From chemistry-request@server.ccl.net Wed May 12 10:06:44 1999 Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA07557 for ; Wed, 12 May 1999 10:06:44 -0400 Received: from out5.ibm.net (out5.ibm.net [165.87.194.243]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA01118 Wed, 12 May 1999 10:03:31 -0400 (EDT) From: jmmckel@ibm.net Received: from puccini (slip-32-100-232-145.ny.us.ibm.net [32.100.232.145]) by out5.ibm.net (8.8.5/8.6.9) with SMTP id OAA98836 for ; Wed, 12 May 1999 14:03:25 GMT Message-ID: <37394423.1349@ibm.net> Date: Wed, 12 May 1999 10:04:35 +0100 Reply-To: jmmckel@ibm.net X-Mailer: Mozilla 3.04 (WinNT; I) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: Permutation code Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello, I am writing an all-possible-subset PLS code. Can anyone point me to a code, or a reference, for listing all possible unique [(i,j| = |j,i)] permutations of P elements taken K at a time? Thanks! John McKelvey From chemistry-request@server.ccl.net Tue May 11 09:52:29 1999 Received: from chris2.u-strasbg.fr (maerker@chris2.u-strasbg.fr [130.79.34.140]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA16056 for ; Tue, 11 May 1999 09:52:26 -0400 Received: (from maerker@localhost) by chris2.u-strasbg.fr (8.8.8/8.8.8) id PAA01212 for chemistry@ccl.net; Tue, 11 May 1999 15:46:16 +0200 From: Christoph Maerker Message-Id: <199905111346.PAA01212@chris2.u-strasbg.fr> Subject: G98 - shmat failed To: chemistry@ccl.net (ccl) Date: Tue, 11 May 1999 15:46:15 +0200 (MEST) Organization: Laboratoire de Chimie biophysique, Institut Le Bel, Universite Louis Pasteur Postal-Address: 4, rue Blaise Pascal, F- 67000 Strasbourg FRANCE Phone: +33/3-88-41-53-19 Fax: +33/3-88-60-63-83 X-Mailer: ELM [version 2.4ME+ PL37 (25)] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 718 Hi all, I ran into trouble on an Origin 2000 with G98 (and G94). Sumitted batch jobs abort within 2 secs with the following message in the log files: shmat failed.: Not enough space shmdt failed.: Invalid argument The output file stopped right after printing the route section. shmat is called in l402, shmdt in l103. Because the same input ran before properly on the very same machine, I think the problem came with the machine and not from Gaussian. Nevertheless, I would like to resolve the problem. Local people recommended to increase memory settings further; did not work either in my case. Therefore: Is anybody out there who knows a strategy to resolve this kind of error ? Thanks a lot, Christoph From chemistry-request@server.ccl.net Tue May 11 15:56:11 1999 Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA20419 for ; Tue, 11 May 1999 15:56:11 -0400 Received: from bobino.sefmedia.com (www.sefmedia.com [207.164.6.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id PAA25197 Tue, 11 May 1999 15:50:02 -0400 (EDT) Received: from ppp-5800-02a-1253.mtl.total.net (ppp-5800-02a-1253.mtl.total.net [216.210.34.253]) by bobino.sefmedia.com (NTMail 4.20.0009/NT6102.00.d8209609) with ESMTP id nhkbaaaa for ; Tue, 11 May 1999 15:51:07 -0400 Reply-To: From: "Bill Hayden" To: Subject: JCCG Date: Tue, 11 May 1999 15:46:04 -0400 Message-ID: <000d01be9be6$e7a22860$c40101c0@zman> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook 8.5, Build 4.71.2173.0 Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 X-Info: Evaluation version of NTMail at bobino.sefmedia.com Chemical Computing Group Inc. has just released the latest edition of its web site, “The Journal of the Chemical Computing Group -JCCG” (http://www.chemcomp.com). Our new edition contains features on: Overview of Molecular Operating Environment (MOE) Version 1999.05: A review of the latest release of MOE. Numeric solution of the Non-Linear Poisson-Boltzmann Equation: A MOE application appearing in the latest release (1999.05) that solves the non-linear Poisson-Boltzmann equation. The results of computational experiments show the method to be accurate and efficient. Flexible Alignment of Small Molecules: Presentation of a method for flexibly aligning a collection of small molecules. The results of several computational experiments suggest the