From chemistry-request@www.ccl.net Fri Sep 18 13:23:07 1998 Received: from mailbox.syr.edu (root@mailbox.syr.edu [128.230.1.5]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id NAA29973 Fri, 18 Sep 1998 13:23:06 -0400 (EDT) Received: from [128.230.59.17] (jello.cat.syr.edu [128.230.59.17]) by mailbox.syr.edu (8.9.0/8.9.0) with ESMTP id NAA09816 for ; Fri, 18 Sep 1998 13:23:07 -0400 (EDT) X-Sender: desingh@mailbox.syr.edu Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Fri, 18 Sep 1998 13:30:56 +0100 To: Computational Chemistry List From: Deepak Singh Subject: Parameters Hi everyone, I am interested in tracking down the revised PM3(tm) parameters for the following elements (for Spartan 5.1) : Ca, Ag, Cu, Fe. Parameters for other metals would be welcome too. Thank you Deepak Singh Deepak Singh Email: desingh@syr.edu Graduate Fellow URL: http://web.syr.edu/~desingh Department of Chemistry, Syracuse University 1-014 Scitech Syracuse NY 13244 Tel: (315) 443 1739, 443 5928 -- work (315) 472 9659 -- home Fax: (315) 443 4070 "Violence is the refuge of the foolish -- Salvor Hardin" From chemistry-request@www.ccl.net Fri Sep 18 15:47:54 1998 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id PAA03115 Fri, 18 Sep 1998 15:47:54 -0400 (EDT) Received: from mail.enter.net (root@mail.enter.net [204.170.70.6]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id PAA25219 for ; Fri, 18 Sep 1998 15:47:51 -0400 (EDT) Received: from satchmo (m40nris-1-4.enter.net [204.170.217.14]) by mail.enter.net (8.8.8/8.8.8) with SMTP id PAA18048; Fri, 18 Sep 1998 15:47:08 -0400 (EDT) Reply-To: From: "Scott Dixon" To: Subject: RE: Reading Mac 3.5's on PC's... Date: Fri, 18 Sep 1998 15:46:20 -0400 Message-ID: <000101bde33d$0216c9c0$123ce1cf@satchmo.daylight.com> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook 8.5, Build 4.71.2377.0 In-Reply-To: <199809171342.AA05312@world.std.com> Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3155.0 Hi, Joe- Dataviz (www.dataviz.com) makes a program called Conversions Plus which allows you to read Mac floppies (or Zip or other disks) on PCs and provides for translation of a variety of Mac formats to PC formats (and vice versa). All you have to do is pop your Mac disk in the PC. I've used it a lot and have had very good luck with it. Regards, Scott Dixon > -----Original Message----- > From: chemistry-request@www.ccl.net > [mailto:chemistry-request@www.ccl.net]On Behalf Of Joe M Leonard > Sent: Thursday, September 17, 1998 9:43 AM > To: chemistry@ccl.net > Subject: CCL:Reading Mac 3.5's on PC's... > > > > Folks, > > Like many, I suspect, I'm facing replacing an OLD Mac, and > since I have this large pile of floppies and datafiles... > > Is there any utility program which can read Mac floppies > on a PC? If so, where can I get a copy...? > > Thanks in advance! > > Joe Leonard > jle@world.std.com > > > --- > Administrivia: This message is automatically appended by the mail exploder: > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > --- > > From chemistry-request@www.ccl.net Fri Sep 18 17:02:05 1998 Received: from panix3.panix.com (GgSTt/HrEEp/Lx6GeCdJtlOLk3TK/PFq@panix3.panix.com [166.84.1.68]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id RAA09106 Fri, 18 Sep 1998 17:02:04 -0400 (EDT) Received: (from kynn@localhost) by panix3.panix.com (8.8.5/8.8.8/PanixU1.4) id RAA29908; Fri, 18 Sep 1998 17:02:00 -0400 (EDT) Date: Fri, 18 Sep 1998 17:02:00 -0400 (EDT) Message-Id: <199809182102.RAA29908@panix3.panix.com> From: "Kynn O. Jones" To: chemistry@www.ccl.net Subject: [Q] On minimal off-lattice models of proteins Over the past decade or so, minimal lattice models have been used to answer fundamental questions about the statistical mechanics of protein folding. These models are basically coarse-grained cartoons of proteins aiming to isolate some fundamental physical features of the problem. (For a review, see E. Shakhnovich, "Theoretical studies of protein folding thermodynamics and kinetics", Curr. Opin. Struct. Biol. 7:29-40, 1997.) There have been some published papers on similarly minimalistic off-lattice models of protein folding, but I have not found much at all by way of technical modeling details. I gather that there are two different approaches to modeling proteins *minimalistically* off-lattice: Monte Carlo and Brownian/Langevin/noisy dynamics. How do these approaches compare? Naively, I would have assumed that MC would be computationally faster; hence I don't quite understand why people bother with BD for this sort of