From chemistry-request@ccl.net Sat Sep 20 03:04:22 2003 Received: from ccl.net (email.ccl.net [192.148.249.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8K74LmK002396 for ; Sat, 20 Sep 2003 03:04:21 -0400 Received: from krakow.ccl.net (krakow.ccl.net [192.148.249.195]) by ccl.net (8.11.6+Sun/8.11.6/OSC 2.1) with ESMTP id h8K74Lm29411 for ; Sat, 20 Sep 2003 03:04:21 -0400 (EDT) Date: Sat, 20 Sep 2003 03:04:20 -0400 (EDT) From: "Dr. Jan K Labanowski" To: chemistry-.at.-ccl.net Subject: Seminars - ACD/Labs North American Users Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=3.5 required=7.0 tests=RCVD_IN_OSIRUSOFT_COM,USER_AGENT_PINE,X_OSIRU_OPEN_RELAY version=2.55 X-Spam-Level: *** X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) ---------- Forwarded message ---------- Date: Thu, 11 Sep 2003 12:30:44 -0400 From: Kelly Sturzenegger To: Jan Labanowski Subject: New Seminars Announced in place of ACD/Labs North American Users Meeting Dear Jan Labanowski: In May you received an e-mail from ACD/Labs informing you that due to SARS-related concerns, we had to postpone our North American Users' Meeting, originally scheduled for June 4-5. We are excited to announce four upcoming Seminars to be held in place of the planned Users' Meeting. There are no registration fees for the seminars and you are welcome to attend as many as you like. 1. NMR Seminar, Oct. 2nd, Princeton, NJ http://www.acdlabs.com/um/naum03/nmr.html 2. MS Seminar, Nov. 4th, East Rutherford, NJ http://www.acdlabs.com/um/naum03/ms.html 3. Chrom Seminar, Nov. 4th, East Rutherford, NJ http://www.acdlabs.com/um/naum03/chrom.html 4. Boston Regional Seminar, Nov. 6th, Cambridge, MA http://www.acdlabs.com/um/boston03/ More information about all ACD/Labs Seminars and Users' Meetings is available on our web site at: http://www.acdlabs.com/um/ We hope you can join us at one of these meetings, and look forward to discussing highlights of our version 7.0 release with you. Sincerely, Kelly Sturzenegger (on behalf of the Organizing Committee) Kelly Sturzenegger Events Coordinator Advanced Chemistry Development, Inc. 90 Adelaide St. W., Suite 600 Toronto, ON M5H 3V9 416-368-3435 X.236 416-368-5596 (Fax) www.acdlabs.com kelly-.at.-acdlabs.com Fall Workshop Schedule http://www.acdlabs.com/um Smash NMR Seminar, September 14 European Users' Meeting, September 23-24 NMR Seminar, October 2 Japanese Users' Meeting, October 23-24 AAPS Medicinal Chemistry Seminar, October 26 MS Seminar, November 4 Chromatography Seminar, November 4 Boston Regional Seminar, November 6 California and West Coast Seminar, November 11 From chemistry-request@ccl.net Fri Sep 19 19:24:53 2003 Received: from rama.ks.uiuc.edu (rama.ks.uiuc.edu [130.126.120.150]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8JNOnmK012961 for ; Fri, 19 Sep 2003 19:24:50 -0400 Received: from verdun.ks.uiuc.edu (verdun.ks.uiuc.edu [130.126.120.129]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id h8JNOjxL007937 for ; Fri, 19 Sep 2003 18:24:50 -0500 (CDT) Received: from localhost (jim@localhost) by verdun.ks.uiuc.edu (8.10.2+Sun/8.9.1) with ESMTP id h8JNOja00775 for ; Fri, 19 Sep 2003 18:24:45 -0500 (CDT) X-Authentication-Warning: verdun.ks.uiuc.edu: jim owned process doing -bs Date: Fri, 19 Sep 2003 18:24:45 -0500 (CDT) From: Jim Phillips To: chemistry.-at-.ccl.net Subject: NAMD 2.5b3 (Parallel MD) Release Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=3.1 required=7.0 tests=RCVD_IN_OSIRUSOFT_COM,USER_AGENT_PINE,X_AUTH_WARNING, X_OSIRU_OPEN_RELAY version=2.55 X-Spam-Level: *** X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear CCL, NAMD is a molecular dynamics program, file compatible with X-PLOR, CHARMM, and AMBER, scalable to hundreds of processors, and available as source code or binaries for a variety of platforms, free of charge. Try it out! It's been 18 months since NAMD 2.4, so there are quite a few changes. I'm planning to have 2.5 final out by the end of the month (when NCSA yanks the Origin 2000s away), so please give this a good thrashing. Thanks! -Jim +--------------------------------------------------------------------+ | | | NAMD 2.5b3 Release Announcement | | | +--------------------------------------------------------------------+ September 19, 2003 The Theoretical and Computational Biophysics Group at the University of Illinois is proud to announce the public release of a new version of NAMD, a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD is distributed free of charge and includes