From chemistry-request@www.ccl.net Thu Mar 25 04:11:17 1999 Received: from indigo ([159.149.79.36]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id EAA02611 Thu, 25 Mar 1999 04:11:12 -0500 (EST) Received: from vega (vega.farma.unimi.it [159.149.79.32]) by indigo (950413.SGI.8.6.12/950213.SGI.AUTOCF) via SMTP id KAA01393 for ; Thu, 25 Mar 1999 10:11:52 +0100 Message-ID: <000301be769f$d9f8ee40$204f959f@vega.farma.unimi.it.farma.unimi.it> From: "Giulio Vistoli" To: Subject: Usage of CHARMm without Quanta interface Date: Thu, 25 Mar 1999 10:14:10 +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 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Dear netters, I find several problems using CHARMm program in batch without Quanta graphic interface. Can anyone send me some informations or example files for minimization or dynamic processes that can show the correct use of CHARMm package in batch. Thank you in advance. Giulio Vistoli From chemistry-request@www.ccl.net Thu Mar 25 07:30:06 1999 Received: from gatekeeper.rp-rorer.co.uk ([195.232.82.242]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id HAA03295 Thu, 25 Mar 1999 07:30:05 -0500 (EST) Received: by gatekeeper.rp-rorer.co.uk id MAA28076 (InterLock SMTP Gateway 3.0 for chemistry@www.ccl.net); Thu, 25 Mar 1999 12:29:56 GMT Received: by gatekeeper.rp-rorer.co.uk (Internal Mail Agent-1); Thu, 25 Mar 1999 12:29:56 GMT Message-Id: <2217D24173C6D111849800008327F8EFA083F8@DAGEX01> From: "McLAY, Iain" To: "'chemistry@www.ccl.net'" Subject: "Quantifying Drug Design" Meeting, Pfizer UK, April 27th Date: Thu, 25 Mar 1999 12:26:16 -0000 Mime-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2232.9) Content-Type: text/plain > The Spring 1999 Meeting of the UK QSAR & ChemoInformatics Group will be > held > at Pfizer on Tuesday 27 April. The focus is on recent efforts to quantify > drug design, with presentations on recognising drug attributes (Chris > Lipinski) and their estimation (Dave Clark, Jens Loesel), design of > combinatorial libraries (Val Gillet), high throughput screening (Jeff > Morris, Tim Clark) and considerations for receptor interactions (Simon > Teague). There will also be a poster session. > > The full programme is accessible via the UK-QSAR web site: > > http://www.iainm.demon.co.uk > > or go straight there with > > http://www.iainm.demon.co.uk/1999spr.htm > > To participate, please send by 12 April your name, address, whether you > will > be driving and title of your poster if presenting, to: > > SK Yeap > Computational Chemistry (PC 557) > Pfizer Central Research > Sandwich, Kent > CT13 9NJ > > e-mail: yeap_sk@sandwich.pfizer.com > tel: 01304-648114 > fax: 01304-658463 > ********************************************************* > Iain McLay > Rhone Poulence Rorer, UK > e-mail: iain.mclay@rp-rorer.co.uk > > From chemistry-request@www.ccl.net Thu Mar 25 14:13:13 1999 Received: from vi0.medc.umn.edu (vwl.medc.umn.edu [128.101.31.230]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id OAA06117 Thu, 25 Mar 1999 14:13:13 -0500 (EST) Received: from vi3.medc.umn.edu (vi3.medc.umn.edu [128.101.31.233]) by vi0.medc.umn.edu (980427.SGI.8.8.8/8.8.8) with ESMTP id NAA20284 for ; Thu, 25 Mar 1999 13:11:36 -0600 (CST) From: Govindan Subramanian Received: (from govindan@localhost) by vi3.medc.umn.edu (980427.SGI.8.8.8/8.8.8) id NAA07406 for chemistry@www.ccl.net; Thu, 25 Mar 1999 13:13:15 -0600 (CST) Message-Id: <199903251913.NAA07406@vi3.medc.umn.edu> Subject: summary : NMR chemical shifts for aminoacids To: chemistry@www.ccl.net Date: Thu, 25 Mar 1999 13:13:15 -0600 (CST) X-Mailer: ELM [version 2.4 PL25] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Hi CCLers, Got two responses for my question regarding computed chemical shifts for aminoacids and peptides. Thanks a lot for the replies. -subramanian.g ===================================================================== References suggested by Dr. David van der Spoel (spoel@xray.bmc.uu.se) Science, 1995, 260, 1491 J. Am. Chem. Soc., 1995, 117, 8823 J. Chem. Phys. 1993, 99, 3629 Ber. Bunsenges. Phys. Chem., 1995, 99, 1001 J. Biomol. NMR., 1996, 6, 341. ===================================================================== ===================================================================== Reference suggested by Dr. Mark J Forster (mforster@nibsc.ac.uk) J. Biomol. NMR., 1995, 5, 217 ===================================================================== From chemistry-request@www.ccl.net Thu Mar 25 15:09:57 1999 Received: from sp2n17.missouri.edu (sp2n17-t.missouri.edu [128.206.2.27]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id PAA06405 Thu, 25 Mar 1999 15:09:57 -0500 (EST) Received: from sp2n3.missouri.edu (sp2n3.missouri.edu [128.206.2.93]) by sp2n17.missouri.edu (8.9.0/8.9.0) with ESMTP id OAA58110 for ; Thu, 25 Mar 1999 14:09:40 -0600 Received: from localhost (c697999@localhost) by sp2n3.missouri.edu (8.9.0/8.9.0) with SMTP id OAA86422 for ; Thu, 25 Mar 1999 14:09:38 -0600 X-Authentication-Warning: sp2n3.missouri.edu: c697999 owned process doing -bs Date: Thu, 25 Mar 1999 14:09:38 -0600 (CST) From: Raelene X-Sender: c697999@sp2n3.missouri.edu To: chemistry@www.ccl.net Subject: questions and mailing list Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi First I was wondering if I could be added to the news group