From owner-chemistry@ccl.net Tue May 30 07:39:00 2006 From: "Godefroid GAHUNGU ggahungu+/-yahoo.fr" To: CCL Subject: CCL:G: Exchange coupling in triradicals within C3 symmetry Message-Id: <-31863-060529184915-25894-up8sq4Sww+3xLge/1mgXww++server.ccl.net> X-Original-From: "Godefroid GAHUNGU" Date: Mon, 29 May 2006 18:49:13 -0400 Sent to CCL by: "Godefroid GAHUNGU" [ggahungu++yahoo.fr] Dear all, My greetings first. In my actual work, I am interested in calculating the exchange coupling (J) values for organic triradicals systems within C3 symmetry. Because of the more extensive electronic degeneracy, ab initio modeling of triradicals seems to be even more complicated than that of diradicals. So far, it is proposed that, from a methodological perspective, a multiconfigurational method should be employed when the triradical orbitals are nearly degenerate, and that Spin-Flipping approach (SF) can be employed to describe triradicals. Through this message, I would like to ask for an assistance about how to proceed, from the geometry optimization (since no crystal structures are not available yet) to the calculation of the J value (let me tell you that there is no experimental J values are available yet). As computational resources, I am intending to use Gaussian 98 or 03 packages, but also have an already installed ORCA program. Would you like to provide me with some details about which appropriate key words to be used within ORCA input files? Thanks ahead for your coming assistance. GAHUNGU Godefroid (Ph.D student) E-mail: ggahungu|*|yahoo.fr Northeast Normal University Chemistry Department Renmin Street, 5268 Changchun-Jilin (PR. China) From owner-chemistry@ccl.net Tue May 30 08:23:00 2006 From: "Mahesh Sundararajan maheshsrajan*_*gmail.com" To: CCL Subject: CCL:G: IRC & TS CALCULATION Message-Id: <-31864-060529162526-16680-zTVpz6486GKUP+dZpE+6jw+*+server.ccl.net> X-Original-From: "Mahesh Sundararajan" Content-Type: multipart/alternative; boundary="----=_Part_12826_11774913.1148918765369" Date: Mon, 29 May 2006 17:06:05 +0100 MIME-Version: 1.0 Sent to CCL by: "Mahesh Sundararajan" [maheshsrajan##gmail.com] ------=_Part_12826_11774913.1148918765369 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Hai: Gaussview03 is a good software to create Gaussian inputs. I hope this helps, Mahesh S On 5/29/06, tarig elshaarani mohamed shaarany_11[A]yahoo.com < owner-chemistry|,|ccl.net> wrote: > > Sent to CCL by: "tarig elshaarani mohamed" [shaarany_11|,|yahoo.com] > > Dear Sir/Mme: > > I am a gradute student from Sudan ,working on theoretical studies > of > Diels_Alder reaction using G03,(following the reaction using density > function theory)..my problem is that; whenever i make my (input)file by > Molder and (export )it to G03 to process calculations,especially when i > use IRC or TS as keywords a message pop up to me reading(insert the > force constant calculations) but when i respond to this by writing(calc > FC ) as key word with IRC or TS, another message pop up reading (input > error)..What do you suggest i should do to overcome this?...Also is > there any software that can prepare the coordinates as Z matrix?.... > > > > > > > > Thank You so much > > Tarig Elshaarani > M.Sc student > University of Khartoum > > > -- > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > > --=20 Dr Mahesh. Sundararajan, School of Chemistry, The University of Manchester. Manchester - M13 9PL. UK Phone: LL: 00 7921213107 Website: http://mch3w.ch.man.ac.uk/theory/staff/student/mbdtsms/index.html ------=_Part_12826_11774913.1148918765369 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline
Hai:
 
Gaussview03 is a good software to create Gaussian inputs.
 
I hope this helps,
 
Mahesh S

 
On 5/29/06, = tarig elshaarani mohamed shaarany_11[A]yahoo.com <owner-chemistry|,|ccl.net> wrote:
Sent to CCL by: "tarig elsh= aarani mohamed" [shaarany_11|,|yahoo.com]

Dear Sir/Mme:

  I am a gradute student from  Sudan ,working on theore= tical studies
of
Diels_Alder reaction using G03,(following the reacti= on using density
function theory)..my problem is that; whenever i make m= y (input)file by
Molder and (export )it to G03 to process calculations,especially when i=
use IRC or TS as keywords a message pop up to me reading(insert the
= force constant calculations) but when i respond to this by writing(calc
FC ) as key word with IRC or TS, another message pop up reading (input<= br>error)..What do you suggest i should do to overcome this?...Also is
t= here any software that can prepare the coordinates as Z matrix?....







