From owner-chemistry@ccl.net Fri Sep 25 06:02:01 2009 From: "Mannan malie_03^-^yahoo.co.in" To: CCL Subject: CCL: I would like to expertise in chemogenomics Message-Id: <-40351-090925044941-19243-kdWw+u8xlPskR7i+9T8E0g.@.server.ccl.net> X-Original-From: Mannan Content-Type: multipart/alternative; boundary="0-461497462-1253864951=:9071" Date: Fri, 25 Sep 2009 13:19:11 +0530 (IST) MIME-Version: 1.0 Sent to CCL by: Mannan [malie_03=-=yahoo.co.in] --0-461497462-1253864951=:9071 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable I would to train myself in chemogenomics. Rightnow I am working in QSAR and molecular dynamics =A0 Is there any one can give=A0=A0=A0basic tutorial in chemogenomics or relate= d information/ source/how to beginwith=A0for a beginner like me. =A0 Mannan. =A0=0A=0A=0A Now, send attachments up to 25MB with Yahoo! India Mail. = Learn how. http://in.overview.mail.yahoo.com/photos --0-461497462-1253864951=:9071 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable

I would to train myself in chemogeno= mics.
Rightnow I am working in QSAR and molecular dynamics
 
Is there any one can give   basic tutorial in chemogeno= mics or related information/ source/how to beginwith for a beginner li= ke me.
 
Mannan.

 

=0A
Yahoo! India has a new look. Take a sneak peek. --0-461497462-1253864951=:9071-- From owner-chemistry@ccl.net Fri Sep 25 06:16:00 2009 From: "Richard Tia richtiagh]~[gmail.com" To: CCL Subject: CCL: Negative Activation energy Message-Id: <-40352-090925060208-25656-FWMCCfQjw99NiXxqmOuQ6g,+,server.ccl.net> X-Original-From: "Richard Tia" Date: Fri, 25 Sep 2009 06:02:01 -0400 Sent to CCL by: "Richard Tia" [richtiagh+/-gmail.com] Dear all, I am computing a certain organometallic cycloaddition reaction and i keep on getting a negative activation energy. I've looked for a stable intermediate in that vicinity of the profile but can't seem to get any. Anybody got any suggestions as to what could be going on and what I can do to remedy that? Thanks is advance. Richard Tia KNUST, Kumasi Ghana From owner-chemistry@ccl.net Fri Sep 25 07:45:01 2009 From: "Jens Spanget-Larsen spanget{:}ruc.dk" To: CCL Subject: CCL:G: Reviews on Density Functionals Message-Id: <-40353-090925073907-20815-rrywwblmWNfTIHntHQ+4RQ(-)server.ccl.net> X-Original-From: Jens Spanget-Larsen Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Fri, 25 Sep 2009 13:38:55 +0200 MIME-Version: 1.0 Sent to CCL by: Jens Spanget-Larsen [spanget * ruc.dk] Dear CCL! The construction of density functionals for a variety of purposes is a popular field, and new density functionals continue to appear. Gaussian09, e.g., contains a listing of about 70 functionals. I am aware of the publications by Reimers et al. (Ann. N.Y. Acad. Sci.1006: 235–251 (2003)) and by Sousa et al. (J. Phys. Chem. A 2007, 111, 10439-10452), but I would be grateful for information on additional reviews, particularly on functionals designed for application in the field of electronic spectroscopy. Yours, Jens >--< ------------------------------------------------------ JENS SPANGET-LARSEN Office: +45 4674 2710 Dept. of Science (18.1) Fax: +45 4674 3011 Roskilde University Mobile: +45 2320 6246 P.O.Box 260 E-Mail: spanget.(-).ruc.dk DK-4000 Roskilde, Denmark http://www.ruc.dk/~spanget ------------------------------------------------------ From owner-chemistry@ccl.net Fri Sep 25 09:01:01 2009 From: "Pascal Muller pascal.jm.muller ~~ gmail.com" To: CCL Subject: CCL: Conformer generation Message-Id: <-40354-090925073050-19740-ml7wDo7lnGCCvO5H0WS/1A() server.ccl.net> X-Original-From: Pascal Muller Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 25 Sep 2009 13:04:12 +0200 MIME-Version: 1.0 Sent to CCL by: Pascal Muller [pascal.jm.muller!A!gmail.com] Dear CLLers, I'm looking for a spl script, for Sybyl, which is able to generate conformers for a database. My spl script using multisearch is working for 10's of