From chemistry-request@server.ccl.net Mon Mar 31 20:27:59 2003 Received: from red.CACheSoftware.com ([12.17.172.66]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h311RxC32758; Mon, 31 Mar 2003 20:27:59 -0500 Received: from dgallagher.cachesoftware.com ([192.168.110.100]) by red.CACheSoftware.com (8.11.6/8.9.3/3) with ESMTP id h311SKK27527; Mon, 31 Mar 2003 17:28:20 -0800 Message-Id: <5.2.0.9.0.20030331171912.027b4ce0@mail.cachesoftware.com> X-Sender: daveg@mail.cachesoftware.com (Unverified) X-Mailer: QUALCOMM Windows Eudora Version 5.2.0.9 Date: Mon, 31 Mar 2003 17:27:22 -0800 To: chemistry@ccl.net From: David Gallagher Subject: SEMINAR: Active-Site Identification, Ligand Design & QSAR, - New SW Tools for Windows Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====================_19679900==.ALT" --=====================_19679900==.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed SEMINAR: Active-Site Identification, Ligand Design and QSAR - New SW Tools for Windows Wednesday April 16th, 2003, 1:30-3:00 pm at Wyndham Garden Hotel, 19333 North Creek Parkway, Bothell, WA A presentation and demonstration of the latest Windows-based tools for analyzing proteins, locating active sites and designing ligands will be offered, including examples of homology modeling, rational drug design, pharmocaphore modeling, 3D sequence alignment and superposition, and novel quantum methods for calculating electronic properties of whole proteins. Quantitative Structure-activity Relationships (QSAR) and fast screening methods for predicting properties such as pKa, water solubility, HIA, Rule-of-5, carcinogenicity, antibacterial activity, etc. will also be reviewed. Sponsored by the CAChe Group, Fujitsu Contact Sarah Achin for Free registration at (503)746-3615 or by email sachin@cachesoftware.com --=====================_19679900==.ALT Content-Type: text/html; charset="us-ascii"

SEMINAR:

Active-Site Identification, Ligand Design
and QSAR - New SW Tools for Windows

Wednesday April 16th, 2003, 1:30-3:00 pm
at Wyndham Garden Hotel,
19333 North Creek Parkway, Bothell, WA

A presentation and demonstration of the latest Windows-based tools for analyzing proteins, locating active sites and designing ligands will be offered, including examples of homology modeling, rational drug design, pharmocaphore modeling, 3D sequence alignment and superposition, and novel quantum methods for calculating electronic properties of whole proteins. Quantitative Structure-activity Relationships (QSAR) and fast screening methods for predicting properties such as pKa, water solubility, HIA, Rule-of-5, carcinogenicity, antibacterial activity, etc. will also be reviewed.

Sponsored by the CAChe Group, Fujitsu
Contact Sarah Achin for Free registration at (503)746-3615
or by email sachin@cachesoftware.com

--=====================_19679900==.ALT-- From chemistry-request@server.ccl.net Tue Apr 1 08:00:14 2003 Received: from web21102.mail.yahoo.com ([216.136.227.104]) by server.ccl.net (8.11.6/8.11.0) with SMTP id h31D0DC27282 for ; Tue, 1 Apr 2003 08:00:13 -0500 Message-ID: <20030401130013.34554.qmail@web21102.mail.yahoo.com> Received: from [193.205.213.88] by web21102.mail.yahoo.com via HTTP; Tue, 01 Apr 2003 15:00:13 CEST Date: Tue, 1 Apr 2003 15:00:13 +0200 (CEST) From: =?iso-8859-1?q?Michele=20Lunelli?