From chemistry-request@www.ccl.net Tue Apr 13 00:02:55 1999 Received: from gateway.bioreason.com (bioreason.trail.com [209.194.109.237]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id AAA20194 Tue, 13 Apr 1999 00:02:52 -0400 (EDT) Received: from bioreason.com (bioreason8 [192.168.1.8]) by gateway.bioreason.com (8.9.3/8.9.3) with ESMTP id WAA03785 for ; Mon, 12 Apr 1999 22:01:41 -0600 Sender: dalke@bioreason.com Message-ID: <3712C189.17D32229@bioreason.com> Date: Mon, 12 Apr 1999 21:01:13 -0700 From: Andrew Dalke Organization: Bioreason, Inc. X-Mailer: Mozilla 4.05 [en] (X11; U; IRIX 6.2 IP22) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: maximum common substructure Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello, I am looking for unix software for finding the maximum common substructure (MCS) of a set of molecules; represented as a graph with typed nodes and edges. My searches so far have come up with: TOPSOM -- TOPological SIMilarity http://baker.mcs.kent.edu/paper/ECCC5.html ToSiM -- Topological Similarities of Molecules. http://echm10.tuwien.ac.at/inst/vk/ (MS Windows?) but I have no other information about ther usefulness of those programs. The examples I've seen, like TOPSOM, convert the problem into a maximum clique detection program. However, they only find the MCS of two molecules and we would like the MCS of a set of molecules. The obvious extension is to compose the compatibility graph (using the TOPSOM nomenclature) with each new molecule's relational line graph, but I worry that the full compatibility graph becomes exponentially large with the number of molecules. Does anyone have advice along these lines? I will summarize the responses, Andrew Dalke dalke@bioreason.com From chemistry-request@www.ccl.net Tue Apr 13 02:02:07 1999 Received: from hermes.fju.edu.tw (hermes.ch.fju.edu.tw [140.136.196.150]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id CAA20558 Tue, 13 Apr 1999 02:01:27 -0400 (EDT) Received: by hermes.fju.edu.tw (AIX 3.2/UCB 5.64/4.03) id AA14317; Tue, 13 Apr 1999 13:42:42 +0800 Date: Tue, 13 Apr 1999 13:42:42 +0800 From: shin@hermes.fju.edu.tw (Shin-Inn Chen) Message-Id: <9904130542.AA14317@hermes.fju.edu.tw> To: chemistry@www.ccl.net Subject: G9x question dear netters: i wonder that is it possible to print out the kinetic energy, attraction to the nuclei, coulomb and exchange interaction of orbitals after SCF calculations. any information will be appreciated. e-mail: shin@hermes.fju.edu.tw shin 1999/4/13 From chemistry-request@www.ccl.net Mon Apr 12 09:08:32 1999 Received: from mail05.rapidsite.net (mail05.rapidsite.net [207.158.192.42]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id JAA10434 Mon, 12 Apr 1999 09:08:31 -0400 (EDT) Received: from www.auditec-newtest.com (209.130.11.42) by mail05.rapidsite.net (RS ver 1.0.2) with SMTP id 9083 for ; Mon, 12 Apr 1999 09:08:17 -0400 (EDT) Received: by localhost with Microsoft MAPI; Mon, 12 Apr 1999 15:10:49 +0200 Message-ID: <01BE84F6.A5C1B7F0.emailcom@auditec-newtest.com> From: Christophe de FILIPPO Reply-To: "emailcom@auditec-newtest.com" To: "'CHEMISTRY@www.ccl.net'" Subject: DISPONIBILITE DE VOS SERVICES APPLICATIFS ET INTERNET Date: Mon, 12 Apr 1999 12:22:37 +0200 Organization: AUDITEC S.A. X-Mailer: Messagerie Internet de Microsoft/MAPI - 8.0.0.4211 MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit X-Loop-Detect: 1 Destinataire : CHEMISTRY@www.ccl.net Les services Web, tendent a prendre une importance capitale dans les relations client fournisseur (Internet), et les relations inter et intra entreprise (Intranet/Extranet). Malheureusement, les services Web dependent d'elements " fragiles " (serveur web, proxy, routeur, etc...) ! Vous devez donc vous poser ces questions : * Combien de clients, collegues ou partenaires ne peuvent se connecter a notre site Web suite a ces indisponibilites ? * Quelle est l'image de marque refletee par notre entreprise si nos services Internet fonctionnent mal ou sont inaccessibles ? * Et si vous faites ou prevoyez de faire du commerce electronique : Quelles sont les pertes de chiffre d'affaire engendrees par les indisponibilites de nos services Internet ? 