molecules, but not for more, and I'm not able to figure why yet. Many thanks, Regards, Pascal From owner-chemistry@ccl.net Fri Sep 25 09:35:01 2009 From: "Tim Cheeseright tim() cresset-bmd.com" To: CCL Subject: CCL: FieldStere 1.1.0 Released Message-Id: <-40355-090925091150-7989-r/QrF3YEqxwUle6vJ3GFsg*|*server.ccl.net> X-Original-From: "Tim Cheeseright" Date: Fri, 25 Sep 2009 09:11:47 -0400 Sent to CCL by: "Tim Cheeseright" [tim(~)cresset-bmd.com] Cresset announces the release of a version 1.1 of its FieldStere bioisostere search system. Following FieldSteres successful release in January this year, Cresset has worked closely with industry leaders to extend its functionality and usability. FieldStere enables computational and medicinal chemists to use field-based chemistry to make smarter business decisions and enable them to escape the constraints imposed by molecular structure. FieldStere provides an innovative way to find bioisosteres - molecules that share a common biological activity but which are structurally diverse. FieldStere finds both known related structures (generating confidence in the results) and non-obvious bioisosteres which give increased novelty and patentability. These bioisosteres can be used to jump between chemotypes or fine-tuned to enhance potency and specificity whilst removing undesirable ADME and physical properties. FieldStere uses Cressets proprietary field technology, which describes chemical structures in terms of the surface and electrostatic properties of the whole molecule and accurately shows how a compound will interact with other molecules. FieldStere 1.1 provides significant new functionality: * Use protein structure data (if available) to limit the search space around your target. * Filter the results interactively to return the precise mix of physicochemical properties required. * Cluster the results by chemotype. * Search the provided database of >600K fragment or create your own using our compound fragmentation tool. To see a FieldStere case study visit www.cresset-bmd.com/fst_atorvastatin.shtml To see FieldStere in action register for a free webinar at www.cresset-bmd.com/cgi-bin/signup.cgi For a free evaluation of FieldStere please contact george]-[cresset-bmd.com Tim Cheeseright tim]-[cresset-bmd.com Cresset BMD BioPark Hertfordshire, AL73AX UK +44 1707 356 120 From owner-chemistry@ccl.net Fri Sep 25 10:29:01 2009 From: "Oellien, F (Frank) frank.oellien * sp.intervet.com" To: CCL Subject: CCL: 5. German Conference on Chemoinformatics Message-Id: <-40356-090925100645-15589-g8vFy990vEF5j1KFEbMYRA++server.ccl.net> X-Original-From: "Oellien, F (Frank)" Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 25 Sep 2009 16:06:27 +0200 MIME-Version: 1.0 Sent to CCL by: "Oellien, F (Frank)" [frank.oellien!^!sp.intervet.com] CALL FOR REGISTRATION 5th German Conference on Chemoinformatics Hotel 'Der Achtermann', Goslar, Germany 8 - 10 November 2009 Dear Colleague, The CIC division of the German Chemical Society wants to inform you = about the upcoming 5. German Conference on Chemoinformatics to be held = in Goslar, Germany, November 8 - 10, 2009 (http://www.gdch.de/gcc2009 = ). The international conference covers plenary talk, regular talks, and = posters in the following sessions: * Chemoinformatics and Drug Discovcery * Chemical Information, Patents, and Databases=20 * Molecular Modelling=20 * Computational Material Science and Nanotechnology=20 Please register now by using the online registration form = (http://www.gdch.de/vas/tagungen/tg/5358/anmeld__e.htm) on our = conference website at www.gdch.de/gcc2009. Please remember that there is = a limit of 200 participants!! The deadline for registration is October = 8, 2009. The final programm is available available as PDF = (http://www.gdch.de/vas/tagungen/tg/5358/gcc_prog_2009.pdf) or online = under http://www.gdch.de/vas/tagungen/tg/5358/program__e.htm Please consider