From chemistry-request@ccl.net Tue Aug 3 03:22:17 2004 Received: from mailer.gwdg.de (mailer.gwdg.de [134.76.10.26]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i738MGMq016022 for ; Tue, 3 Aug 2004 03:22:16 -0500 Received: from vrlab03.mpibpc.gwdg.de ([134.76.211.99] helo=mpi-bpc.mpg.de) by mailer.gwdg.de with esmtp (Exim 4.34) id 1Brufy-0000kn-Kw for chemistry*at*ccl.net; Tue, 03 Aug 2004 10:29:38 +0200 Message-ID: <410F4CF2.7090007*at*mpi-bpc.mpg.de> Date: Tue, 03 Aug 2004 10:29:38 +0200 From: Vlad Cojocaru User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.4) Gecko/20030624 Netscape/7.1 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry*at*ccl.net Subject: drug design course Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Virus-Scanned: (clean) by exiscan+sophie X-Spam-Status: No, hits=0.9 required=7.5 tests=MY_BAD_DOT autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear CCL-ers, Could somebody indicate a good short course on drug design within the european union? I am a graduate student working on MD simulations and I would like to participate in such a course. I tried searching but I didnt find anything. Thank you in advance vlad -- Vlad Cojocaru Max Planck Institute for Biophysical Chemistry Department: 060 Am Fassberg 11, 37077 Goettingen, Germany tel: ++49-551-201.1327 e-mail: Vlad.Cojocaru*at*mpi-bpc.mpg.de home tel: ++49-551-9963204 From chemistry-request@ccl.net Tue Aug 3 09:03:43 2004 Received: from armstrong.ociweb.com (63-254-221-196.ip.mcleodusa.net [63.254.221.196]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i73E3fMq005083 for ; Tue, 3 Aug 2004 09:03:41 -0500 Received: from [192.168.1.9] (110-122.bestdsl.net [216.162.110.122]) by armstrong.ociweb.com (8.11.6/8.11.6) with ESMTP id i73EB7C15999; Tue, 3 Aug 2004 09:11:09 -0500 Mime-Version: 1.0 X-Sender: masterpop.-at-.balbes.com Message-Id: Date: Tue, 3 Aug 2004 09:10:08 -0500 To: chemistry.-at-.ccl.net From: "Lisa M. Balbes, Ph.D." Subject: Conformers, 2D to 3D algorithms Cc: lisa.-at-.balbes.com Content-Type: text/plain; charset="iso-8859-1" ; format="flowed" X-Spam-Status: No, hits=0.8 required=7.5 tests=MY_DSL autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i73E3hMq005090 I am trying to determine what algorithm(s) are considered state of the art in 2D to 3D structure conversion, and in conformer searching/generation. I am especially interested in answers to the following questions. Conformers ---------- 1) What algorithms are available? 2) Which one or ones is/are considered best? 3) What software are these implemented in? Any open-source or public domain? 4) Are there "gold standard" test sets for performance? 2D -> 3D -------- 1) What are the standard file formats? Where do the files usually come from? 2) What sort of questions are being asked and answered using this technique? 3) What software are these implemented in? Again, any open-source or public domain stuff? 4) Are there "gold standard" test sets for performance? I would appreciate opinions, literature references, marketing materials...whatever anyone cares to share. Please respond to me directly, and I'll be happy to post a summary to the list. Lisa -- ------------------------------------------------------------------------------------------------------------------------------- Lisa M. Balbes, Ph.D. lisa.-at-.balbes.com http://www.balbes.com/ Balbes Consultants Scientific Writing Services since 1992 American Chemical Society - Career Consultant and Presenter; COMP division WebMaven Chair, Washington University APAP, St Louis South Committee CIC SIG Manager, St Louis Society for Technical Communication Technical Coordinator, Cyberworkshop Committee, American Needlepoint Guild Treasurer, Cub Scout Pack 352 and Advancement Coordinator, Boy Scout Troop 352 From chemistry-request@ccl.net Tue Aug 3 15:30:21 2004 Message-ID: <40FB88B8.5060909.-at-.ua.ac.be> From: Karla Tersago MIME-Version: 1.0 To: chemistry.-at-.ccl.net Subject: basis set for Iridium Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Dear CCL-ers, Currently, I'm trying to perform some geometry optimisations on Ir-complexes, but it seems difficult to me to find a useful basis set to perform DFT calculations with Gausian03. Can anyone please suggest me which basis set is useful for this kind of calculations (on Iridium)? And can anyone please help me with the following problem: I tried the WTBS "Well-Tempered Basis Set" for Iridium obtained from the EMSL Basis Set Library, but got the following error: (Enter /afs/islab/brabo/gaussian/g03/l502.exe) UHF open shell SCF: Requested convergence on RMS density matrix=1.00D-08 within 128 cycles. Requested convergence on MAX density matrix=1.00D-06. Requested convergence on energy=1.00D-06. No special actions if energy rises. Using DIIS extrapolation, IDIIS= 1040. Integral symmetry usage will be decided dynamically. 