From chemistry-request@server.ccl.net Tue Jul 24 06:06:53 2001 Received: from titanium.mater.unimib.it (ricci@[149.132.191.100]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6OA6p515188 for ; Tue, 24 Jul 2001 06:06:53 -0400 Received: from localhost (ricci@localhost) by titanium.mater.unimib.it (8.8.6 (PHNE_14041)/8.8.6) with SMTP id MAA21327 for ; Tue, 24 Jul 2001 12:06:51 +0200 (METDST) Date: Tue, 24 Jul 2001 12:06:50 +0200 (METDST) From: Davide Ricci To: chemistry@ccl.net Subject: DQS and G98 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I recently built a pc's cluster to do parallel calculations with g98 (by Linda). The g98 parallel version is installed but I've some problems: 1) I installed the DQS (on the master and on the clients) and I created some queues, but all the serial jobs are queued only on the master. I'm running the qmaster demon on the server and the dqs_execd demon on the clients 2) To run gaussian jobs I need some scrips. Does someone have these scripts? Could you help me, please? Thank you very much Davide Ricci (Phd. student) ******************************* Ricci Davide * * davide.ricci@mater.unimib.it * * UNIVERSITA' MILANO BICOCCA * Via Cozzi 53 * * ITALY * * ******************************* From chemistry-request@server.ccl.net Tue Jul 24 05:17:46 2001 Received: from sun2.ruf.uni-freiburg.de ([132.230.1.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6O9Hi518652 for ; Tue, 24 Jul 2001 05:17:45 -0400 Received: from uni-freiburg.de (PC2-IR4.physchem.uni-freiburg.de [132.230.171.109]) by sun2.ruf.uni-freiburg.de (8.9.3+Sun/8.9.1) with ESMTP id LAA04526 for ; Tue, 24 Jul 2001 11:17:41 +0200 (MET DST) Message-ID: <3B5D3DE8.3922A92F@uni-freiburg.de> Date: Tue, 24 Jul 2001 11:20:40 +0200 From: Oliver Hucke X-Mailer: Mozilla 4.5 [en] (WinNT; I) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: water in ligand docking Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers, we are performing ligand docking calculations with the program FlexX. Within the binding site there are ~20 water molecules visible in the crystal structure. Since FlexX considers the binding site as rigid, we have to decide which of these water molecules to keep as part of the receptor. (Unfortunately the 'particle mode' of FlexX did not produce satisfactory results) We are very interested in recommendations on how to select the water molecules and/or in any experience/references concerning the subject of considering water molecules in the binding site in ligand docking calculations. We will summarize the answers, of course. Kind regards, Tom Steinbrecher ______________________________________ Inst. fuer Physikalische Chemie II Universitaet Freiburg Albertstr. 23a D-79104 Freiburg Tel. : +49-761-203-5130 (/-6179) Fax. : +49-761-203-6189 email: hucke@uni-freiburg.de ______________________________________ From chemistry-request@server.ccl.net Tue Jul 24 07:00:01 2001 Received: from c2bapps2.btconnect.com ([193.113.209.22]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f6OB00517054 for ; Tue, 24 Jul 2001 07:00:01 -0400 Received: from patriot (actually host host217-32-147-5.hg.mdip.bt.net) by c2bapps2 with SMTP (XT-PP); Tue, 24 Jul 2001 11:59:30 +0100 From: "Roma Oakes" To: "ccl" Subject: RE: addition of downloaded basis set help! Date: Tue, 24 Jul 2001 11:55:08 +0100 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2911.0) In-Reply-To: Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 Thanks to all who helped me with this - the calculation is running (still!) and I think that it must be going okay - since the molecule has optimised and now I'm just waiting for the frequency calculations to finish - looks like it may be a long wait. thanks again Roma Oakes -----Original Message----- From: Roma Oakes [mailto:r.e.oakes@btconnect.com] Sent: 18 July 2001 08:21 To: ccl Subject: addition of downloaded basis set help! Dear all I am fairly new to computational chem. (6 months). I use Gaussian 98 on both a Linux and a windows system. Can someone explain, (in very simple terms) and one step at a time, how to get g98 to use a basis set that I have downloaded from http://www.dl.ac.uk/emsl_pnl/basisform.html It downloaded as a .rtf. I have located where the basis sets are stored on Linux (can't find them at all in the windows version!) I know that I need to use additional keywords but I can't figure out exactly what they ought to be - and where they should be put. All help gratefully received Roma Oakes r.oakes@qub.ac.uk From chemistry-request@server.ccl.net Tue Jul 24 07:39:57 2001 Received: from dire.bris.ac.uk ([137.222.10.60]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6OBdu517512 for ; Tue, 24 Jul 2001 07:39:56 -0400 Received: from eis.bris.ac.uk by dire.bris.ac.uk with SMTP-PRIV with ESMTP; Tue, 24 Jul 2001 12:39:53 +0100 