the conference dinner on Tuesday evening during your = travel planing. Furthermore, there will be 3 workshops in front of the conference on = Sunday afternoon by Chemical Computing Group, CCDC and the OCHEM team, = Helmholtz Zentrum, Munich. We will inform you about the details (times, = lecture halls, ..) on website. In addition a free-software session will be held on Sunday afternoon. Visit the conference website at www.gdch.de/gcc2009 for more information = or access directly the Call-for-Paper PDF = http://www.gdch.de/vas/tagungen/tg/einlad5358.pdf Unfortunately, the last-minute-poster submission has to be closed before = the end of the official deadline, because the limit of 60 posters has = already been reached. I hope to see you in Goslar.=20 Frank Oellien GDCh CIC Division Chair=20 Mit freundlichen Gr=FC=DFen / With kind regards=20 Dr. Frank Oellien BioChemInformatics Scientist Intervet Innovation GmbH Zur Propstei 55270 Schwabenheim, Germany E-Mail: frank.oellien]-[sp.intervet.com Phone: +49 (6130) 948 365 =09 Fax: +49 (6130) 948 517 =09 =20 Home http://www.intervet.com Sitz der Gesellschaft: Schwabenheim Amtsgericht Mainz, HRB 23 166 = Gesch=E4ftsf=FChrer: Dr. Peter Schmid -------------------------------------- This message and any attachments are solely for the intended recipient. If you are not the intended recipient, disclosure, copying, use or distribution of the information included in this message is prohibited -- please immediately and permanently delete. -------------------------------------- From owner-chemistry@ccl.net Fri Sep 25 11:22:01 2009 From: "Aimee Tomlinson altomlinson-.-ngcsu.edu" To: CCL Subject: CCL:G: severe error message #2070 Message-Id: <-40357-090925093307-19705-P8kL3WMZvVRsvCjv3vv8LA-*-server.ccl.net> X-Original-From: "Aimee Tomlinson" Date: Fri, 25 Sep 2009 09:33:03 -0400 Sent to CCL by: "Aimee Tomlinson" [altomlinson*o*ngcsu.edu] I have seen this error before and it was a problem with linking. I cannot identify what the problem is this time. It seems to break down upon inclusion of larger atom (e.g. Sulfur). I tried to run a simple calculation on thiophene and here is the log file: Entering Link 1 = C:\G03W\l1.exe PID= 3240. Copyright (c) 1988,1990,1992,1993,1995,1998,2003,2004, Gaussian, Inc. All Rights Reserved. This is the Gaussian(R) 03 program. It is based on the the Gaussian(R) 98 system (copyright 1998, Gaussian, Inc.), the Gaussian(R) 94 system (copyright 1995, Gaussian, Inc.), the Gaussian 92(TM) system (copyright 1992, Gaussian, Inc.), the Gaussian 90(TM) system (copyright 1990, Gaussian, Inc.), the Gaussian 88(TM) system (copyright 1988, Gaussian, Inc.), the Gaussian 86(TM) system (copyright 1986, Carnegie Mellon University), and the Gaussian 82(TM) system (copyright 1983, Carnegie Mellon University). Gaussian is a federally registered trademark of Gaussian, Inc. This software contains proprietary and confidential information, including trade secrets, belonging to Gaussian, Inc. This software is provided under written license and may be used, copied, transmitted, or stored only in accord with that written license. The following legend is applicable only to US Government contracts under FAR: RESTRICTED RIGHTS LEGEND Use, reproduction and disclosure by the US Government is subject to restrictions as set forth in subparagraphs (a) and (c) of the Commercial Computer Software - Restricted Rights clause in FAR 52.227-19. Gaussian, Inc. 340 Quinnipiac St., Bldg. 40, Wallingford CT 06492 --------------------------------------------------------------- Warning -- This program may not be used in any manner that competes with the business of Gaussian, Inc. or will provide assistance to any competitor of Gaussian, Inc. The licensee of this program is prohibited from giving any competitor of Gaussian, Inc. access to this program. By using this program, the user acknowledges that Gaussian, Inc. is engaged in the