mailing list. Second, I have a question: I am studying a large Rhodium complex using Ab initio MO and DFT. I have noticed that the virials are high - 2.5-3.5. Does anyone know if this is "normal" for such systems or, if it is not, why the V/T is so high? Thanks, Raelene Lawrence *********************************************************************** The underlying physical laws necessary for the mathematical theory of a large part of physics and the whole of chemistry are thus completely known, and the difficulty is only that the exact application of these laws leads to equations much too complicated to be soluble. P.A.M. Dirac (1929) Aaaaaggghhhh... A.R. Lawrence (1999) *********************************************************************** A. R. Lawrence Plummer Group 125 Chemistry Bldg University of Missouri - Columbia E-mail: c697999@showme.missouri.edu From chemistry-request@www.ccl.net Thu Mar 25 18:00:06 1999 Received: from causul.u-strasbg.fr (root@causul.u-strasbg.fr [130.79.34.67]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id SAA00561 Thu, 25 Mar 1999 18:00:05 -0500 (EST) Received: from chimie.u-strasbg.fr (marc@localhost [127.0.0.1]) by causul.u-strasbg.fr (8.8.8/8.8.8) with ESMTP id AAA28879 for ; Fri, 26 Mar 1999 00:04:01 +0100 Sender: marc@causul.u-strasbg.fr Message-ID: <36FAC0E0.E39002F0@chimie.u-strasbg.fr> Date: Fri, 26 Mar 1999 00:04:00 +0100 From: Marc Baaden X-Mailer: Mozilla 4.5 [en] (X11; I; Linux 2.0.36 i586) X-Accept-Language: en MIME-Version: 1.0 To: "'Computational Chemistry List'" Subject: Calculation of tensor averages Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers, I am working on the calculation of NMR shielding tensors by QM methods. I have calculated shielding tensors for two conformations of the same molecule. Now I am looking for a way to calculate the average tensor for a given nucleus assuming that the two conformers have equal probability. The problem I encounter is that the geometries of the two conformers are different (bond distances, angles etc.) and that they are differently oriented in space. How can one calculate the average tensor ? More precisely: - Does a "unique" reference frame exist, such that one can simply calculate an average element by element : = (Aij + Bij) / 2 And how is it defined ? - Has anybody already come across this problem ? And are there literature references ? I would be very grateful for any hints, literature references or comments. Thank you in advance. Marc Baaden -- Marc Baaden - Labo MSM (UMR 7551) - http://crypt.u-strasbg.fr/marc mailto:baaden@chimie.u-strasbg.fr - FAX (+49) 89 666 171 68 68 ICQ# 11466242 - Tel: (+33) 3 88 41 60 86 or (+33) 6 03 24 26 56 From chemistry-request@www.ccl.net Thu Mar 25 20:02:28 1999 Received: from havana.ks.uiuc.edu (havana.ks.uiuc.edu [130.126.120.73]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id UAA01183 Thu, 25 Mar 1999 20:02:27 -0500 (EST) Received: from istanbul.ks.uiuc.edu (istanbul.ks.uiuc.edu [130.126.120.95]) by havana.ks.uiuc.edu (8.9.1/8.9.1) with ESMTP id TAA23719 for ; Thu, 25 Mar 1999 19:02:29 -0600 (CST) Received: from localhost (jim@localhost) by istanbul.ks.uiuc.edu (8.8.7/8.6.9) with ESMTPid TAA01549 for ; Thu, 25 Mar 1999 19:02:30 -0600 X-Authentication-Warning: istanbul.ks.uiuc.edu: jim owned process doing -bs Date: Thu, 25 Mar 1999 19:02:30 -0600 (EST) From: Jim Phillips X-Sender: jim@istanbul To: chemistry@www.ccl.net Subject: ANNOUNCE: NAMD 2.0 Release Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII +--------------------------------------------------------------------+ | | | NAMD 2.0 Release Announcement | | | +--------------------------------------------------------------------+ March 25, 1999 The Theoretical 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. NAMD2 is a major improvement over NAMD 1.5, in both speed and simulation features. This is a binary-only release of NAMD2. We still have some additional code cleanup before releasing the source in a couple of weeks. NAMD2 is available via the web at http://www.ks.uiuc.edu/Research/namd/. Mail any questions or comments to namd@ks.uiuc.edu. ---------------------------------------------------------------------- New Features in NAMD 2.0 - Reads CHARMM (or X-PLOR) formatted parameter files. - Supports periodic and non-periodic MD simulations. - Particle mesh Ewald full electrostatics for periodic simulations. - Triple timestepping. - Rigid bonds to hydrogen atoms. - Fixed atoms implemented efficiently, no unnecessary force calculations. - Berendsen and Langevin piston constant pressure methods. - Steered Molecular Dynamics (SMD) features. ---------------------------------------------------------------------- Problems? For problems or questions, send email to namd@ks.uiuc.edu. If you think you have found a bug, please include what machine you are running on, and, if possible, a dump of the program output and/or a copy of your input files. Your feedback will help us improve NAMD2. ---------------------------------------------------------------------- NAMD2 Known Deficiencies - PME does not parallelize well and has had limited testing. - NAMD2 requires X-PLOR or CHARMM to produce the .psf structure input files. If you don't have one of these, you probably can't use NAMD2 yet. ----------------------------------------------------------------------