From chemistry-request@server.ccl.net Tue Feb 4 12:28:01 2003 Received: from f04n01.cac.psu.edu ([128.118.141.31]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h14HS0I19329 for ; Tue, 4 Feb 2003 12:28:00 -0500 Received: from ra.chem.psu.edu (ra.chem.psu.edu [128.118.199.40]) by f04n01.cac.psu.edu (8.9.3/8.9.3) with ESMTP id MAA57850 for ; Tue, 4 Feb 2003 12:27:59 -0500 Content-Type: text/plain; charset="us-ascii" From: Rajarshi Guha Reply-To: rajarshi@presidency.com To: chemistry@ccl.net Subject: drawing molecules with specific conformations Date: Tue, 4 Feb 2003 12:30:02 -0500 X-Mailer: KMail [version 1.4] MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Message-Id: <200302041230.07616.rajarshi@presidency.com> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi, I'm using Hyperchem to draw molecules. However there are a number of molecules in which 2 substituents only differ in their conformations. In these cases when I click 'Add hydrogen and Build model', Hyperchem will swap the position of the two substituents. Has anybody gotten around this problem? Are there any other drawing programs which can allow me to draw conformations properly? Thanks, - -- - ------------------------------------------------------------------- Rajarshi Guha GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE - ------------------------------------------------------------------- Artificial intelligence has the same relation to intelligence as artificial flowers have to flowers. -- David Parnas -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.0.7 (GNU/Linux) iD8DBQE+P/ifG7nmNJuHVu4RAg80AJ9aWG6H9QMSkJycVeAMX7O69Pwn1wCgrj+F CdtC85/Vh8+nze4NCzMsCok= =fUUN -----END PGP SIGNATURE----- From chemistry-request@server.ccl.net Tue Feb 4 12:48:06 2003 Received: from sandmail01.sd.accelrys.com ([209.120.169.30]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h14Hm5I22507 for ; Tue, 4 Feb 2003 12:48:05 -0500 To: CHEMISTRY@ccl.net Cc: Elizabethc@accelrys.com Subject: Accelrys Customer Training in April MIME-Version: 1.0 X-Mailer: Lotus Notes Release 5.0.9a January 7, 2002 Message-ID: From: "Jeff Nauss" Date: Tue, 4 Feb 2003 09:48:03 -0800 X-MIMETrack: Serialize by Router on sandmail01/Server/Accelrys(Release 5.0.9 |November 16, 2001) at 02/04/2003 09:48:05 AM, Serialize complete at 02/04/2003 09:48:06 AM, Serialize by Router on sandmail01/Server/Accelrys(Release 5.0.9 |November 16, 2001) at 02/04/2003 09:48:06 AM Content-Type: text/plain; charset="us-ascii" Accelrys Inc. are holding the following training workshops at locations in the US and Europe during April 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. Material Science: Introduction to Materials Studio 1st April San Diego, CA Introduction to Quantum Mechanics Modeling using Materials Studio 2nd - 3rd April San Diego, CA Workshop on Structure Solution from Powder Diffraction Data 4th April San Diego, CA For course details and registration see: http://www.accelrys.com/training/matsci/schedule.html Macromolecular Modeling: Introduction to Life Science Modeling with InsightII 8th-9th April Burlington, MA Homology Base Protein Design 10th-11th April Burlington, MA For course details and registration see: http://www.accelrys.com/training/macro/schedule.html Cheminformatics: Accord for Excel 7th April Cambridge, UK Accord for Access 8th April Cambridge, UK Accord Database Explorer 9th April Cambridge, UK For course details and registration see: http://www.accelrys.com/training/cheminf/schedule.html Rational Drug Design: Introduction to Cerius2 for Life Sciences 8th-9th April San Diego, CA Small Molecule and Drug Design with Cerius2 10th-11th April San Diego, CA Introduction to Cerius2 for Life Sciences 15th-16th April Burlington, MA Pharmacophore Generation with Catalyst 17th-18th April Burlington, MA For course details and registration see: http://www.accelrys.com/training/rdd/schedule.html -- 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 From chemistry-request@server.ccl.net Wed Feb 5 02:47:58 2003 Received: from yangtze.hku.hk ([147.8.148.244]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h157lvI26612 