From chemistry-request@server.ccl.net Fri Jan 25 03:47:14 2002 Received: from gw1-mail.cict.fr (IDENT:root@[195.220.59.20]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0P8lEc01521 for ; Fri, 25 Jan 2002 03:47:14 -0500 Received: from gw1-mail.cict.fr (IDENT:root@localhost.cict.fr [127.0.0.1]) by gw1-mail.cict.fr (8.11.6/8.11.6) with ESMTP id g0P8lBn19596 for ; Fri, 25 Jan 2002 09:47:11 +0100 Received: from irsamc.ups-tlse.fr (irsamc.ups-tlse.fr [130.120.88.41]) by gw1-mail.cict.fr (8.11.6/8.11.6) with ESMTP id g0P8lBM19589 for ; Fri, 25 Jan 2002 09:47:11 +0100 Received: from irsamc4 (irsamc4.ups-tlse.fr [130.120.88.67]) by irsamc.ups-tlse.fr (8.9.3/8.9.3) with ESMTP id JAA12111 for ; Fri, 25 Jan 2002 09:46:53 +0100 Date: Fri, 25 Jan 2002 09:46:56 +0100 (CET) From: GUTIERREZ Fabien X-X-Sender: gutierre@irsamc4.ups-tlse.fr To: chemistry@ccl.net Subject: Re: CCL:g98: installation linux In-Reply-To: <000001c1a50c$e1a8a100$1200a8c0@chem.wsu.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi all i have succeeded in compiling gaussian rev A9 on i386 system with redhat using g77,intel compiler and pgf77 with tuned blas library like atlas , the one's from greg henry and last with intel libraries . moreover it can run in shared memory improving time calculations . if my experience could be of any help to some of you Fabien -- **************************************** * M Fabien GUTIERREZ * * Laboratoire de Physique Quantique * * Universite Paul Sabatier * * 118 route de Narbonne * * 31062 TOULOUSE Cedex * * * * fabien.gutierrez@irsamc.ups-tlse.fr * * Tel : 05.61.55.60.31 Bureau * **************************************** From chemistry-request@server.ccl.net Fri Jan 25 07:27:14 2002 Received: from gip.u-picardie.fr ([193.49.184.17]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0PCREc06037 for ; Fri, 25 Jan 2002 07:27:14 -0500 Received: from labo5 (labo5.sa.u-picardie.fr [195.83.150.83]) by gip.u-picardie.fr (Postfix) with SMTP id 66DBB7F9B for ; Fri, 25 Jan 2002 13:27:12 +0100 (CET) X-Sender: fyd-phar@mailx.u-picardie.fr X-Mailer: Windows Eudora Light Version 1.5.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@ccl.net From: FyD Subject: Solvation models and dG in GAMESS Message-Id: <20020125122712.66DBB7F9B@gip.u-picardie.fr> Date: Fri, 25 Jan 2002 13:27:12 +0100 (CET) Dear All, I would like to compare free energy, dG of 2 conformations, in solvant and in vacuo. - In vacuo, dG is obtained from the dE corrected for ZPE, enthalpy thermal effect and entropy obtained (from thermochemistry at 298K). - In condensed phase, I tried 3 solvation models in GAMESS: COSMO, SCRF and PCM: * COSMO and SCRF report total energy (a.u.)... * PCM reports directly the free energy (Kcal/Mol)... Why PCM directly reports free energy and COSMO/SCRF only total energy ? Could you give me some review references on this topic ? Thanks, regards, Francois From chemistry-request@server.ccl.net Fri Jan 25 11:06:11 2002 Received: from ribotargets.com ([194.129.39.11]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0PG6Ac17392 for ; Fri, 25 Jan 2002 11:06:10 -0500 Received: from szilva (helo=localhost) by echo.ribotargets.com with local-esmtp (Exim 3.13 #1) id 16U8ou-0004d3-00 for CHEMISTRY@ccl.net; Fri, 25 Jan 2002 16:03:16 +0000 Date: Fri, 25 Jan 2002 16:03:16 +0000 (GMT) From: Szilveszter Juhos To: CHEMISTRY@ccl.net Subject: Re: CCL:Conformation representation Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL Members, Here are the references I've collected (though not all the papers are yet here so I can not proove their usefulness) about 3D conformation: Ash, S.; Cline, M. A.; Homer, R. W.; Hurst, T.; Smith, G. B. SYBYL Line Notation (SLN): a versatile language for chemical structure representation. J. Chem. Inf. Comput. Sci. 1997, 37 71-79. Hiroko Satoh, Hiroyuki Koshino, Kimito Funatsu, and Tadashi Nakata; Novel Canonical Coding Method for Representation of Three-Dimensional Structures, Journal of Chemical Information and Computer Sciences; 