method's utility for the elucidation of pharmacophores and comparative field analysis. In addition to the above features you will also find the following departments: About CCG: a brief history of Chemical Computing Group; Products: a listing of CCG applications; Support & Training: information on our customer support and training; In the News: CCG press releases; Where We Will Be: Scientific Conferences, meetings and seminars where CCG will be speaking and/or exhibiting; Past JCCG Features: a collection of past JCCG features; Japan: information on our Japanese distribtion. http://www.chemcomp.com info@chemcomp.com Thanks, Bill William A. Hayden Vice President Chemical Computing Group hayden@chemcomp.com http://www.chemcomp.com (514) 393 1055 From chemistry-request@server.ccl.net Wed May 12 01:54:59 1999 Received: from mail.sun.ac.za (mail.sun.ac.za [146.232.128.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id BAA03359 for ; Wed, 12 May 1999 01:54:57 -0400 Received: from land.sun.ac.za ([146.232.216.2]) by mail.sun.ac.za with esmtp (Exim 2.10 #1) id 10hRvj-0001Bx-00; Wed, 12 May 1999 07:51:43 +0200 Received: from SUN_LAND/SpoolDir by land.sun.ac.za (Mercury 1.44); 12 May 99 07:51:23 +0200 Received: from SpoolDir by SUN_LAND (Mercury 1.44); 12 May 99 07:51:19 +0200 Received: from maties.sun.ac.za (146.232.209.1) by land.sun.ac.za (Mercury 1.44) with ESMTP; 12 May 99 07:51:14 +0200 Sender: jan@sun.ac.za Message-ID: <373908F8.317939CE@maties.sun.ac.za> Date: Wed, 12 May 1999 07:52:08 +0300 From: Jan Dillen Reply-To: jlmd@maties.sun.ac.za Organization: University of Stellenbosch X-Mailer: Mozilla 4.07C-SGI [en] (X11; I; IRIX 6.5 IP32) MIME-Version: 1.0 To: Juan Frau Munar CC: CHEMISTRY@ccl.net Subject: Re: CCL:Animations in Power Point References: <3736B0C3.167E@originqf.uib.es> Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Juan Frau Munar wrote: > > Hello everybody > > I would like to have an active molecule in a Power Point´s slide. We > would like to get the molecule rotating 360º during the presentation. > It is something similar to the animations we can see on the web (MDL > format). Any ideas? > Try MSI's WebLab Viewer (http://www.msi.com). Greetings Jan Dillen. From chemistry-request@server.ccl.net Wed May 12 02:50:40 1999 Received: from hermes.bmc.uu.se (hermes.bmc.uu.se [130.238.39.159]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id CAA03768 for ; Wed, 12 May 1999 02:50:38 -0400 Received: from alpha2.bmc.uu.se ([130.238.37.65]) by hermes.bmc.uu.se (post.office MTA v2.0 0813 ID# 0-17733) with SMTP id AAA16072 for ; Wed, 12 May 1999 08:41:44 +0200 Received: from ronja.bmc.uu.se by alpha2.bmc.uu.se; (5.65v3.2/1.1.8.2/30Jan97-1111AM) id AA25410; Wed, 12 May 1999 08:47:26 +0200 Date: Wed, 12 May 1999 08:47:25 +0200 (W. Europe Daylight Time) From: John Marelius To: chemistry@ccl.net Subject: Re: CCL:Free MM Code In-Reply-To: <373837A4.18630F8B@bif1.creighton.edu> Message-Id: X-X-Sender: john@alpha2.bmc.uu.se 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 server.ccl.net id CAA03769 Hi, When it comes to MD simulations of solvated biomolecules I can recommend the new program Q developed by J. Åqvist & co-workers. It is designed for free energy calculations and empirical valence bond simulations in biomolecular systems. It can be used with several different force fields and is relatively easy to use. see http://aqvist.bmc.uu.se John Marelius +-----------------------------------------------------------------+ | John Marelius | | Dept. of Molecular Biology, Uppsala University | | E-mail: John.Marelius@molbio.uu.se | | address: Box 590, S-751 24 Uppsala, Sweden | +-----------------------------------------------------------------+ From chemistry-request@server.ccl.net Wed May 12 15:48:50 1999 Received: from pnl.gov (relay.pnl.gov [130.20.128.34]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA12452 for ; Wed, 12 May 1999 15:48:46 -0400 Received: from lowton.pnl.gov by pnl.gov (PMDF V5.1-12 #28154) with SMTP id <01JB3ZEG19DS91ZWZG@pnl.gov> for chemistry@ccl.net; Wed, 12 May 1999 12:44:50 PDT Received: from lowton.pnl.gov by lowton.pnl.gov (SMI-8.6/SMI-SVR4) id MAA27103; Wed, 12 