for ; Wed, 5 Feb 2003 02:47:57 -0500 Received: from localhost (martin@localhost) by yangtze.hku.hk (8.11.6/8.9.3) with ESMTP id h157xrL14647 for ; Wed, 5 Feb 2003 15:59:58 +0800 Date: Wed, 5 Feb 2003 15:59:53 +0800 (HKT) From: Ma Chi Chiu To: CHEMISTRY@ccl.net Subject: Question Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I have a question regarding using Charmm. Actually, I would like to calculate the vibrational mode of a molecule with Force Field. However, I am not sure whether Charmm can handle this kind of calculation or not. Can anyone give me some hints or idea about that? Whether Charmm can calculate the vibrational properties (mode) of a molecule or not? If so, how? Thank you very much Martin From chemistry-request@server.ccl.net Wed Feb 5 04:57:20 2003 Received: from guppy.vub.ac.be ([134.184.129.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h159vJI10529 for ; Wed, 5 Feb 2003 04:57:19 -0500 Received: from mach.vub.ac.be (mach.vub.ac.be [134.184.129.3]) by guppy.vub.ac.be (8.9.1b+Sun/3.17.1.ap (guppy)) id KAA01965; Wed, 5 Feb 2003 10:57:03 +0100 (MET) for Received: from algcpc10 ([134.184.24.76]) by mach.vub.ac.be (8.9.3/3.13.3.ap (mach)) id KAA04668; Wed, 5 Feb 2003 10:57:02 +0100 (MET) for Message-ID: <015c01c2ccfc$b0f02bf0$4c18b886@vub.ac.be> From: "DFT 2003" To: Subject: 10th International Conference on the Application of Density Functional Theory in Chemistry and Physics Date: Wed, 5 Feb 2003 10:55:18 +0100 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 5.00.2919.6700 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2919.6700 Dear Colleagues, It is a pleasure and an honour for me to inform you that the registration for the 10th International Conference on the Application of Density Functional Theory in Chemistry and Physics, which will be held in Brussels > from September 07 to 12, 2003, is now open. All information concerning registration, accomodation, abstract submission, proceedings, ... can be found on the conference web site : http://www.vub.ac.be/dft2003/ Hoping to meet you in Brussels, with best regards, P. Geerlings Prof. Dr. Paul GEERLINGS Free University of Brussels Faculty of Sciences Department of General Chemistry (ALGC) Pleinlaan 2 1050 Brussels - Belgium Tel. : +32.2.629.33.14 Fax. : +32.2.629.33.17 email : dft2003@vub.ac.be From chemistry-request@server.ccl.net Wed Feb 5 09:21:26 2003 Received: from yangtze.hku.hk ([147.8.148.244]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h15ELPI20427 for ; Wed, 5 Feb 2003 09:21:26 -0500 Received: from localhost (xjwang@localhost) by yangtze.hku.hk (8.11.6/8.9.3) with ESMTP id h15EXKM15055 for ; Wed, 5 Feb 2003 22:33:25 +0800 Date: Wed, 5 Feb 2003 22:33:20 +0800 (HKT) From: Wang Xiujun To: chemistry@ccl.net Subject: Question about wavefunction in G98 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear All, I want calculate some molecules. In the calculation, I want to fix a part of wavefunction and change another part. Who can tell me whether I can do this by Gaussian98 or other software? Thank you! -- Wang Xiujun The University of Hong Kong From chemistry-request@server.ccl.net Wed Feb 5 10:35:55 2003 Received: from mustang.mpi.com ([63.244.250.132]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h15FZtI22692 for ; Wed, 5 Feb 2003 10:35:55 -0500 Received: from thunderbolt.mpi.com (thunderbolt.mpi.com [199.93.192.55]) by mustang.mpi.com (Switch-2.2.2/Switch-2.2.0) with ESMTP id h15FZsh05712; Wed, 5 Feb 2003 10:35:54 -0500 (EST) Received: from US-VS1.corp.mpi.com (us-be2.corp.mpi.com [199.93.195.21]) by thunderbolt.mpi.com (Switch-3.0.1/Switch-3.0.0) with ESMTP id h15FZqg9006466; Wed, 5 Feb 2003 10:35:52 -0500 (EST) X-MimeOLE: Produced By Microsoft Exchange V6.0.6249.0 content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="US-ASCII" Subject: RE: Benchmarks Date: Wed, 5 Feb 2003 10:35:52 -0500 Message-ID: <9C5166762F311146951505C6790A9CF832FF73@US-VS1.corp.mpi.com> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: Benchmarks Thread-Index: AcLNFms4fEiobjECQueZQ1kRy1+8AAAFXiVA From: "Stradella, Omar" To: , Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h15FZtI22693 John, You are probably thinking about the component of the SPECFP suite of benchmarks called "fpppp". See: http://www.spec.org/cpu95/CFP95/145.fpppp/ Omar Stradella >-----Original Message----- >From: jmmckel@attglobal.net [mailto:jmmckel@attglobal.net] >Sent: Tuesday, February 04, 2003 11:25 AM >To: chemistry@ccl.net >Subject: CCL:Benchmarks > >Folks, > >Once upon a time there was used a piece of cde from Gaussian70, I >believe, for cpu benchmarks. I believe the code was part of the two >electron integral code. Does anyone remember any of this and/or could >point me to it? > >Suggestions for other useful scientific cpu tests are also welcome, >particularly if public domain, and would stress the cpu and cpu-memory >communication. > >Thanks! > >John McKelvey > > > >-= 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 Wed Feb 5 12:17:15 2003 Received: from cascara.uvic.ca ([142.104.5.28]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h15HHFI26121 for ; Wed, 5 Feb 2003 12:17:15 -0500 Received: from unix6.uvic.ca (unix6.uvic.ca [142.104.5.87]) by cascara.uvic.ca (8.12.6/8.12.6) with ESMTP id h15HH8O4449262; Wed, 5 Feb 2003 09:17:08 -0800 Date: Wed, 5 Feb 2003 09:17:08 -0800 (PST) From: Roy Jensen To: chemistry@ccl.net Subject: Plotting basis functions In-Reply-To: Message-ID: References: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-UVic-Virus-Scanned: OK - Passed virus scan by Sophos (sophie) on cascara X-Scanned-By: MIMEDefang 2.19 (www . roaringpenguin . com / mimedefang) All I am trying to plot the 6-31G basis functions for carbon along one coordinate (eventually two for p functions). 'Trying' is the right word... I am using the cartesian expression given in Levine, 5th, p 487, which appears to be the general form of those found in other texts. The basis set information comes from the EMSL library. About the only thing that works is that all the functions go to zero at large distance from the nucleus. Looking along one axis, the 1s (6G) function looks correct. However, the 2s (3G) function has a probability near zero at the nucleus while the 2p function does not have a zero probability at the nucleus! The 1s(6G), 2s(3G), and 2p(3G) _do not_ integrate to unity!?. They are close, between 0.86 and 1.13, but this is too large for errors in the integration routine (MathCad, from -5 a0 to 5 a0 along all coordinates). As a check, the 1G functions do integrate to unity. Any hints would be appreciated! I presume the 6-31G set was not optimized on hydrogenic orbitals, but shouldn't there be some resemblance? Roy Jensen -----BEGIN PGP PUBLIC KEY BLOCK----- Comment: available at www.consol.ca ------END PGP PUBLIC KEY BLOCK------ From chemistry-request@server.ccl.net Wed Feb 5 13:56:50 2003 Received: from smtp.unc.edu ([152.2.1.241]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h15IuoI28873 for ; Wed, 5 Feb 2003 13:56:50 -0500 Received: from chastity.isis.unc.edu (chastity.isis.unc.edu [152.2.1.128]) by smtp.unc.edu (8.12.2/8.12.2) with ESMTP id h15IuaJg003660 (version=TLSv1/SSLv3 cipher=EDH-RSA-DES-CBC3-SHA bits=168 verify=NOT); Wed, 5 Feb 2003 13:56:36 -0500 (EST) Date: Wed, 5 Feb 2003 13:56:36 -0500 From: Judit Sztaray X-X-Sender: szj@chastity.isis.unc.edu To: help@gaussian.com cc: chemistry@ccl.net Subject: transition dipole moment Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII To whom it may concern: I had a small problem during using Gaussian98. I would like to calculate the transition dipole moment, and our group have used the Iop(7/33=1) keyword before all the time, that suppose to calculate this. But they have used it for mp2 level only, and now I wanted to calculate this at HF level, and it's completly missing .. as there were no such an input-parameter .. the other parts of the output file seem OK to me. Can it be, that the HF does not have this options? or is this just a small bug? Unfortunately the iop(7/33) is not listed in the Overlay Options. Thanks for helping: Judit Sztaray From chemistry-request@server.ccl.net Wed Feb 5 15:47:41 2003 Received: from mailshell.com ([209.157.66.231]) by