2000; 40(3); 622-630. Hiroko Satoh, Hiroyuki Koshino, Kimito Funatsu, and Tadashi Nakata; Representation of Molecular Configurations by CAST Coding Method, Journal of Chemical Information and Computer Sciences; 2001; 41(5); 1106-1112. J. H. Schuur, P. Selzer, J. Gasteiger J. The Coding of the Three-dimensional Structure of Molecules by Molecular Transforms and Its Application to Structure - Spectra Correlations and Studies of Biological Activity, Chem. Inf. Comput. Sci., 36, 334-344 (1996) Bravi, G.; Gancia, E.; Zaliani, A. MS-WHIM, New 3D Theoretical Descriptors Derived from Molecular Surface Properties: A Comparative 3D QSAR Study in A Series of Steroids. Computer-aided Mol. Design 1997, 11. 79-? R.Todeschini and P.Gramatica, "3D-modelling and prediction by WHIM descriptors. Part 5. Theory development and Chemical Meaning of WHIM Descriptors", Quant. Struct.-Act. Relat. 16, 113-119 (1997) Valentin Steinhauer; Chemical Information in 3D Space, Journal of Chemical Information and Computer Sciences; 1996; 36(5); http://www.daylight.com/meetings/mug98/Yang/lenguas/tdt.html and the CIF format was also mentioned although I think other format(s) will be more appropiate for me. With the help of Quoc-Tuan Do, Deepak, Joao Aires de Sousa, Edward Griffiths and Andrea Zaliani (hoping not leaving anybody out). Thanks for the replies, now I just have to read myself through all the papers. Szilva From chemistry-request@server.ccl.net Fri Jan 25 14:02:43 2002 Received: from pcserver.iqm.unicamp.br ([143.106.51.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0PJ2gc25697 for ; Fri, 25 Jan 2002 14:02:43 -0500 Received: from localhost (localhost.iqm.unicamp.br [127.0.0.1]) by pcserver.iqm.unicamp.br (Postfix) with ESMTP id A21BC3EFC for ; Fri, 25 Jan 2002 17:02:37 -0200 (BRST) Received: from iqm.unicamp.br (safita.iqm.unicamp.br [143.106.51.106]) by pcserver.iqm.unicamp.br (Postfix) with ESMTP id 844853EF3 for ; Fri, 25 Jan 2002 17:02:35 -0200 (BRST) Sender: smv@pcserver.iqm.unicamp.br Message-ID: <3C51BA58.DEF2BC62@iqm.unicamp.br> Date: Fri, 25 Jan 2002 17:04:40 -0300 From: "Sergio M. Vechi" X-Mailer: Mozilla 4.76 [pt_BR] (X11; U; Linux 2.2.17-14cl i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: classical md nwchem input Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Virus-Scanned: by AMaViS perl-11 Dear CCL Members, I have some experience in molecular dynamics (md) simulations with my own programs and just now I become a NWChem user. I want to perform a classical NVE md simulation for pure liquids/mixtures with NWChem. I have the force field parameters: bond angles, bond lenghts, site charges and Lennard Jones parameters of the models. I can write the molecular cartesian coodinates too. I would appreciate your help in the construction of a NWChem input file since there are some information regarding user defined models that I could not find in the Tutorial/User Documentation. Thanks in advance, S M Vechi From chemistry-request@server.ccl.net Fri Jan 25 19:22:31 2002 Received: from france.chem.duke.edu ([152.3.169.99]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0Q0MVc04261 for ; Fri, 25 Jan 2002 19:22:31 -0500 Received: from yang3.chem.duke.edu (yang5.chem.duke.edu [152.3.169.205]) by france.chem.duke.edu (8.9.3/8.9.3) with SMTP id TAA13318 for ; Fri, 25 Jan 2002 19:22:29 -0500 (EST) From: Hong Organization: Duke Unversity To: chemistry@ccl.net Subject: 3-D fast sine-transform Date: Fri, 25 Jan 2002 19:09:54 -0500 X-Mailer: KMail [version 1.0.28] Content-Type: text/plain MIME-Version: 1.0 Message-Id: <02012519223102.08110@yang3.chem.duke.edu> Content-Transfer-Encoding: 8bit Dear cclers, I need to use 3-D fast sine transform (FST) in my codes, but I can only find 1-D FST code. A simple way to do 3d FST is build it from 1-D FST. That's what I am using now. I suspect that's not the optimal way and I wonder whether there are more efficient implimentations. Could you give me some suggestions or advice? Thanks! Hong Jiang