= Subject: HindRot and degrees of freedom To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear CCLers, After a frequency calculation in G98W, i tried to identify the internal rotation modes with the option freq=hindrot, but the program stops with the message "Problem with the number of degrees of freedom". I tried different calculation: freq=(analytic,hindrot) freq=(numeric,hindrot) and freq=(readFC,hindrot) with the same result. The last part of the output file is as follow: Full mass-weighted force constant matrix: Low frequencies --- -6.0075 -3.1832 -0.0183 -0.0070 0.0035 2.0224 Low frequencies --- 23.7749 39.3650 49.3116 Hindered Internal Rotation Analysis Internal coordinate list checked Check for planar centers 2 1 3 10 359.995 3 2 4 6 359.999 6 3 7 8 359.999 8 6 9 27 359.999 9 1 8 25 360.000 10 2 11 21 360.000 11 10 12 13 359.974 13 11 14 16 359.994 16 13 17 18 359.998 18 16 19 21 359.957 21 10 18 22 360.000 23 24 25 29 360.000 25 9 23 26 360.000 27 8 28 29 360.000 29 23 27 30 360.000 Check reduced barrier height. Cut-off : V/RT = 33.7559 Bond 2 - 10 frozen. Estimated reduced barrier height : V/RT = 34.0576 For a periodicity of : 2 Check for ring deformation Number of internal rotation degrees of freedom = 8 NNew= 83 NTest= 8 NB= 26 IFrz= 0 IBar= 1 ICyc= 0 Problem with the number of degrees of freedom Error termination via Lnk1e in C:\Programmi\G98W\l716.exe. Job cpu time: 0 days 15 hours 14 minutes 4.0 seconds. File lengths (MBytes): RWF= 521 Int= 0 D2E= 0 Chk= 8 Scr= 1 Do you have any suggestion to overcome this problem? Best Regards, Michele Lunelli ______________________________________________________________________ Yahoo! Cellulari: loghi, suonerie, picture message per il tuo telefonino http://it.yahoo.com/mail_it/foot/?http://it.mobile.yahoo.com/index2002.html From chemistry-request@server.ccl.net Tue Apr 1 09:24:09 2003 Received: from ultra3000.if.sc.usp.br ([143.107.228.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h31EO8C30035 for ; Tue, 1 Apr 2003 09:24:08 -0500 Received: from joselap (zappa.if.sc.usp.br [143.107.228.35]) by ultra3000.if.sc.usp.br (8.11.6/8.11.0) with ESMTP id h31ELoE06231; Tue, 1 Apr 2003 11:21:50 -0300 Message-ID: <002a01c2f85a$6e0a7780$0201a8c0@joselap> From: "JOSE" To: "Ian Hovell" , References: <216FE3CA3D4DD611AE2600105AD16BDFD56AED@correio.cetem.gov.br> Subject: Re: CCL:Problems with convergence Date: Tue, 1 Apr 2003 11:24:39 -0300 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1106 X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 Hi Ian, as long as I know, you should have less variables in your z-matrix (only most important geometric parameters) and optimize the structure before SCF calculation. regards, Jose --- Original Message ----- From: "Ian Hovell" To: Sent: Monday, March 31, 2003 4:48 PM Subject: CCL:Problems with convergence > Dear CCLers, > I am having problems with the convergence of the molecule below. I have > tried, without sucess, all of the options found in the reference manual for > SCF calculations. I feel I must be doing something wrong. Any help would be > extremely welcome since I'm rapidly losing my hair over this problem. > > TIA > Ian > P.S. Will summarise answers if there is interest. > > > %mem=6MW > %nproc=1 > %chk=solutes.chk > # opt rhf/3-21g* scrf=(scipcm,dielectric=35.6) geom=connectivity > > Solvated Solutes : quinolinol > > 0 1 > C > C 1 B1 > C 2 B2 1 A1 > C 3 B3 2 A2 1 > D1 > C 4 B4 3 A3 2 > D2 > N 5 B5 4 A4 3 > D3 > C 6 B6 5 A5 4 > D4 > C 7 B7 6 A6 5 > D5 > C 8 B8 7 A7 6 > D6 > C 5 B9 4 A8 3 > D7 > O 8 B10 7 A9 6 > D8 > H 3 B11 2 A10 1 > D9 > H 4 B12 3 A11 2 > D10 > H 1 B13 2 A12 3 > D11 > H 2 B14 1 A13 10 > D12 > H 7 B15 6 A14 5 > D13 > H 9 B16 8 A15 7 > D14 > H 11 B17 8 A16 7 > D15 > > B1 1.356319 > B2 1.417031 > B3 1.355411 > B4 1.413911 > B5 1.360091 > B6 1.297613 > B7 1.412651 > B8 1.355149 > B9 1.404556 > B10 1.373424 > B11 1.071439 > B12 1.070129 > B13 1.072393 > B14 1.071859 > B15 1.073740 > B16 1.070263 > B17 0.964342 > A1 120.664144 > A2 120.217668 > A3 120.288571 > A4 119.422755 > A5 119.925604 > A6 122.763646 > A7 118.806597 > A8 119.630176 > A9 121.864491 > A10 119.329860 > A11 122.198637 > A12 120.846283 > A13 120.120605 > A14 117.591735 > A15 119.665739 > A16 113.351613 > D1 -0.003573 > D2 0.005337 > D3 179.993576 > D4 -179.986182 > D5 0.002305 > D6 -0.011149 > D7 -0.000978 > D8 179.992503 > D9 179.996463 > D10 -179.998392 > D11 -179.998655 > D12 179.995120 > D13 -179.994506 > D14 -179.996324 > D15 -0.165861 > > 1 2 2.0 10 1.5 14 1.0 > 2 3 1.5 15 1.0 > 3 4 2.0 12 1.0 > 4 5 1.5 13 1.0 > 5 6 1.5 10 1.5 > 6 7 2.0 > 7 8 1.5 16 1.0 > 8 9 2.0 11 1.0 > 9 10 1.5 17 1.0 > 10 > 11 18 1.0 > 12 > 13 > 14 > 15 > 16 > 17 > 18 > > Ian Hovell - Ph.D. > NUCLEO DE MODELAGEM MOLECULAR-NMM > Centro de Tecnologia Mineral - CETEM > Ministerio da Ciência e da Tecnologia- MCT > Avenida Ipê, No 900 - Cidade Universitaria > Ilha do Fundão Rio de Janeiro RJ Brasil > CEP 21941-590 > tel 00 55 (xx) 3865 - 7216 > Fax 00 55 (xx) 22602837 ou 2290-4286 > e-mail hovell@cetem.gov.br > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > From chemistry-request@server.ccl.net Tue Apr 1 06:01:20 2003 Received: from brown.csi.cam.ac.uk ([131.111.8.14]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h31B1JC24057 for ; Tue, 1 Apr 2003 06:01:20 -0500 Received: from prayer by brown.csi.cam.ac.uk with local (Exim 4.12) id 190JVz-0005SZ-00 for chemistry@ccl.net; Tue, 01 Apr 2003 12:01:15 +0100 From: "Dr P. Murray-Rust" To: chemistry@ccl.net Subject: Re: CCL:(chemical) markup languages for writing scientific documents Date: 01 Apr 2003 12:01:15 +0100 X-Mailer: Prayer v1.0.6 X-Originating-IP: [131.111.121.103] Mime-Version: 1.0 Content-Type: text/plain; format=flowed; charset=ISO-8859-1 Message-Id: On Mar 31 2003, Marc Baaden wrote: > > Dear colleagues, > > jkl@ccl.net said: > >> On more directly Web related matters, two sessions at the ACS had > >> relevance, one on XML in Chemistry, and another on "The Scientific > >> Article in the digital World". > > > .. not immediately directly related, but still of relevance (I hope): > > what > kind of authoring environment would be best adapted to the task of > writing scientific papers, reports, abstracts etc. ? > > I have recently been playing around with docbook and refdb (both come in > SGML and XML flavours), and was amazed how far one could get with those > already. > > Especially for *computational* chemistry, docbook has all the nice tags > for inclusion of code, screenshots, etc. XML can revolutionise any scientific domain as it encourages interoperability through consistency of syntax and sharable ontologies. This is already happening in biosciences and we believe that it can do the same for comp chem. At the ACS meeting Henry Rzepa and I and presented our extensions to CML (Chemical Markup Language) which may answer some of these questions. We are close to a distribution kit for which the current position is: - CML has been widely tested and implemented for managing molecules and their properties, both experimental and computed. Many of the OpenSource toolkits (e.g. OpenBabel, JChemPaint, Jmol, CDK, JOElib, bkchem, etc. ) support both input and output of CML. [We would be happy to hear from authors of such systems and advise them on implementing CML]. There is an open CMLDOM in JUMBO4. CML2 (CML is schema form) is available and a publication has been accepted for J. Chem. Inf. Comp. Sci. - CML interoperates with most major XML languages, especially DocBook, XHTML, SVG (for