Original-From: Daniel Glossman-Mitnik Content-Type: multipart/alternative; boundary=000e0cd1fada6af0c00475716c8a Date: Thu, 8 Oct 2009 13:25:17 -0600 MIME-Version: 1.0 Sent to CCL by: Daniel Glossman-Mitnik [dglossman . gmail.com] --000e0cd1fada6af0c00475716c8a Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Dear netters: Does anyone know where the Quantum Chemistry Literature Database results have been published *after* 2005? =C2=BFor a similar database? Thanks in advance. Best regards, Daniel ***************************************************************************= ********************************** Dr. Daniel Glossman-Mitnik: Centro de Investigaci=C3=B3n en Materiales Avanzados, SC Grupo NANOCOSMOS - Nanotecnolog=C3=ADa Computacional, Simulaci=C3=B3n y M= odelado Molecular Miguel de Cervantes 120 - Complejo Industrial Chihuahua - Chihuahua, Chih 31109, Mexico Phone: +52 614 4391151 Secretary/FAX: +52 614 4394852 Lab: +52 614 4394805 E-mail: daniel.glossman###cimav.edu.mx dglossman###gmail.com WWW: http://www.cimav.edu.mx/cv/daniel.glossman http://blogs.cimav.edu.mx/daniel.glossman ***************************************************************************= ********************************** --000e0cd1fada6af0c00475716c8a Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Dear netters:

Does anyone know where the Quantum Chemistry Liter= ature Database results have been
published after 2005?
=
=C2=BFor a similar database?

Thanks in advance. Best regards,
Daniel

***********************************************= **************************************************************
Dr. Danie= l Glossman-Mitnik:
Centro de Investigaci=C3=B3n en Materiales Avanzados,= SC
Grupo NANOCOSMOS =C2=A0- =C2=A0Nanotecnolog=C3=ADa Computacional, Simulaci= =C3=B3n y Modelado Molecular
Miguel de Cervantes 120 - Complejo Industri= al Chihuahua - Chihuahua, Chih 31109, Mexico
Phone: +52 614 4391151 =C2= =A0 =C2=A0 Secretary/FAX: +52 614 4394852 =C2=A0 =C2=A0 Lab: +52 614 439480= 5
E-mail: =C2=A0daniel.glossm= an###cimav.edu.mx =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0dglossman###gmail.com
WWW: =C2=A0http://www.cimav.edu.mx/cv/daniel.gloss= man
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0http://blogs.cimav.edu.mx/daniel.glossman*************************************************************************= ************************************
--000e0cd1fada6af0c00475716c8a-- From owner-chemistry@ccl.net Thu Oct 8 22:36:00 2009 From: "Fabio Paranhos fabioparanho- -gmail.com" To: CCL Subject: CCL: TS optimization Message-Id: <-40443-091006221300-9942-UZ1TQc86t5Y7AiMc9n8K8w[*]server.ccl.net> X-Original-From: Fabio Paranhos Content-Type: multipart/alternative; boundary=0015175cac181cefe404754dd8aa Date: Tue, 6 Oct 2009 21:58:25 -0300 MIME-Version: 1.0 Sent to CCL by: Fabio Paranhos [fabioparanho]*[gmail.com] --0015175cac181cefe404754dd8aa Content-Type: text/plain; charset=ISO-8859-1 Hi, do you maind to post the output file? Ciao. -- We belong not where we are, but rather who we are. (FLPC) --0015175cac181cefe404754dd8aa Content-Type: text/html; charset=ISO-8859-1 Hi,

do you maind to post the output file?

Ciao.

--
We belong not where we are, but rather who we are. (FLPC)
--0015175cac181cefe404754dd8aa-- From owner-chemistry@ccl.net Thu Oct 8 23:11:00 2009 From: "Cory Pye cpye,+,ap.smu.ca" To: CCL Subject: CCL:G: Third derivative of energy in Gaussian Message-Id: <-40444-091008160434-7567-chjIumZ7QNyLJ1SK6RPr/g^server.ccl.net> X-Original-From: Cory Pye Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Thu, 8 Oct 2009 15:52:23 -0300 (ADT) MIME-Version: 1.0 Sent to CCL by: Cory Pye [cpye[A]ap.smu.ca] Silvio, Freq=Cubic does a numerical differentiation of the analytic second derivatives. -Cory On Thu, 8 Oct 2009, Silvio a Beccara s.abeccara=-=gmail.com wrote: > > Sent to CCL by: Silvio a Beccara [s.abeccara_+_gmail.com] > Dear friends, > > I'd need to know whether it is possible, with Gaussian 03, to obtain the > (possibly analytic) third derivatives of molecular total energy with respect > to atomic positions. I've already tried the Freq and Polar keywords, but I > don't seem to be able to find the information I need. > > Kind regards > > > Silvio a Beccara > University of Trento - Italy> > ************* ! Dr. Cory C. Pye ***************** ! Associate Professor *** ** ** ** ! Theoretical and Computational Chemistry ** * **** ! Department of Chemistry, Saint Mary's University ** * * ! 923 Robie Street, Halifax, NS B3H 3C3 ** * * ! cpye],[crux.stmarys.ca http://apwww.stmarys.ca/~cpye *** * * ** ! Ph: (902)-420-5654 FAX:(902)-496-8104 ***************** ! ************* ! Les Hartree-Focks (Apologies to Montreal Canadien Fans)