   Thank You so much

Tarig Els= haarani
M.Sc student
University of Khartoum


--


=
-=3D This is automatically added to each message by the mailing script = =3D-
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-- Dr Mahesh. Sundararajan,
School of Chemistry,
The University of Ma= nchester.
Manchester - M13 9PL.
UK

Phone:

LL: 00 7921213107
=
Website:
http://mch3w.ch.man.ac.uk/theory/staff/student/mbdtsms/= index.html =20 ------=_Part_12826_11774913.1148918765369-- From owner-chemistry@ccl.net Tue May 30 09:46:00 2006 From: "Pradipta Bandyopadhyay pradipta]~[iitg.ernet.in" To: CCL Subject: CCL: Ergodicity check for biomolecular simulation ! Message-Id: <-31865-060530093227-32462-ETImp6Ur5gQD+z2RUdVkjA:_:server.ccl.net> X-Original-From: "Pradipta Bandyopadhyay" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Tue, 30 May 2006 19:01:28 +0530 (IST) MIME-Version: 1.0 Sent to CCL by: "Pradipta Bandyopadhyay" [pradipta*iitg.ernet.in] Hi, I am looking for references which deal with testing ergodicity of biomolecular simulations and/or checking the 'overlap' of two different trajectories for same system. For liquid simulations, I know of Mountain and Thirumalai paper (J. Phys. Chem., 93, 6975, 1989). Is there any similar paper for protein simulations? Thanks, Pradipta ----------------------------------------------------------------------------------- This email was sent from IIT Guwahati Webmail. If you are not the intended recipient, please contact the sender by email and delete all copies; your cooperation in this regard is appreciated. http://www.iitg.ernet.in From owner-chemistry@ccl.net Tue May 30 11:37:00 2006 From: "Judith Bandy jbandy]_[inforsense.com" To: CCL Subject: CCL: FREE WEBCAST: How Workflows Help Biotechs Cut Data Analytics Costs Message-Id: <-31866-060530113334-7782-KO8sCNpFF+vPawe6+Gya2w:-:server.ccl.net> X-Original-From: "Judith Bandy" Date: Tue, 30 May 2006 11:33:31 -0400 Sent to CCL by: "Judith Bandy" [jbandy(a)inforsense.com] You are invited to join a free webcast..... _____________________________________ Event: How Workflows Help Biotechs ... Reduce the cost of high quality, high volume data analysis by using InforSense KDE Date and Time: Wednesday, June 14, 2006 3:00pm UK /10:00am EST/7:00am PST 6:00pm UK /1:00pm EST/10:00am PST Presenter(s): Anthony Arvanites, Cheminformatics, Cambria BioSciences Robin Munro, Director Strategic Application Development, InforSense Duration: 1 hour Register Here to Join the Live Webcast: http://www.inforsense.com/webcast_jun06_14.html Description: Streamlining High-throughput Analytics Biotechnology companies typically combine demanding research tasks with rapidly evolving business requirements. Informatics plays a key role in this work, but IT resources are often limited. The challenge for many growing biotechnology companies is how to develop a cost-effective IT capability that can evolve with changing business needs. InforSense KDE enables companies to deal with this challenge by using a workflow-based integrative analytics methodology that defines and streamlines key information-driven research processes. With InforSense KDE, sophisticated informatics applications can be easily built by scientists themselves at the speed of research, without the need for additional IT knowledge and support. Analytic workflows can be deployed to research scientists as easy-to-use solutions, stored to track information-based decision-making, and used to support more effective collaboration with partners. InforSense is successfully working with many life science companies, including Cambria Biosciences, a Boston-based biotechnology company, to lower the cost and time required for high volume data analyses. In this webcast, showing a case study by Anthony Arvanites from Cambria Biosciences, you will discover how InforSense KDE delivers: - Cost-effective high throughput analytics without programming - Secure, streamlined and automated data analysis using in-database analytics - Knowledge capture and application through easy development and implementation of in-house SOPs - Reduced IT costs through leveraging and optimising existing IT investments - IP tracking by capturing how a decision is made - not just the results Cambria BioSciences is an innovative biotechnology company that combines the power of genetics, physiological disease models and high-throughput chemical screening to discover new drug leads and how they work. The company has a focused research agenda requiring intensive analytical work but has limited IT resources. In 2005, Cambria acquired InforSense KDE as the main tool for implementing their data analysis tasks. Cambria rapidly implemented a custom portal