graphics) and MathML for parsable maths. We have proof of concept for compound documents such as theses, journal articles and compound data cards. - CML has been extended to reactions (CMLReact) and we are currently working with the EBI (Eur. Bioinf. Inst.) on enzyme-based reactions. - CML can manage spectral data (CMLSpect) including annotation of peaks and peak groups - CML has been extended to computational chemistry (CMLComp) to provide an infrastructure for the computational process. This includes job control and input, program output, XMLisation of manuals (so far MOPAC and GULP) and creation of ontologies (dictionaries) - generally one per program. We would be happy to hear from early adopters and program authors who wish to explore XML for comp chem. We are also developing Java, C and F77 libraries for XMLising program output. CML home page is http://www.xml-cml.org and software/specifications will be distributed from http://cml.sourceforge.net. Peter Murray-Rust From chemistry-request@server.ccl.net Tue Apr 1 05:30:45 2003 Received: from mail.alquds.edu ([62.90.24.150]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h31AUTC23283 for ; Tue, 1 Apr 2003 05:30:30 -0500 Received: from mail.alquds.edu (localhost [127.0.0.1]) by mail.alquds.edu (8.11.6+Sun/8.11.6) with ESMTP id h31AVjv08090 for ; Tue, 1 Apr 2003 12:32:03 +0200 (IST) From: "Omar Deeb/science college" To: chemistry@ccl.net Subject: computational chemistry unit Date: Tue, 1 Apr 2003 12:31:45 +0200 Message-Id: <20030401102422.M91095@mail.alquds.edu> X-Mailer: Open WebMail 1.90 20030304 X-OriginatingIP: 62.90.24.137 (f2538) MIME-Version: 1.0 Content-Type: text/plain; charset=windows-1256 X-MailScanner: Found to be clean X-MailScanner-Information: Please contact the ISP for more information Dear ccl users, We are trying to construct a computational chemistry unit in the dept. of chemistry and chemical technology at Alquds university. We are lookibg for any suggestions how to build this unit. If any one has an experience in this field, we will be more pleased to take these suggestions into considerations. Thanks a lot Dr. Omar Deeb Alquds University Jerusalem e-mail : omardeeb@science.alquds.edu From chemistry-request@server.ccl.net Tue Apr 1 10:44:47 2003 Received: from ChE.UDel.Edu ([128.175.117.64]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h31FilC32497 for ; Tue, 1 Apr 2003 10:44:47 -0500 Received: from chem.udel.edu (struppi.che.udel.edu [128.175.117.107]) by ChE.UDel.Edu (8.9.3p2/8.9.3) with ESMTP id KAA13238 for ; Tue, 1 Apr 2003 10:44:47 -0500 (EST) Message-ID: <3E89B442.1010409@chem.udel.edu> Date: Tue, 01 Apr 2003 10:46:10 -0500 From: Stephen Garrison User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.0; en-US; rv:0.9.4) Gecko/20011019 Netscape6/6.2 X-Accept-Language: en-us MIME-Version: 1.0 To: chemistry@ccl.net Subject: Linux Settings for G98 performance Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit I am not sure if anyone on this list will have any recommendations, but I have not heard anything from the LUG so far. So, I figured it was worth a shot. I am trying to eek out as much performance as I can from machines in a cluster for which I am responsible and wondering if anyone here has some recomendations on the Linux file system and swap parameters. Each machine is a Dual AMD MP1800 with 1.5GB of memory. There is a maximum of 2 jobs running on each machine and many of the jobs that we run can use 400MB+ of memory and write 15GB of scratch files to disk. When two heavy jobs (CCSD(T) with large memory (but combined less than 1.5GB) and disk usage) are running on