source code. NAMD development is supported by the NIH National Center for Research Resources. NAMD 2.5b3 has several advantages over NAMD 2.4: - Improved parallel scaling and serial performance. - Trajectory reading and interaction energy analysis. - Improved constant pressure simulation and coordinate wrapping. NAMD is available from http://www.ks.uiuc.edu/Research/namd/. For your convenience, NAMD has been ported to and will be installed on the machines at the NSF-sponsored national supercomputing centers. If you are planning substantial simulation work of an academic nature you should apply for these resources. Benchmarks for your proposal are available at http://www.ks.uiuc.edu/Research/namd/performance.html The Theoretical and Computational Biophysics Group encourages NAMD users to be closely involved in the development process through reporting bugs, contributing fixes, periodical surveys and via other means. Questions or comments may be directed to namd.-at-.ks.uiuc.edu. We are eager to hear from you, and thank you for using our software! From chemistry-request@ccl.net Fri Sep 19 16:29:36 2003 Received: from sandmail01.sd.accelrys.com (fw1.sd.accelrys.com [209.120.169.30]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8JKT4mK007090 for ; Fri, 19 Sep 2003 16:29:04 -0400 In-Reply-To: To: Subject: Re: CCL:Hydrogens in InsightII MIME-Version: 1.0 X-Mailer: Lotus Notes Release 6.0.1CF1 March 04, 2003 Message-ID: From: Jeff Nauss Date: Fri, 19 Sep 2003 13:29:04 -0700 X-MIMETrack: Serialize by Router on sandmail01/Server/Accelrys(Release 6.0.2CF1|June 9, 2003) at 09/19/2003 13:29:05, Serialize complete at 09/19/2003 13:29:05 Content-Type: text/plain; charset="US-ASCII" X-Spam-Status: No, hits=-0.5 required=7.0 tests=IN_REP_TO version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) I think the simplest way would be to use in InsightII Molecule | Display and turn off the display of the hydrogens. Then go to Molecule | Put with the Displayed toggle on. Only the visible atoms are written to the file and you retain your original structure. Though your suggestion will certainly work if the file is already created. Jeff -- 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.-at-.accelrys.com http://www.accelrys.com/training "Peter Gannett" Sent by: "Computational Chemistry List" 09/19/2003 04:49 AM To , cc Subject CCL:Hydrogens in InsightII Francois: It would probably be easier to write the pdb file and then use the egrep command with the -v option, which can be used to exclude all lines containing hydrogens, and then dump it to a new file. Pete Gannett >>> FyD 09/18/03 08:24PM >>> Dear All, I would interested in knowing 'the command' in insightII which allows to automatically REMOVE all the hydrogens (of an oligonucleotide) in order to save the structure (to the PDB format) without these hydrogens, keeping only the heavy atoms. Thanks, regards, Francois -= This is automatically added to each message by the mailing script =- To send e-mail to subscribers of CCL put the string CCL: on your Subject: line and send your message to: CHEMISTRY.-at-.ccl.net Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST.-at-.ccl.net HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs If your mail is bouncing from CCL.NET domain send it to the maintainer: Jan Labanowski, jkl.-at-.ccl.net (read about it on CCL Home Page) -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@ccl.net Sat Sep 20 02:44:57 2003 Received: from front1.chartermi.net (front1.chartermi.net [24.213.60.123]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8K6iQmK001348 for ; Sat, 20 Sep 2003 02:44:26 -0400 Received: from [24.236.135.230] (HELO master.bw01.kressworks.com) by front1.chartermi.net (CommuniGate Pro SMTP 3.5.9a) with ESMTP id 156584257 for chemistry.-at-.ccl.net; Sat, 20 Sep 2003 02:44:25 -0400 Content-Type: text/plain; charset="us-ascii" From: CCL To: Subject: B3LYP functional specification of constants Date: Sat, 20 Sep 2003 02:38:17 +0000 User-Agent: KMail/1.4.3 MIME-Version: 1.0 Message-Id: <200309200238.18038.ccl.-at-.kressworks.com> X-Spam-Status: No, hits=0.3 required=7.0 tests=DATE_IN_PAST_03_06,USER_AGENT_KMAIL version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h8K6ivmK001419 While investigating prior to doing some extensive B3LYP calculations, I've noticed that GAMESS and MOLPRO use 0.08 times the Slater Exchange in the B3LYP functional while NWCHEM and GAUSSIAN use 0.8. Which is correct? I will summarize to the list. Thanks. Jim