From chemistry-request@ccl.net Mon Oct 4 09:37:23 2004 Received: from maya.uab.es (maya.uab.es [158.109.0.6]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i94EbMWx016506 for ; Mon, 4 Oct 2004 09:37:22 -0500 Received: from CONVERSION-DAEMON.maya.uab.es by maya.uab.es (PMDF V6.2-X20 #30859) id <0I5200L01E06K5/at/maya.uab.es> for chemistry/at/ccl.net; Mon, 04 Oct 2004 16:38:36 +0200 (MEST) Received: from klingon.uab.es (klingon.uab.es [158.109.14.5]) by maya.uab.es (PMDF V6.2-X20 #30859) with ESMTP id <0I5200ED7E05X4/at/maya.uab.es> for chemistry/at/ccl.net; Mon, 04 Oct 2004 16:38:29 +0200 (MEST) Received: from astult.qf.uab.es ([158.109.14.42] helo=klingon.uab.es) by klingon.uab.es with esmtp (Exim 4.30) id 1CETeO-00025p-WB for chemistry/at/ccl.net; Mon, 04 Oct 2004 16:17:17 +0200 Date: Mon, 04 Oct 2004 16:44:53 +0200 From: Marc Noguera Julian Subject: problems with turbomole To: chemistry/at/ccl.net Message-id: <416161E5.5080401/at/klingon.uab.es> MIME-version: 1.0 Content-type: text/plain; format=flowed; charset=ISO-8859-1 Content-transfer-encoding: 7BIT X-Accept-Language: en-us, en User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.6) Gecko/20040113 X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hello all, I am having problems with TURBOMOLE package. I am trying to calculate gradient for nth excited state in the case of ethylene (for testing). Output follows: 2e-integral 1st. derivatives will be neglected if expon. factor < 0.100000E-06 outer boundary for 2e-integral derivative neglection is 0.139334E-13 nfun > 10 not supported by nfun > 10 which is given by the two-electron contribution to gradient calculation Thanks in advance Marc From chemistry-request@ccl.net Mon Oct 4 05:42:16 2004 Received: from x403b0a96.ip.e-nt.net (x403b0a96.ip.e-nt.net [64.59.10.150]) by server.ccl.net (8.12.8/8.12.8) with SMTP id i94AgE51005861 for ; Mon, 4 Oct 2004 05:42:15 -0500 To: chemistry/at/server.ccl.net From: "Analisa Narcisa" Reply-To: "Analisa Narcisa" Date: Mon, 04 Oct 2004 06:49:55 -0500 Subject: CorelDraw $100, AD0BE Ph0toshop $80, Symantec Norton Antivirus $15 & more S0ftwares, all countries shiiping leaving later Message-ID: MIME-Version: 1.0 X-MimeOLE: Produced By Microsoft Exchange V6.0.5437.1 Content-Type: multipart/alternative; boundary="--261268149.908968688877422996.2887" X-Spam-Status: No, hits=4.4 required=7.5 tests=HTML_40_50,HTML_FONT_BIG, HTML_MESSAGE,SARE_ADLTOBFU,SARE_ADLTSUB1 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net ----261268149.908968688877422996.2887 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 8bit carry threw national familiar condition confidence pay during mere sea minute luckily law beautiful ----261268149.908968688877422996.2887 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 8bit search dress week busy paid soul person let , year son playing . excite daughter building drew returned became eleven any hundred

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obliged placed brought ; voice grade seven worthy says education miserable hung reply paid responsible affect cause ----261268149.908968688877422996.2887-- From chemistry-request@ccl.net Mon Oct 4 09:41:47 2004 Received: from mail1.rrz.Uni-Koeln.DE (mail1.rrz.Uni-Koeln.DE [134.95.100.208]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i94EfjWx016804 for ; Mon, 4 Oct 2004 09:41:46 -0500 Received: from [127.0.0.1] (vpn82-61.vpn.Uni-Koeln.DE [134.95.82.61]) by mail1.rrz.Uni-Koeln.DE (8.12.11/8.12.11) with ESMTP id i94EqiIO023675 (version=TLSv1/SSLv3 cipher=RC4-MD5 bits=128 verify=NOT); Mon, 4 Oct 2004 16:52:56 +0200 (MEST) Message-ID: <416163C1.4080807^at^uni-koeln.de> Date: Mon, 04 Oct 2004 16:52:49 +0200 From: Christoph Steinbeck User-Agent: Mozilla Thunderbird 0.8 (Windows/20040913) X-Accept-Language: en-us, en MIME-Version: 1.0 To: CCL List , CHMINF-L^at^LISTSERV.INDIANA.EDU, cic-members^at^chemie.uni-erlangen.de Subject: 18th CIC-Workshop "Recent Developments in Chemoinformatics" Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit X-Virus-Scanned: by amavisd-new X-Spam-Status: No, hits=0.4 required=7.5 tests=MY_BAD_DOT,SMILEY autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net We are approaching the registration deadline for the 18th annual workshop of the "Chemistry-Information-Computers" section of the German Chemical Society (GDCh). Surrounded by the Upper Middle Rhine UNESCO