From chemistry-request@server.ccl.net Fri Jan 25 19:13:22 2002 Received: from mtiwmhc25.worldnet.att.net ([204.127.131.50]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0Q0DMc03650 for ; Fri, 25 Jan 2002 19:13:22 -0500 Received: from DopeTec ([138.23.156.82]) by mtiwmhc25.worldnet.att.net (InterMail vM.4.01.03.27 201-229-121-127-20010626) with ESMTP id <20020126001315.FUGB28783.mtiwmhc25.worldnet.att.net@DopeTec> for ; Sat, 26 Jan 2002 00:13:15 +0000 Message-ID: <004401c1a5bb$e47ae050$01000001@DopeTec> From: "Donald Keidel" To: Subject: gaussian- linux error PGI: Undefined variable Date: Fri, 25 Jan 2002 16:18:13 -0000 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0041_01C1A5BB.E3493E20" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2600.0000 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 This is a multi-part message in MIME format. ------=_NextPart_000_0041_01C1A5BB.E3493E20 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hello CCL members, I am getting the error: PGI: Undefined variable. Does anyone know what = that means? I want to thank everyone for all there help on my = installation problems. Thanks again in advance and have a good day. Don=20 --------------------------------------------------- Donald J. Keidel University of California, Riverside Department of Biochemistry and Molecular Biology Riverside, CA 92521 phone: (909) 787-5493 fax: (909) 787-4434 dkeidel397@att.net webpage: www.biochemistry.ucr.edu/gru/gradstudents/don_keidel/index.htm ------=_NextPart_000_0041_01C1A5BB.E3493E20 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hello CCL members,
 
I am getting the error:  PGI: = Undefined=20 variable.  Does anyone know what that means?  I want to thank = everyone=20 for all there help on my installation problems.  Thanks again in = advance=20 and have a good day.
 
Don
---------------------------------------------------
Donald = J.=20 Keidel
University of California, Riverside
Department of = Biochemistry and=20 Molecular Biology
Riverside, CA 92521
phone:  (909)=20 787-5493
fax:  (909) 787-4434
dkeidel397@att.net
webpage: www.biochemistry.ucr.edu/gru/gradstudents/don_keidel/index.htm<= BR>
------=_NextPart_000_0041_01C1A5BB.E3493E20-- From chemistry-request@server.ccl.net Fri Jan 25 17:47:57 2002 Received: from sd.accelrys.com ([146.202.0.254]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0PMlvc31846 for ; Fri, 25 Jan 2002 17:47:57 -0500 Received: (from jnauss@localhost) by sd.accelrys.com (8.11.0/8.11.0) id g0PNsMw09128 for chemistry@ccl.net; Fri, 25 Jan 2002 15:54:22 -0800 Received: from jnauss1-pc.accelrys.com (jnauss1-pc.sd.accelrys.com [172.30.51.68]) by sd.accelrys.com (8.11.0/8.11.0) with ESMTP id g0PNsLT09083 for ; Fri, 25 Jan 2002 15:54:21 -0800 Message-Id: <5.1.0.14.0.20020125135611.040fee80@sparky2.sd.accelrys.com> X-Sender: jnauss@sparky2.sd.accelrys.com X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Fri, 25 Jan 2002 13:56:36 -0500 To: chemistry@ccl.net From: Jeff Nauss Subject: Accelrys Life Science Customer Training in Tel Aviv Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Accelrys will be holding two 2-day workshops at the Tel Aviv University in Tel Aviv, Israel. On February 18-19, the "CHARMm Workshop" will be offered. This workshop will provide a more in-depth coverage of molecular mechanics and dynamics focusing on the use of CHARMm. Both command line usage as well as use in InsightII will be covered. No experience is necessary but knowledge of InsightII will be helpful. On February 20-21, the workshop "Structure-Based Drug Design with InsightII" will be conducted. This workshop is for experienced users of InsightII who are interested in docking and drug design. The focus will be on detailed studies of single ligand interactions with specific receptors. Extensive experience or completion of the "Introduction to Life Science Modeling with InsightII" workshop is required. Fees for each 2-day course are US$1000 commercial, US$500 government, and