Received: from localhost (localhost [127.0.0.1]) by eis.bris.ac.uk (8.11.4/8.11.3) with SMTP id f6OBd5110509 for ; Tue, 24 Jul 2001 12:39:05 +0100 (BST) Date: Tue, 24 Jul 2001 12:39:04 +0100 (BST) From: F Schambach To: chemistry@server.ccl.net Subject: still Autodock 3.05 Problems Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I've been trying to get Autodock distribution 3.05 to work on either a Red Hat Linux machine and on a SGI running IRIX 6.3 . The problem I have when I try to dock into my protein structure is that Autodock always docks my small ligand on top of protein residues in positions that are obviously impossible. That occurs on both systems with all kinds of ligands, with the precompiled binaries, with the ones I compiled myself, with standard mkgpf3/mkdpf3 files, I changed the grid spacing to 0.05 and made the grid big enough to include the whole active site and my ligand isn't docked on the edge of the box. Why does Autodock dock on top of residues ? Anybody having similiar problems ? Thank you very much, Felix Schambach, University of Bristol, Dept of Biochemistry f.schambach@bris.ac.uk From chemistry-request@server.ccl.net Mon Jul 23 19:36:05 2001 Received: from kafka.net.nih.gov ([165.112.130.10]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6NNa4527614 for ; Mon, 23 Jul 2001 19:36:04 -0400 Received: from I.T.S.ME ([129.43.27.170]) by kafka.net.nih.gov (8.11.3/8.10.1) with ESMTP id f6NNa4D11641; Mon, 23 Jul 2001 19:36:04 -0400 (EDT) Date: Mon, 23 Jul 2001 19:33:40 -0400 (Eastern Daylight Time) From: "M. Nicklaus" To: CHEMISTRY@ccl.net cc: mn1@helix.nih.gov Subject: Chemistry Databases/Services (Small Molecule) on the Web Message-ID: X-X-Sender: mn1@helix.nih.gov MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I'm trying to compile a list of all the Web sites offering chemical structural databases (small molecule) that have at least one of the following capabilities: - Search by (sub-) structure - Display of the structure, at least in 2D (not just a name) - Download/save a structure in a computer-readable format (SD, PDB...) - Retrieve/dump large parts of the database (or even the entire DB) in bulk form, again in a computer-readable format - Perform some kind of calculation on the structure (e.g. physicochemical properties etc.) - At least 100 molecules available - Accessible with just a Web browser, possibly with some easily obtainable plugin (this excludes services that require a special application, such as SciFinder) These sites may be academic, commercial, government, non-profit. Required fees or subscription is not a disqualifier, but should be noted. I already have a certain number of such URLs; but I want to make sure that I don't overlook anything. I'll post a summary of course. TIA, Marc ------------------------------------------------------------------------ Marc C. Nicklaus, Ph.D. NIH/NCI at Frederick E-mail: mn1@helix.nih.gov Bldg 376, Rm 207 Phone: (301) 846-5903 376 Boyles Street Fax: (301) 846-6033 FREDERICK, MD 21702 USA Head, Computer-Aided Drug Design MiniCore Facility Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute at Frederick, National Institutes of Health http://rex.nci.nih.gov/RESEARCH/basic/medchem/mcnbio.htm ------------------------------------------------------------------------ From chemistry-request@server.ccl.net Tue Jul 24 03:47:28 2001 Received: from web14610.mail.yahoo.com ([216.136.224.242]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f6O7lS532426 for ; Tue, 24 Jul 2001 03:47:28 -0400 Message-ID: <20010724074724.69999.qmail@web14610.mail.yahoo.com> Received: from [128.235.16.159] by web14610.mail.yahoo.com; Tue, 24 Jul 2001 00:47:24 PDT Date: Tue, 24 Jul 2001 00:47:24 -0700 (PDT) From: Naomi Zirkind Subject: Raman spectra of glucose To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii BS"D I am looking for Raman spectra of glucose at excitation wavelengths in the infrared region (longer than 830 nm). If any of you has such information, please let me know via e-mail. Thank you. Dr. Naomi Zirkind New Jersey Institute of Technology Newark, New Jersey __________________________________________________ Do You Yahoo!? Make international calls for as low as $.04/minute with Yahoo! Messenger http://phonecard.yahoo.com/ From chemistry-request@server.ccl.net Tue Jul 24 10:26:18 2001 Received: from ns02.sbphrd.com (firewall-user@[208.198.64.