World Heritage Site (http://www.welterbe-mittelrheintal.de/), we will be discussing recent developments in Chemoinformatics. The meeting place will be Hotel Jakobsberg (http://www.jakobsberg.de) > from November 14th - 16th. The deadline for the registration is October 11th. Poster submission is possible until October 31st, after October 11th obviously only for registered participants :-) This year's key topics are - Pharmaceutical Chemoinformatics - Theoretical Chemistry and Modeling - Computer-Assisted Structure Elucidation - Metabolomics and Biomarker Talks will be given either in German or in English. Please register at http://www.cic-workshop.de, where you can also find the 2nd circular with the complete conference program. In case of questions or problems with the registration do not hesitate to contact me. With best regards, Christoph Steinbeck -- Dr. habil. Christoph Steinbeck (c.steinbeck^at^uni-koeln.de) Head of the Junior Research Group for Applied Bioinformatics Cologne University BioInformatics Center (http://www.cubic.uni-koeln.de) Z|lpicher Str. 47, 50674 Cologne Tel: +49(0)221-470-7426 Fax: +49 (0) 221-470-7786 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. From chemistry-request@ccl.net Mon Oct 4 00:53:50 2004 Received: from lgsx13.lg.ehu.es (lgsx13.lg.ehu.es [158.227.2.28]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i945rm51023987 for ; Mon, 4 Oct 2004 00:53:49 -0500 Received: from lgsx13.lg.ehu.es (localhost [127.0.0.1]) by lgsx13.lg.ehu.es (8.12.10/8.12.10) with ESMTP id i9464wAD012356 for ; Mon, 4 Oct 2004 08:04:58 +0200 (CEST) Received: from Teiresias.sq.ehu.es (sqpq13.sq.ehu.es [158.227.161.13]) by lgsx13.lg.ehu.es (8.12.10/8.12.10) with ESMTP id i9464rLX012313 for ; Mon, 4 Oct 2004 08:04:57 +0200 (CEST) From: Txema Organization: EHU To: chemistry)at(ccl.net Subject: Xeon Noconas and Gaussian Date: Mon, 4 Oct 2004 08:04:47 +0200 User-Agent: KMail/1.5.4 MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Content-Disposition: inline Message-Id: <200410040804.47378.pobmelat)at(sq.ehu.es> X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi there! We are planing to buy some new computers and considering the xeon noconas option. Anybody has any experience with these processors and Gaussian g98 in parallel? Txema Mercero EHU / UPV From chemistry-request@ccl.net Mon Oct 4 05:19:32 2004 Received: from gveu50.emea.givaudan.com (mail-external3.givaudan.com [57.66.141.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i94AJV51004875 for ; Mon, 4 Oct 2004 05:19:32 -0500 To: Matt Thompson Cc: chemistry!at!ccl.net Subject: Re: CCL:Glasses for printed stereo imagaes MIME-Version: 1.0 X-Mailer: Lotus Notes Release 5.0.11 July 24, 2002 Message-ID: From: andras.borosy!at!givaudan.com Date: Mon, 4 Oct 2004 12:30:37 +0200 X-MIMETrack: Serialize by Router on gvedoh01/H/Givaudan(Release 5.0.12 |February 13, 2003) at 04/10/2004 12:30:43 Dear Matt, Thanks a lot. I think to order PokeScope soon. Aldrich and VCH do not sell stereoviewers anymore. Bye, Dr. Andras Borosy Seniour Scientist Delivery Systems, Fragrance Research Givaudan Schweiz AG Ueberlandstr. 138 8600 D=FCbendorf Switzerland tel: + 41-1-8242164 fax: +41-1-8242926 e-mail: andras.borosy!at!givaudan.com Matt Thompson 01.10.2004 18:21 To: andras.borosy!at!givaudan.com cc: Subject: Re: CCL:Glasses for printed stereo imagaes On Fri, 2004-10-01 at 08:32, andras.borosy!at!givaudan.com wrote: > Dear Colleagues, > > Do you happen to know where one can buy special glasses for printed > stereo images? I assume you mean things like stereoscopic or stereopticon images? If so, I know someone who really likes the PokeScope: http://www.pokescope.com/pokescopeinfo.html But, there are a plethora of other achromatic viewers out there: http://www.berezin.com/3d/viewers1.htm That site also has lots of anaglyph (red/cyan type images) and Pulfrich glasses too. I've never ordered from them, so YMMV. Matt -- Learning just means you were wrong and they were right. - Aram Matt Thompson -- http://ucsub.colorado.edu/~thompsma/ 440 UCB, Boulder, CO 80309-0440 JILA A510, 303-492-4662 From chemistry-request@ccl.net Mon Oct 4 21:22:37 2004 Received: from hercules88.mit.edu (HERCULES88.MIT.EDU [18.63.2.20]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i952MbF2015373 for ; Mon, 4 Oct 2004 21:22:37 -0500 Received: from localhost (usagi@localhost) by hercules88.mit.edu (SGI-8.9.3/8.9.3) with ESMTP id WAA23375 for ; Mon, 4 Oct 2004 22:32:03 -0400 (EDT) Date: Mon, 4 Oct 2004 22:32:03 -0400 From: Bryan Matthew Wong To: chemistry~at~ccl.net Subject: help with 2D PES scan of CH3-NH2 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hello. I'm trying to do a 2D relaxed potential energy scan in Gaussian 98 of methylamine: CH3-NH2. Specifically, I am trying to map out the 2D PES of the internal rotor (between CH3-NH2) and the inversion of the nitrogen. I.e., for every torsional angle, I want the energy of inversion for various inversion angles. I can't think of a good way to do this without constraining more than 2 variables using the modredundant command. I originally thought using dummy atoms might help with this, but the modredundant command doesn't work with dummy atoms. Is there any hope of doing this in Gaussian. Thanks, Bryan usagi~at~hercules88.mit.edu From chemistry-request@ccl.net Mon Oct 4 10:21:56 2004 Received: from mhub-c2.tc.umn.edu (mhub-c2.tc.umn.edu [160.94.128.32]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i94FLtWx019771 for ; Mon, 4 Oct 2004 10:21:56 -0500 Received: from pobox.com (abacavir.pharmacy.umn.edu [160.94.172.208] (may be forged)) by mhub-c2.tc.umn.edu with ESMTP; Mon, 4 Oct 2004 10:33:07 -0500 (CDT) X-Umn-Remote-Mta: [N] abacavir.pharmacy.umn.edu [160.94.172.208] #+HF+LO+TS+AU Message-ID: <41616E1A.2010802{at}pobox.com> Date: Mon, 04 Oct 2004 10:36:58 -0500 From: Eric Bennett User-Agent: Mozilla/5.0 (X11; U; IRIX64 IP30; en-US; rv:1.4.1) Gecko/20040326 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry{at}ccl.net CC: Yong Liang Yang Subject: Re: CCL:Nativeness RMSD References: In-Reply-To: Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=1.0 required=7.5 tests=IMPRONONCABLE_1 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Yong Liang Yang wrote: > Dear Colleagues: > > I would like to calculate the nativeness RMSD of docked > structures from a small molecules database with the native > ligand (reference structure) from crystal structure. In another word, > I want to calculate RMSD of two different structures without translating > or changing the orientation of second structure. > > However, most RMSD algorithms try to translate the orientation of > second structure and minimize the distance. Could someone recommend > some packages or codes which could calculate nativeness RMSD? Many > thanks and appreciate it. (I have posted this topic on Autodock list) There's almost certainly a better way, but you can trick ProFit into doing this: http://acrmwww.biochem.ucl.ac.uk/software/ In ProFit you use the "ZONE" command to specify the range of residues to fit and you can use an "ATOMS" command to narrow the fitting to certain kinds of atoms (CA to fit only alpha carbons for example). You have to fit before you get an RMS. But after you fit, you can change the atoms used to calculate the RMS using the "RATOMS" command and you will get a new RMS calculated *without* translating the atoms. So to trick ProFit you'd have to add a couple dummy atoms with identical coordinates to each structure and do a "superimpose" that has no effect (because the atoms are already in identical positions) using just those atoms. Since ZONE has to be over more than one residue, you'd have to have one of your dummy atoms in a residue numbered differently from the ligand. Then calculate the RMS over all the other atoms using RATOMS; no new superposition will be performed. You might want to give your dummy atoms a unique PDB atom name so you can select just those atoms with the ATOMS command. While this is somewhat clunky, if you are handy with unix shell scripts you can automate this process to add the dummy atoms AND do the actual fitting in ProFit since ProFit is a command line program. You will have to use the -h option for ProFit if your ligand is defined using HETATM records. If you happen to have access to the commercial Maestro interface from Schrodinger, it will also calculate RMS without superposition if you check the "Calculate in place" box. This is much easier than playing games with ProFit but you have to buy the software. -- Eric Bennett, Center for Drug Design, U of Minnesota The fact is, we're in deep trouble in Iraq. - Sen. Hagel, R-Neb We made serious mistakes [in Iraq]. Sen. McCain, R-Ariz This is the incompetence in the administration. - Sen. Lugar, R-Ind