May 1999 12:37:11 -0700 Date: Wed, 12 May 1999 12:37:11 -0700 (PDT) From: kim Subject: Re: CCL:PM3tm-summary-later comment To: chemistry@ccl.net Cc: rissers-c@battelle.org, paneth@ck-sg.p.lodz.pl Reply-to: kim Message-id: <199905121937.MAA27103@lowton.pnl.gov> MIME-version: 1.0 X-Mailer: dtmail 1.2.0 CDE Version 1.2 SunOS 5.6 sun4u sparc Content-type: TEXT/plain; charset=us-ascii Content-MD5: S1xd2oZIZlcwBAiiJK8Icg== dear piotr, after reading your pm3(tm) commentary, it left me wondering about the pm3(tm) in general. looking further into cro3 problem, and comparing the hyperchem and spartan implementations (using molecules with the same symmetry, geom. optimized) on a pc i had the following results: spartan hyperchem bond lengths: 1.63 1.63 heat of formation -79.14 kcal/mol -185.44 kcal/mol total energy -1132.304 ev -1132.369 ev so while the heats of formation are vastly different, the electronics portions of both programs would seem to yield very similar results. however, it would seem the energetic points of reference for computing the heats of formation for the two programs are very different (anybody have some comment on these discrepancies?) regarding the h-h repulsion, since there aren't hydrogens involved...that shouldn't be the difference. i checked with spartan using the hhon and hhoff keywords, and there was no difference there. the end of your message sounded like pm3(tm) might become a hopeless morass, but now the problem seems rather localized. it would be nice if this discrepancy could be resolved, but, it would require some detailed information from wavefunction. the last time i checked, the publication regarding the details of the pm3(tm) development has not hit print. excerpted: > The difference between implementations in the above-mentioned programs was > pointed out: in Spartan correction for H-H repulsion is added by default in > calculations containing tms. (Unfrotunately I couldn't check if this was my > problem since the keyword turning it off does not work in PC Spartan Pro). > > Finally, thanks to Alan Shusterman, we were able to compare data for CrO3. > C3v geometry gave in all versions of Spartan (unix, mac, pc) heat of > formation of -79.14 kcal/mol while Hyperchem yielded -185.5 kcal/mol > (experimental data: about -52 kcal/mol JPC 1996, 100, 6354) - geometrical > results are the same from both programs. > last note: the author has no connection with either hypercube or wavefunction. ================================================ = = = Kim F. Ferris = = Pacific Northwest National Laboratory = = Environmental and Health Sciences = = P.O. Box 999; Mailstop K2-44 = = Richland, WA 99352 = = = = Voice (509) 375-3754 = = Fax (509) 375-2186 = = = = e-mail: kim@darter.pnl.gov = = kim.ferris@pnl.gov = = = ================================================ From chemistry-request@server.ccl.net Wed May 12 21:02:10 1999 Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id VAA15004 for ; Wed, 12 May 1999 21:02:10 -0400 Received: from hermes.combichem.com (hermes.combichem.com [207.158.48.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id UAA06238 Wed, 12 May 1999 20:58:48 -0400 (EDT) Received: from combichem.com ([10.2.100.8]) by hermes.combichem.com (Post.Office MTA v3.1.2 release (PO205-101c) ID# 0-49457U200L100S0) with ESMTP id AAA80; Wed, 12 May 1999 17:57:04 -0700 Message-ID: <373A2319.E6FAB288@combichem.com> Date: Wed, 12 May 1999 17:55:53 -0700 From: asmellie@combichem.com (Andrew Smellie) X-Mailer: Mozilla 4.5 [en] (WinNT; I) X-Accept-Language: en MIME-Version: 1.0 To: ccl Subject: Predicting feature properties.... Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Does anyone know of computational methods to predict feature properties of small organic fragments. For example, I'd like to be able to predict whether a heteroatom in the context of molecule could act as a donor or acceptor? Another example would be predicting hydrophobic regions or atoms in the molecule. I'd be happy to summarize all replies. Thanks, Andrew -- Dr. Andrew Smellie, CombiChem Inc. 1804 Embarcadero Road, Palo Alto, CA 94303 Phone: (650)-842-0560 FAX: (650-842-0575 email: asmellie@combichem.com