17171 words used for storage of precomputed grid. Keep R1 and R2 integrals in memory in canonical form, NReq= 2402437. IEnd= 41974 IEndB= 41974 NGot= 111411200 MDV= 110218373 LenX= 110218373 Symmetry not used in FoFDir. MinBra= 0 MaxBra= 3 Meth= 1. IRaf= 0 NMat= 1 IRICut= 1 DoRegI=T DoRafI=F ISym2E= 0 JSym2E=0. Choose: IPath= 0 Avail=F Cost= 0 Choose: IPath= 1 Avail=T Cost= 68851820 Choose: IPath= 2 Avail=F Cost= 0 Choose: IPath= 3 Avail=F Cost= 0 Choose: IPath= 4 Avail=T Cost= 356895164 Choose: IPath= 5 Avail=T Cost= 390455112 Choose: IPath= 6 Avail=F Cost= 0 Choose: IPath= 7 Avail=F Cost= 0 Choose: IPath= 8 Avail=F Cost= 0 Choose: IPath= 9 Avail=F Cost= 0 Choose: IPath=10 Avail=F Cost= 0 Choose: IPath=11 Avail=T Cost= 68851820 Choose: IPath=12 Avail=F Cost= 0 Choose: IPath=13 Avail=F Cost= 0 Choose: IPath=14 Avail=T Cost= 356895164 Choose: IPath=15 Avail=F Cost= 0 Choose: IPath=16 Avail=F Cost= 0 Choose: IPath=17 Avail=F Cost= 0 Choose: IPath=18 Avail=F Cost= 0 Choose: IPath=19 Avail=F Cost= 0 Choose: IPath=20 Avail=F Cost= 0 Choose: IPath=21 Avail=F Cost= 0 Choose: IPath=22 Avail=F Cost= 0 Choose: IPath=23 Avail=F Cost= 0 Choose: IPath=24 Avail=F Cost= 0 Choose: IPath=25 Avail=F Cost= 0 Choose: IPath=26 Avail=F Cost= 0 Choose: IPath=27 Avail=F Cost= 0 Choose: IPath=28 Avail=F Cost= 0 Choose: IPath=29 Avail=T Cost= -1803080948 Choose: IPath=30 Avail=F Cost= 0 Choose: IPath=31 Avail=F Cost= 0 Choose: IPath=32 Avail=F Cost= 0 Choose: IPath=33 Avail=F Cost= 0 Choose: IPath=34 Avail=F Cost= 0 Choose: IPath=35 Avail=F Cost= 0 Choose: IPath=36 Avail=F Cost= 0 Choose: IPath=37 Avail=F Cost= 0 Choose: IPath=38 Avail=F Cost= 0 Choose: IPath=39 Avail=F Cost= 0 Choose: IPath=40 Avail=F Cost= 0 Choose: IPath=41 Avail=F Cost= 0 Choose: IPath=42 Avail=F Cost= 0 Choose: IPath=43 Avail=F Cost= 0 Choose: IPath=44 Avail=F Cost= 0 Choose: IPath=45 Avail=F Cost= 0 Choose: IPath=46 Avail=F Cost= 0 Choose: IPath=47 Avail=F Cost= 0 Choose: IPath=48 Avail=F Cost= 0 Choose: IPath=49 Avail=F Cost= 0 Overflow in Choose. Error termination via Lnk1e in /afs/islab/brabo/gaussian/g03/l502.exe at Fri Jul 16 13:46:22 2004. Job cpu time: 0 days 0 hours 10 minutes 52.7 seconds. File lengths (MBytes): RWF= 11 Int= 0 D2E= 0 Chk= 1 Scr= 1 Thank you for your help, Karla -- ----------------------------------------------------------------------------- Karla Tersago Structural Chemistry Group, Department of Chemistry University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium E-mail: karla.tersago.-at-.ua.ac.be /Phone:+32(03)8202366/Fax:+32(03)8202310 ----------------------------------------------------------------------------- From chemistry-request@ccl.net Tue Aug 3 12:04:32 2004 Received: from www.eyesopen.com (208-41-78-163.client.dsl.net [208.41.78.163]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i73H4UMq014349 for ; Tue, 3 Aug 2004 12:04:30 -0500 Received: from eyesopen.com (208-41-78-162.client.dsl.net [208.41.78.162]) (authenticated) by www.eyesopen.com (8.11.6/8.11.6) with ESMTP id i73GpD730803 for ; Tue, 3 Aug 2004 10:51:13 -0600 Message-ID: <410FC757.7070909!at!eyesopen.com> Date: Tue, 03 Aug 2004 11:11:51 -0600 From: George Vacek Organization: OpenEye Scientific Software User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.0.2) Gecko/20030208 Netscape/7.02 X-Accept-Language: en-us, en MIME-Version: 1.0 To: CHEMISTRY!at!ccl.net Subject: OpenEye Workshop: Rapid lead identification with ROCS and FRED Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=0.8 required=7.5 tests=MY_DSL autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net OpenEye will be hosting a training workshop at the ACS National Meeting in Philadelphia. If you plan to attend that meeting and would like an introduction to ROCS and FRED, please consider attending our workshop. Title: Rapid lead identification with ROCS and FRED Wednesday, August 25, 3:30-6:00pm Room 305, Pennsylvania Convention Center, ACS National Meeting in LA Attendance is free but seating is limited and strictly enforced by ACS. Register to attend at www.chemistry.org/expoplanner Abstract: The chemistry of molecular interactions boils down to shape and electrostatics. This workshop focuses on rapid lead identification in drug discovery using OpenEye software developed under that philosophy. It will begin with a brief overview of OpenEye's complete offering, before focusing on FRED and ROCS. FRED offers extremely fast, exhaustive docking of ligands within a protein active site, while the ligand-based ROCS provides rapid 3D molecular shape similarity searches. Either can be guided by known pharmacophore features. The workshop will include some theory, example cases, software demonstrations and the opportunity for hands-on tutorial. Regards, George Vacek VP, Business Development OpenEye Scientific Software