server.ccl.net (8.11.6/8.11.0) with SMTP id h15KlfI31079 for ; Wed, 5 Feb 2003 15:47:41 -0500 Received: (qmail 28437 invoked by uid 99); 5 Feb 2003 20:47:41 -0000 Message-ID: <1044478061.3e41786d3f7b3@www.mailshell.com> Date: Wed, 05 Feb 2003 12:47:41 -0800 X-Priority: 3 (Normal) From: To: chemistry@ccl.net Subject: external basis sets in GAMESS In-Reply-To: <9C5166762F311146951505C6790A9CF832FF73@US-VS1.corp.mpi.com> MIME-Version: 1.0 Content-Type: text/plain Content-Transfer-Encoding: 8bit User-Agent: Mailshell.com I'm trying to include some non-builtin basis sets into PC-GAMESS (version 6.2). None of the methods described in the manual seem to work, so I'd appreciate any help from folks who succeeded in this. Thanks - Zoli Fekete _______________________________________________________ The FREE service that prevents junk email http://www.mailshell.com From chemistry-request@server.ccl.net Wed Feb 5 16:06:44 2003 Received: from exchange.neokimia.com ([132.210.158.207]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h15L6iI31383 for ; Wed, 5 Feb 2003 16:06:44 -0500 content-class: urn:content-classes:message Subject: RE: Benchmarks MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 5 Feb 2003 16:05:21 -0500 X-MimeOLE: Produced By Microsoft Exchange V6.0.6249.0 Message-ID: X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: Benchmarks Thread-Index: AcLNV2/QzssPdEe3RTas/DBqK3U5RwABAClg From: "Axel Mathieu" To: , Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h15L6jI31384 I can't answer your question about Gaussian, although I have used ScienceMark to benchmark several of my stations. It may not be the best benchmark available but it can give you a good idea of the performance of your machines. To tell you the truth, I can't remember the source of their code (if they used previously coded algorithms or if they coded it themselves). You'll find it at: http://www.sciencemark.org/ Axel -----Original Message----- From: jmmckel@attglobal.net [mailto:jmmckel@attglobal.net] Sent: 4 février, 2003 11:25 To: chemistry@ccl.net Subject: CCL:Benchmarks Folks, Once upon a time there was used a piece of cde from Gaussian70, I believe, for cpu benchmarks. I believe the code was part of the two electron integral code. Does anyone remember any of this and/or could point me to it? Suggestions for other useful scientific cpu tests are also welcome, particularly if public domain, and would stress the cpu and cpu-memory communication. Thanks! John McKelvey -= 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 Wed Feb 5 19:18:08 2003 Received: from kafka.net.nih.gov ([165.112.130.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h160I7I02013 for ; Wed, 5 Feb 2003 19:18:07 -0500 Received: from I.T.S.ME ([129.43.27.170]) by kafka.net.nih.gov (/8.10.1) with ESMTP id h160I6sE009873; Wed, 5 Feb 2003 19:18:06 -0500 (EST) Date: Wed, 5 Feb 2003 19:16:13 -0500 (Eastern Standard Time) From: "M. Nicklaus" To: chemistry@ccl.net cc: mn1@helix.nih.gov Subject: Temperature monitoring Message-ID: X-X-Sender: mn1@helix.nih.gov MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII We have a Linux cluster consisting of dual XP1900+ Athlon nodes. We've found them to be quite heat-sensitive. We would therefore like to monitor component temperature in them (ideally selectively for CPU, memory etc.) to pinpoint where the problems lies, and at what temperatures the nodes become likely to go down. What kind of approaches - both hardware and software - have people found to be effective for this goal? Useful answers will be summarized. Thanks in advance, Marc ------------------------------------------------------------------------ Marc C. Nicklaus, Ph.D. NIH/NCI at Frederick E-mail: mn1@helix.nih.gov Bldg 376, Rm 207 Phone: (301) 846-5903 376 Boyles Street Fax: (301) 846-6033 FREDERICK, MD 21702 USA Head, Computer-Aided Drug Design MiniCore Facility Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute at Frederick, National Institutes of Health http://rex.nci.nih.gov/RESEARCH/basic/medchem/mcnbio.htm ------------------------------------------------------------------------