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From chemistry-request@www.ccl.net Mon Apr 12 15:26:54 1999 Received: from chm-pluto.ulaval.ca (chm-pluto.ulaval.ca [132.203.2.10]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id PAA13497 Mon, 12 Apr 1999 15:26:54 -0400 (EDT) Received: from OXYGENE (unverified [132.203.70.8]) by serveur_chimie.chm.ulaval.ca (EMWAC SMTPRS 0.83) with SMTP id ; Mon, 12 Apr 1999 15:26:46 -0400 Date: Mon, 12 Apr 1999 15:26:46 -0400 Message-Id: <3.0.16.19990412152646.3adf3c3e@serveur_chimie.chm.ulaval.ca> X-Sender: mroberge@serveur_chimie.chm.ulaval.ca X-Mailer: Windows Eudora Pro Version 3.0 (16) To: chemistry@www.ccl.net From: Mathieu Roberge Subject: Biosym Command Language (for macros in InsightII) Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by www.ccl.net id PAA13498 Hi there ! I am looking for documentation about the BCL (Biosym Command Language) used in InsightII for the programming of macros. The manual from MSI do contain something, but the ones I got are quite old (v4.0.0.). I'm interested in anything that might be of use (command list, examples, etc.). Mathieu Roberge ------------------------------------------------------- Dept. Chimie, Université Laval 2450 Place Prével, #2 Cite universitaire, Ste-Foy Ste-Foy, Québec Quebec, Canada, G1K 7P4 G1V 2X3 (418) 656-2131 poste 4210 (418) 650-7199 ------------------------------------------------------- Mathieu.Roberge@chm.ulaval.ca From chemistry-request@www.ccl.net Mon Apr 12 16:42:35 1999 Received: from unomail.unomaha.edu (unomail.unomaha.edu [137.48.1.6]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id QAA18236 Mon, 12 Apr 1999 16:42:35 -0400 (EDT) From: Douglas_Stack/CAS/UNO/UNEBR@unomail.unomaha.edu Received: by unomail.unomaha.edu(Lotus SMTP MTA v4.6.3 (733.2 10-16-1998)) id 86256751.0071A04A ; Mon, 12 Apr 1999 15:41:06 -0500 X-Lotus-FromDomain: UNIVERSITY OF NEBRASKA To: Bill Glauser cc: chemistry@www.ccl.net Message-ID: <86256751.00719D57.00@unomail.unomaha.edu> Date: Mon, 12 Apr 1999 15:40:55 -0500 Subject: Re: CCL:G:Jaguar Mime-Version: 1.0 Content-type: text/plain; charset=us-ascii Content-Disposition: inline The orginal post refered to G92. Does Jaguar's speed advantage hold in comparasion to G94 and the newly releasesd G98? How does Q-Chem compare to either programs. It would be nice to see a review of the lastest release of all three programs for large systems on a similar platform. Douglas E. Stack Assistant Professor Department of Chemistry University of Nebraska at Omaha Omaha, NE 68182-0109 (402) 554-3647 (402) 544-3647 (fax) Douglas_Stack@unomaha.edu From chemistry-request@www.ccl.net Mon Apr 12 18:34:48 1999 Received: from mx.seanet.com (dns2.seanet.com [199.181.164.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id SAA18829 Mon, 12 Apr 1999 18:34:47 -0400 (EDT) Received: from littlegeek ([150.215.141.175]) by mx.seanet.com (8.9.3/Seanet-8.7.3) with SMTP id PAA21031 for ; Mon, 12 Apr 1999 15:34:42 -0700 (PDT) Message-ID: <001401be8535$55df96f0$af8dd796@wrq.com> From: "Mark Thompson" To: References: <199904121626.MAA11998@www.ccl.net> Subject: Re: CCL:G:Jaguar Date: Mon, 12 Apr 1999 15:39:21 -0700 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Geez, could we please avoid marketing messages and infomercials to this forum? ----- Original Message ----- From: Bill Glauser To: Sent: Monday, April 12, 1999 9:26 AM Subject: CCL:G:Jaguar > Dear Gavin, ...marketing content deleted for sanity.... From chemistry-request@www.ccl.net Mon Apr 12 19:31:08 1999 Received: from smurf.chem.usu.edu (smurf.chem.usu.edu [129.123.3.85]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id TAA19307 Mon, 12 Apr 1999 19:31:07 -0400 (EDT) Received: from localhost (pczyryca@localhost) by smurf.chem.usu.edu (950413.SGI.8.6.12/950213.SGI.AUTOCF) via ESMTP id QAA10458; Mon, 12 Apr 1999 16:33:45 -0700 Date: Mon, 12 Apr 1999 16:33:45 -0700 From: "Przemyslaw G. Czyryca" To: chemistry@infomeister.usc.eduB cc: chemistry@www.ccl.net Subject: Re: CCL:summary: Computational Chemistry vs Theoretical In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII > A good test of "computation" vs "theory" is to imagine what would > happen if we suddenly had INFINITELY fast and powerful computers (the > starting point of a discussion in Physics Today some time back). If > we had INFINITELY fast and powerful computers that were extremely easy > to use, computational chemistry would quickly disappear. I disagree. This example is founded on a statement that we have a complete, reliable theory of electronic structure and that there are also reliable, universal algorithms of, say, optimization or TS search. This is not the case. We are not only limited with lack of CPU power, but the existing theories are good only within their particular areas of applicability. Thus the role of a computational chemist is not only choosing a good compromise between time and accuracy. Moreover, with INFINITE memory and CPU power we are able to have (i believe) a system with INFINITE artifical intelligence! Such a system would also create unemployment for theoretical chemists :-) Regards, P.C. From chemistry-request@www.ccl.net Tue Apr 13 10:20:25 1999 Received: from ChE.UDel.Edu (che.udel.edu [128.175.117.64]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA23754 Tue, 13 Apr 1999 10:20:22 -0400 (EDT) Received: from localhost (hloucha@localhost) by ChE.UDel.Edu (8.8.8/8.8.8) with SMTP id KAA05028; Tue, 13 Apr 1999 10:20:25 -0400 (EDT) Date: Tue, 13 Apr 1999 10:20:25 -0400 (EDT) From: Matthias Hloucha To: chemistry@www.ccl.net cc: hloucha@ChE.UDel.Edu Subject: Proteins, Electrostatics Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Colleagues, it be would be very helpful for me, if you could give me an advice where to find a code to calculate the electrostatic part of the interaction between two proteins in electrolyte solution. Keywords: PDB structure, Henderson Hasselbalch equation -> charges linarized Poisson Boltzmann equation, sphere approximation -> U Thanking you very much for your kind consideration, Yours Matthias From chemistry-request@www.ccl.net Tue Apr 13 13:08:40 1999 Received: from voicenet.com (mail12.voicenet.com [207.103.0.6]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id NAA25650 Tue, 13 Apr 1999 13:08:39 -0400 (EDT) Date: Tue, 13 Apr 1999 13:08:39 -0400 (EDT) Message-Id: <199904131708.NAA25650@www.ccl.net> Received: (qmail 4683 invoked from network); 13 Apr 1999 17:08:38 -0000 Received: from dialup502-pri.voicenet.com (HELO billag.voicenet.com) (207.103.81.130) by mail12.voicenet.com with SMTP; 13 Apr 1999 17:08:38 -0000 X-Sender: billag@popmail.voicenet.com X-Mailer: Windows Eudora Light Version 1.5.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: Douglas_Stack/CAS/UNO/UNEBR@unomail.unomaha.edu From: Bill Glauser Subject: CCL:G:Jaguar Cc: chemistry@www.ccl.net Dear Douglas, Schrodinger, Inc. doesn't have access to G94 or G98 - that's why the comparison was run versus G92. I have not heard anything about Q-Chem one way or the other. But from anecdotal reports, we hear that Jaguar's speed advantages do hold in comparison with G94 and G98. Certainly there will be some changes, but the qualitative speedups are expected to remain more or less the same. Schrodinger, Inc. would very much like to see a comparison among the latest versions of the leading ab initio programs for treating large systems (run on the same platform). And we have always made Jaguar available (upon request) for a trial period for anyone wanting to perform benchmarking or any other form of testing. Best regards, Bill ---- At 03:40 PM 4/12/99 -0500, you wrote: >The orginal post refered to G92. Does Jaguar's speed advantage hold in >comparasion to G94 and the newly releasesd G98? >How does Q-Chem compare to either programs. It would be nice to see a review of >the lastest release of all three programs for large systems on a similar >platform. > > >Douglas E. Stack >Assistant Professor >Department of Chemistry >University of Nebraska at Omaha >Omaha, NE 68182-0109 >(402) 554-3647 >(402) 544-3647 (fax) >Douglas_Stack@unomaha.edu ---- William A. Glauser / Schrodinger, Inc. / 800-207-7482 / 610-869-0578 610-869-0577 (fax) / billg@schrodinger.com / http://www.schrodinger.com From chemistry-request@www.ccl.net Tue Apr 13 14:40:30 1999 Received: from ex1.ncsa.uiuc.edu (ex1.ncsa.uiuc.edu [141.142.3.16]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id OAA26281 Tue, 13 Apr 1999 14:40:29 -0400 (EDT) Received: from mx1.ncsa.uiuc.edu (mx1.ncsa.uiuc.edu [141.142.3.15]) by ex1.ncsa.uiuc.edu (8.9.3/8.9.3) with ESMTP id NAA17791 for ; Tue, 13 Apr 1999 13:40:30 -0500 (CDT) Received: from mckelvey (mckelvey.ncsa.uiuc.edu [141.142.41.30]) by mx1.ncsa.uiuc.edu (8.9.2/8.9.2) with SMTP id NAA20792 for ; Tue, 13 Apr 1999 13:40:30 -0500 (CDT) Message-Id: <3.0.5.32.19990413134027.009957f0@pop.ncsa.uiuc.edu> X-Sender: mckelvey@pop.ncsa.uiuc.edu X-Mailer: QUALCOMM Windows Eudora Pro Version 3.0.5 (32) Date: Tue, 13 Apr 1999 13:40:27 -0500 To: chemistry@www.ccl.net From: John McKelvey Subject: Linux and ATA/UDMA Disks Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" X-md5sum: 0d4ec840c1db49efd9ea0f2dd0a7c66e X-md5sum-Origin: mx1.ncsa.uiuc.edu Greetings! Someone just cautioned me about using Ultra DMA ATA drives with Linux. Comments on this are most welcome! I'd hate to build a ayatem I could not use! I wish to use ATA-4 drives (ATA-66's) with an INTEL 450MHZ system. Tnanks! John McKelvey NCSA From chemistry-request@www.ccl.net Tue Apr 13 16:44:45 1999 Received: from giasbma.vsnl.net.in (giasbma.vsnl.net.in [202.54.4.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id QAA27186 Tue, 13 Apr 1999 16:44:42 -0400 (EDT) Received: from giasbmc.vsnl.net.in (giasbmc [202.54.4.6]) by giasbma.vsnl.net.in (8.8.8/8.8.8) with SMTP id CAA23488 for ; Wed, 14 Apr 1999 02:23:37 +0500 (IST) Date: Wed, 14 Apr 1999 01:55:32 -0500 (GMT) From: Amit Galande To: chemistry@www.ccl.net Subject: random vs rational screening Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hallo! Can anybody tell me that if suppose 10000 molecules are there in my diversity,all can not be screened so when deciding number molecules those are to be chosen from 10000 , how many are selected 1) When rational approach is used 2)When random approaches are used (irrespetive of which molecules are to be chosen) Can you please suggest me any references regarding this Thanking you in ANTICIPATION From chemistry-request@www.ccl.net Tue Apr 13 22:18:58 1999 Received: from mail-01.telis.org (mail-01.telis.org [204.71.76.230]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id WAA28306 Tue, 13 Apr 1999 22:18:57 -0400 (EDT) Received: from [208.140.81.69] (s02-pm19.snaustel.campuscwix.net [208.140.81.69]) by mail-01.telis.org (8.9.0/8.8.8) with ESMTP id TAA04847 for ; Tue, 13 Apr 1999 19:19:29 -0700 (PDT) X-Sender: gammadas@mail.telis.org Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 13 Apr 1999 21:20:57 -0500 To: chemistry@www.ccl.net From: Goutam Das Subject: curve fitting program Dear CCLer's Do anyone of you have suggestions regarding a good curve fitting program(Windows/Mac). I have used Origin and think it is quite powerful, but I would like to know what else is available. Any pointer to software reviews (preferably web accessible) would be very valuable. Thanx in advance. Goutam Das GOUTAM DAS Research Scientist BETZDEARBORN (A division of Hercules) PO BOX 4300, 9669 GROGANS MILL ROAD THE WOODLANDS, TX 77387-4300, USA # 281.367.6201 xt 425///email:gammadas@telis.org