US$400 academic. However, register for both courses and receive a 25% discount for the second course. Registration is on-line at URL http://www.accelrys.com/training/lifesci/registration.php. Further detailed information about this and other Accelrys training workshops can be found at the Accelrys website (http://www.accelrys.com/training/lifesci/schedule.html). Please do not hesitate to contact us should you have any questions. Please note that on 1 June, MSI, Synopsys, Oxford Molecular, and GCG became Accelrys. Thank you very much. Jeffrey L. Nauss +1-858-799-5555 -- Jeffrey L. Nauss, PhD Phone: (858) 799-5555 Life Science Customer Training Fax: (858) 799-5100 Accelrys Inc. E-mail: jnauss@accelrys.com 9685 Scranton Road http://www.accelrys.com/training/lifesci/ San Diego, CA 92121-3752 From chemistry-request@server.ccl.net Fri Jan 25 20:33:05 2002 Received: from ccl.net ([192.148.249.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0Q1X5c07537 for ; Fri, 25 Jan 2002 20:33:05 -0500 Received: from arlen.ccl.net (arlen.ccl.net [192.148.249.10]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with ESMTP id UAA24215; Fri, 25 Jan 2002 20:33:00 -0500 (EST) Date: Fri, 25 Jan 2002 20:33:01 -0500 (EST) From: Jan Labanowski To: chemistry@ccl.net, Microelectronics@AtomicScaleDesign.net Subject: CHEMKIN Training Dates - USA 2002 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII ---------- Forwarded message ---------- Date: Fri, 25 Jan 2002 17:15:53 -0800 (PST) From: Reaction Design To: jkl@ccl.net Subject: CHEMKIN Training Dates - USA 2002 ================================================================= Reaction Design Offers CHEMKIN Training in San Diego, CA, USA ================================================================= TITLE: CHEMKIN Fundamentals and Applications DATES: May 7-8, 2002 July 9-10, 2002 September 10-11, 2002 November 13-14, 2002 LOCATION: ExecuTrain of San Diego 10180 Telesis Court San Diego, CA 92021 USA __________________________________________________________________ =============== COURSE OVERVIEW =============== (see below for Course Abstract) Day 1: 9:00 a.m. - 5:30 p.m. Introduction to CHEMKIN Gas-phase and Surface Fundamentals Day 2: 9:00 a.m. - 5:30 p.m. Solving Industry-relevant Problems with CHEMKIN For more information, visit: http://www.reactiondesign.com/ps_training.html __________________________________________________________________ ============= REGISTRATION: ============= Please note: Pre-registration is required. We cannot accommodate walk-ins. To register: Download a registration form from our web site at: http://www.reactiondesign.com/pdfdocs/ps_registration.pdf - OR - Call: (858) 550-1920 x15 and ask for Training Registration - OR - Send an e-mail to mailto:training@reactiondesign.com requesting a registration form. We will need the following information: - Name, Title, Company, Address, Phone and e-mail address of each registrant - How payment will be made: Purchase Orders, VISA, MasterCard or checks are accepted (Checks must be drawn on a US bank in US dollars) Registration will not be confirmed until a PO or payment is received. __________________________________________________________________ ===== COST: ===== $1100 per student Registrants will receive a free 30-day evaluation license for the CHEMKIN software upon course completion. *** Ask about discounted pricing for 2 or more individuals from the same organization. *** Register 30 days in advance and receive a $100 discount. __________________________________________________________________ ================ COURSE ABSTRACT: ================ Title: CHEMKIN Fundamentals and Applications The CHEMKIN Collection of software represents a widely accepted standard for modeling chemical kinetics in a variety of chemical processes, including combustion, catalysis, chemical conversion, as well as deposition and etching of materials for microelectronics and materials processing. 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