business of creating and licensing software in the field of computational chemistry and represents and warrants to the licensee that it is not a competitor of Gaussian, Inc. and that it will not use this program in any manner prohibited above. --------------------------------------------------------------- Cite this work as: Gaussian 03, Revision D.01, M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, J. A. Montgomery, Jr., T. Vreven, K. N. Kudin, J. C. Burant, J. M. Millam, S. S. Iyengar, J. Tomasi, V. Barone, B. Mennucci, M. Cossi, G. Scalmani, N. Rega, G. A. Petersson, H. Nakatsuji, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, M. Klene, X. Li, J. E. Knox, H. P. Hratchian, J. B. Cross, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann, O. Yazyev, A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, P. Y. Ayala, K. Morokuma, G. A. Voth, P. Salvador, J. J. Dannenberg, V. G. Zakrzewski, S. Dapprich, A. D. Daniels, M. C. Strain, O. Farkas, D. K. Malick, A. D. Rabuck, K. Raghavachari, J. B. Foresman, J. V. Ortiz, Q. Cui, A. G. Baboul, S. Clifford, J. Cioslowski, B. B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R. L. Martin, D. J. Fox, T. Keith, M. A. Al-Laham, C. Y. Peng, A. Nanayakkara, M. Challacombe, P. M. W. Gill, B. Johnson, W. Chen, M. W. Wong, C. Gonzalez, and J. A. Pople, Gaussian, Inc., Wallingford CT, 2004. ****************************************** Gaussian 03: IA32W-G03RevD.01 13-Oct-2005 25-Sep-2009 ****************************************** %mem=1500MB %chk=C:\G03W\RAE\CON_A5a\thiophene.chk --------------------------- # opt am1 geom=connectivity --------------------------- 1/14=-1,18=50,26=3,38=1,57=2/1,3; 2/9=110,17=6,18=5,40=1/2; 3/5=2,11=9,12=1,16=1,25=1,30=1/1; 4/5=3,11=1,20=5,22=1,24=3,35=1/1,2; 6/7=2,8=2,9=2,10=2/1; 7//16; 1/14=-1,18=50/3(3); 2/9=110/2; 6/7=2,8=2,9=2,10=2/1; 99//99; 2/9=110/2; 3/5=2,11=9,12=1,16=1,25=1,30=1/1; 4/5=5,11=1,16=3,20=5,22=1,24=3,35=1/1,2; 7//16; 1/14=-1,18=50/3(-4); 2/9=110/2; 6/7=2,8=2,9=2,10=2/1; 99//99; For some reason it breaks down at the |1.exe. Any help would be appreciated. From owner-chemistry@ccl.net Fri Sep 25 12:37:01 2009 From: "Jan Labanowski janl=-=speakeasy.net" To: CCL Subject: CCL: COMP Symposia, Spring 2010 ACS National Meeting (March 21st-25th, 2010, SF) Message-Id: <-40358-090925123444-28538-EtCAPjz+f9WC7hfUeBdJ7w:server.ccl.net> X-Original-From: Jan Labanowski Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 25 Sep 2009 12:34:30 EDT MIME-Version: 1.0 Sent to CCL by: Jan Labanowski [janl-#-speakeasy.net] CCL Members may be interested in this (I received my personal copy as a "Ca= rd Carrying Member" of COMP): Dear COMP Member: The COMP symposia for the Spring 2010 ACS National Meeting (March 21st to 25th, 2010) in San Francisco are: Advances in Conformational Sampling (Oral) Drug Discovery (Oral) Generalized Ensemble Simulation Methods (Oral) Molecular Mechanics (Oral) Molecular Pharmaceutics (Oral) Quantum Chemistry (Oral) Scripting & Programming (Oral) Thomas Kuhn Paradigm Shift (Oral) Chemical Computing Group Excellence Award (Poster) Hewlett-Packard Scholar Awards (Poster) Poster Session (Poster) As you maybe aware, the ACS has retired OASYS and is now using PACS for abstract submission. To submit an abstract you will need to use your ACS ID at http://abstracts.acs.org . Abstract submission deadline is October 19th, 2009. Please allow extra time to submit your abstract as this is a new system. Instructions on how to obtain an ACS ID are provided on the main page of the PACS website ( http://abstracts.acs.org ). =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D Jan Moderatoire Extraordinaire de CCL (Pardon my English...) P.S. On a private note from Jan... Please submit the interesting meetings t= o the Computational Chemistry List conference site (you have the link under each message, please read it). It is free and your support is welcome {:-)}.