the same machine, performance is severely degraded. The load on the machines appears to spike when the jobs are writing scratch files to the disk. I have seen values for the parameters to tune bdflush, buffermem, and kswapd, but generally only for use with Oracle. I was wondering if anyone here had done some tuning of these parameters and/or had any recommendations given our situation and setup. I realize that the best thing will be to try out various values and get real world numbers, but I am looking for some direction or indication of what I might look at first and parameter values likely to improve performance. Thanks for any help you can provide. From chemistry-request@server.ccl.net Tue Apr 1 11:15:43 2003 Received: from sandmail01.sd.accelrys.com ([209.120.169.30]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h31GFgC00780 for ; Tue, 1 Apr 2003 11:15:42 -0500 To: CHEMISTRY@ccl.net Cc: "Elizabeth Crookenden" Subject: Accelrys Customer training for June MIME-Version: 1.0 X-Mailer: Lotus Notes Release 6.0.1 February 07, 2003 Reply-To: "Elizabeth Crookenden" Message-ID: From: "Jeff Nauss" Date: Tue, 1 Apr 2003 08:15:40 -0800 X-MIMETrack: Serialize by Router on sandmail01/Server/Accelrys(Release 5.0.9 |November 16, 2001) at 04/01/2003 08:15:42 AM, Serialize complete at 04/01/2003 08:15:42 AM Content-Type: text/plain; charset="US-ASCII" Accelrys Inc. are holding the following training workshops at locations in the US and Europe during June 2003. These events are designed to help you get more value from your Accelrys software, helping you to better accomplish your research goals. Costs are $600 per day for commercial, $450 per day for government and $330 per day for academic. Cheminformatics: Accord Developer Studio 2nd-3rd June 2003, San Diego, CA DS Accord Chemistry Cartridge 4th June 2003, San Diego, CA Accord Grid Control 5th June 2003, San Diego, CA Accord CombiChem Add-on 6th June 2003, San Diego, CA For course details and registration see: http://www.accelrys.com/training/cheminf/schedule.html Macromolecular Modeling: Introduction to Life Science Modeling with InsightII 10th-11th June 2003, San Diego, CA Homology Base Protein Design 12th-13th June 2003, San Diego, CA CHARMm 16th-17th June 2003, San Diego, CA Structure Based Drug Design with InsightII 18th-19th June 2003, San Diego, CA For course details and registration see: http://www.accelrys.com/training/macro/schedule.html Material Science: Introduction to Materials Studio 12th June 2003, Cambridge UK Workshop on Structure Solution from Powder Diffraction Data 13th June 2003, Cambridge UK Introduction to Polymer Modeling using Materials Studio 16th-17th June 2003, Cambridge UK Introduction to Quantum Mechanics Modeling using Materials Studio 18th-19th June 2003, Cambridge UK For course details and registration see: http://www.accelrys.com/training/matsci/schedule.html Rational Drug Design: DS MedChem Explorer 23rd June 2003, San Diego, CA Introduction to Cerius2 for Life Sciences 24th-25th June 2003, San Diego, CA Small Molecule and Drug Design with Cerius2 26th-27th June 2003, San Diego, CA For course details and registration see: http://www.accelrys.com/training/rdd/schedule.html Elizabeth Crookenden Training Co-ordinator Accelrys Ltd 334 Cambridge Science Park Cambridge CB4 0WN UK Telephone number: +44 (0) 1223 228691 Fax number: +44 (0) 1223 228501 Web: http://www.accelrys.com -- Jeffrey L. Nauss, Ph.D. Manager, Discovery Studio Training Accelrys Inc. 9685 Scranton Road San Diego, CA 92121-3752 Phone: 858-799-5555 Fax: 858-799-5100 E-mail: jnauss@accelrys.com http://www.accelrys.com/training