of analytic applications, including compound inventory, high content screening analysis and predictive ADME, without needing to expand its IT resources. Cambria report savings in IT resources of around 35% through providing scientists with deployed applications built using InforSense KDE. Register Here to Join the Live Webcast: http://www.inforsense.com/webcast_jun06_14.html InforSense Ltd 459a Fulham Road Chelsea, London SW10 9UZ - UK InforSense - USA 25 Moulton Street, Cambridge, MA 02138 - USA www.inforsense.com 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 products names are trademarks of their respective holders. From owner-chemistry@ccl.net Tue May 30 17:51:00 2006 From: "Jozsef Csontos jozsefcsontos**creighton.edu" To: CCL Subject: CCL: negative bsse content Message-Id: <-31867-060530174746-9707-ZWRW2t5blh62dMU1PTqiKw(~)server.ccl.net> X-Original-From: Jozsef Csontos Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Tue, 30 May 2006 16:47:29 -0500 Mime-Version: 1.0 Sent to CCL by: Jozsef Csontos [jozsefcsontos[a]creighton.edu] Dear List Members, I was calculating intermolecular interaction energies using the counterpoise method to correct the results for bsse (3 dimer centered basis set calcs). The bsse contents were also calculated (2 more monomer centered basis set calcs). If I'm not mistaken I can get the bsse content if I subtract the non-bsse corrected energy from the bsse corrected one. This imply that the bsse content should be positive. I am using quite large basis set considering the investigated systems (~50 atoms, cc-pVTZ, aug-cc-pVTZ) and the BSSE content is usually small, less than 1kcal/mol; the interaction energies are in the 2-8 kcal/mol range. The level of theory are lmp2 and dft. However, in some cases (mainly lmp2 calcs) I got small negative (~ -0.3,-0.5 kcal/mol) bsse contents. Do you have any idea, how the bsse content can come to be negative? Thanks, Jozsef -- Jozsef Csontos, Ph.D. Department of Biomedical Sciences Creighton University, Omaha, NE From owner-chemistry@ccl.net Tue May 30 18:51:00 2006 From: "Lisa Subissati lsubissati-,-chemcomp.com" To: CCL Subject: CCL: Press Release: Chemical Computing Group, Excellence Award Winner Announcement Message-Id: <-31868-060530102702-12345-YFhVYmupf9miDiQXlN/oKA]_[server.ccl.net> X-Original-From: "Lisa Subissati" Date: Tue, 30 May 2006 14:41:59 -0400 Sent to CCL by: "Lisa Subissati" [lsubissati++chemcomp.com] [Converted from PDF attachment to text by CCL Admin] Chemical Computing Group 1010 Sherbrooke St. West, Suite 910 Montreal, CA H3A 2R7 2006 Press Release Chemical Computing Group Announces Excellence Award Winners at the 2006 ACS in San Francisco, CA. MONTREAL, May 30, 2006 - Chemical Computing Group (CCG) and the American Chemical Society's (ACS) Division of Computers in Chemistry (COMP) congratulate the winners of the CCG Excellence Awards at the 232nd ACS National Meeting in San Francisco, California. The well-regarded CCG Excellence Award honors graduate students who have excelled in the field of computational chemistry. Winners are selected according to the distinction and relevance of their research, as well as the quality of supporting materials. CCG will finance each awardee for travel costs to San Francisco for the Fall 2006 ACS; will recognize their research at the Awards Presentation during the COMP Division Poster Session on Tuesday September 12, 2006; and will give a one-year license for their software, the Molecular Operating Environment. For more information on how to submit for the 2007 ACS Award in Chicago, please contact Andrew Good at: Andrew.Good|*|bms.com Fall 2006 ACS San Francisco, CA Winners: Ying Wei, Northeastern University High-recall, high-precision prediction of protein binding sites >from 3D structure Sara E. Nichols, Yale University Shrinking residues for enhanced Monte Carlo sampling for proteins Timothy H. Click, University of Oklahoma Locating alpha-helices and beta-strands using recently-developed protocols Johannes Hachmann, Cornell University Quadratic Scaling Multireference Correlation in Polyenes and Long Molecules with the Local Density Matrix Renormalization Group Zhi Wang, Emory University Quantum Chemical Molecular Dynamics Study of Catalyst-Free SWNT Growth >from SiC-derived Carbon Kind regards, Lisa Subissati Marketing .. Chemical Computing Group .. 1010 Sherbrooke St. West, Suite 910 .. Montreal, CA H3A 2R7 .. Tel: 514 393 1055 ext. 43 .. Fax: 514 874 9538 .. www.chemcomp.com ----------------------------------------------------- CCG's 3rd User Group Meeting June 27th - 30th, 2006 Montreal, Canada www.chemcomp.com/ugm-2006.htm -----------------------------------------------------