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6OEQH520233 for ; Tue, 24 Jul 2001 10:26:18 -0400 Received: by ns02.sbphrd.com; id KAA22547; Tue, 24 Jul 2001 10:26:13 -0400 (EDT) From: Received: from unknown(139.136.64.5) by ns02.sbphrd.com via smap (V5.0) id xma022492; Tue, 24 Jul 01 10:26:03 -0400 Received: from uksmtp01.ha.uk.sbphrd.com (uksmtp01.ha.uk.sbphrd.com [139.136.216.185]) by phinet.sbphrd.com (8.9.1b+Sun/8.9.1) with ESMTP id KAA13687; Tue, 24 Jul 2001 10:26:06 -0400 (EDT) Subject: OMG Life Sciences Research Task Force seeks your guidance To: bioinformatics@sdsc.edu, lifesciences@omg.org, chemistry@ccl.net, tc@omg.org Date: Tue, 24 Jul 2001 10:25:15 -0400 Message-ID: X-MIMETrack: Serialize by Router on UKSMTP01/SERVERS/PHRD/SB_PLC(Release 5.0.5 |September 22, 2000) at 24/07/2001 15:26:01 MIME-Version: 1.0 Content-type: text/plain; charset=us-ascii We apologize to those who receive multiple copies of this email. Please distribute this announcement to all interested parties. ======================================================================== The Object Management Group has issued a new Request for Information (RFI) in the life sciences research area. Authored by the Life Sciences Research (LSR) Domain Task Force (DTF), the new RFI is a general request. We want to know what to focus on next. The RFI can be found at http://doc.omg.org/lifesci/2001-04-15 RFI submissions are due by 20 August 2001. The primary reason for issuing a new RFI is to take advantage of the OMG's new Model Driven Architecture (MDA). By leveraging its modeling specifications, such as UML, the OMG has significantly broadened its architectural approach. New technology submissions will be required to have a middleware-independent model, with one or more corresponding models for specific middleware platforms such as CORBA, Enterprise Java Beans, XML, or SOAP. For more information about MDA see http://www.omg.org/mda. Two revised submission efforts (Gene Expression and Chemical Structures) are already using the MDA approach and will include XML-based solutions. The RFI also highlights the technology adoptions from LSR, * Biomolecular Sequence Analysis * Genomic Maps * Bibliographic Query Service * Macromolecular Structure and the RFPs underway * Chemical Structure Access & Representation * Gene Expression * Laboratory Equipment Control Interface Specification * Biomolecular Sequence Analysis Entities Please contact any of the LSR co-chairs if you have questions about the RFI or the LSR DTF. * David Benton (W_David_Benton@gsk.com) * Karl Konnerth (konnerth@incyte.com) * Scott Markel (smarkel@netgenics.com) You can also find out more about the LSR at http://lsr.omg.org/ From chemistry-request@server.ccl.net Tue Jul 24 12:57:41 2001 Received: from server.mldnet.com (root@[212.56.192.20]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6OGvb523432 for ; Tue, 24 Jul 2001 12:57:38 -0400 Received: from ppp-212.56.193.135.mldnet.com (ppp-212.56.193.135.mldnet.com [212.56.193.135]) by server.mldnet.com (8.9.3/8.9.3) with ESMTP id TAA06538; Tue, 24 Jul 2001 19:57:20 +0300 Date: Tue, 24 Jul 2001 20:02:50 +0300 From: Mike Peleah X-Mailer: The Bat! (v1.53d) Reply-To: Mike Peleah X-Priority: 3 (Normal) Message-ID: <35525882.20010724200250@yahoo.com> To: chemistry@ccl.net, Gamess-L@gl.ciw.edu Subject: DIIS and SOSCF MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear chemistry, I have a question regarding GAMESS--which SCF option: DIIS or SOSCF is better for use? For my personal observations it seems that using DIIS accelerate convergence better than SOSCF. Also, I would like to read original articles on DIIS but the only reference I have is P.Pulay J.Comput.Chem. 3, 556-560(1982). Unfortunatelly, J.Comput.Chem. completely unavailable in our library (and I our country I think). Could anybody give me other references on DIIS, preferably in J.Chem.Phys J.Am.Chem.Soc. and smth like that. Thanks. Best regards, Mike mailto:MikePeleah@yahoo.com From chemistry-request@server.ccl.net Tue Jul 24 18:14:14 2001 Received: from smtp014.mail.yahoo.com ([216.136.173.58]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f6OMED528280 for ; Tue, 24 Jul 2001 18:14:13 -0400 Received: from ch-12.psnet.ucla.edu (HELO TPT20) (128.97.147.212) by smtp.mail.vip.sc5.yahoo.com with SMTP; 24 Jul 2001 22:14:12 -0000 X-Apparently-From: Reply-To: From: "Roi Baer" To: "Mike Peleah" , , Subject: RE: DIIS and SOSCF Date: Wed, 25 Jul 2001 01:15:39 +0200 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) In-Reply-To: <35525882.20010724200250@yahoo.com> Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 Dear Mike, Try: Bowler and Gillan Chem Phys Lett 325 (2000) 473 Roi Roi Baer, Chaim Weizmann Institute of Chemistry, and the Lise Meitner Center for Quantum Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904 Israel ======================================= Tel (W): +972 (2) 658-6114 Fax (W): +972 (2) 651-3742 Tel/Fax (H): +972 (2) 678-8367 ======================================= email: Roi.Baer@huji.ac.il URL: http://www.fh.huji.ac.il/~roib ======================================= _________________________________________________________ Do You Yahoo!? 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