modeling. (One possibility that occurs to me is that BD may be considered more convincing as a model of specific kinetic details, as opposed to merely a means to sample conformational space; or maybe off-lattice MC requires much more parameter tweaking to get it to work than BD.) I would appreciate opinions from those familiar with the ins and outs of both techniques (particularly within the context of minimal protein models). Has anyone reviewed in print the relative merits of off-lattice MC vs. BD? I'll post a summary of the responses I get. Thanks in advance, KJ ------- End of forwarded message ------- From chemistry-request@www.ccl.net Fri Sep 18 19:44:23 1998 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id TAA10558 Fri, 18 Sep 1998 19:44:23 -0400 (EDT) Received: from freon.chem.swin.edu.au (freon.chem.swin.edu.au [136.186.11.20]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id TAA00177 for ; Fri, 18 Sep 1998 19:44:18 -0400 (EDT) Received: from localhost (marg@localhost) by freon.chem.swin.edu.au (980427.SGI.8.8.8/970903.SGI.AUTOCF) via SMTP id JAA02260; Sat, 19 Sep 1998 09:52:23 -0700 (PDT) Date: Sat, 19 Sep 1998 09:52:23 -0700 (PDT) From: Margaret Wong To: chemistry@ccl.net Subject: Re: CCL:Reading Mac 3.5's on PC's... In-Reply-To: <199809171342.AA05312@world.std.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello Joe and CCL'ers Executor from http://www.ardi.com is very useful (both PC and linux) and my students use it on a regular basis to get info from the mac to a PC running windows or NT or to a Mac to a pc running linux. > Like many, I suspect, I'm facing replacing an OLD Mac, and > since I have this large pile of floppies and datafiles... > > Is there any utility program which can read Mac floppies > on a PC? If so, where can I get a copy...? cheers Margaret _ Dr Margaret Wong V marg@freon.chem.swin.edu.au _-_|\ \_ (_)o Chemistry Dept ) ( mgw@stan.xx.swin.oz.au / \ To: chemistry@www.ccl.net Subject: Re: CCL:Re: Parameterization In-Reply-To: <35FFFC8F.6F59@uno.edu> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Wed, 16 Sep 1998, Howard Alper wrote: > Now I have some questions about parameterization to create forcefields > for MD simulations. Specifically, I am interested in parameterizing > Nitromethane. While any information regarding a set of parameters > (bond, angle, torsion, out-of-plane,charges,van der Waals, etc) would > be welcome, we are interested in generating the neccesary parameters, > and in a form suitable for use in CHARMM. To this end I have several > questions: I've omitted the questions, because I'm not answering them directly, but supplying some references from Alex MacKerell's web site at http://www.pharmacy.umab.edu/~alex/research.html The papers below describe the development of various topology and parameter sets which are distributed with the academic version of CHARMM; additional citations and the parameter sets themselves (in CHARMM format) are also available on the web page. Typically, force constants for bond stretching and angle bending are derived from published IR/Raman spectroscopic data, after conversion to the CHARMM system of units. Atomic point charges and VDW radii parameters require extensive ab initio calculations, while torsions are usually parameterized to match experimentally determined rotational barriers and/or conformational distributions. MacKerell, Jr., A. D.; Bashford, D.; Bellott, M.; Dunbrack Jr., R.L.; Evanseck, J.D.; Field, M.J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F.T.K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D.T.; Prodhom, B.; Reiher, III, W.E.; Roux, B.; Schlenkrich, M.; Smith, J.C.; Stote, R.; Straub, J.; Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. All-atom empirical potential for molecular modeling and dynamics Studies of proteins. Journal of Physical Chemistry B, 1998, 102, 3586-3616. Yin, D. and MacKerell, Jr. A.D. Combined Ab initio/Empirical Approach for the Optimization of Lennard-Jones Parameters. Journal of Computational Chemistry, 1998, 19: 334-338. Pavelites, J.J., Bash, P.A., Gao, J. and MacKerell, Jr., A.D. A Molecular Mechanics Force Field for NAD+, NADH, and the Pyrophosphate Groups of Nucleotides. Journal of Computational Chemistry, (1997) 18:221-239. A.D. MacKerell Jr., J. Wi-rkiewicz-Kuczera and M. Karplus, An All-Atom Empirical Energy Function for the Simulation of Nucleic Acids, Journal of the American Chemical Society (1995) 117:11946-11975. -- Rick Venable =====\ |=| "Eschew Obfuscation" FDA/CBER Biophysics Lab |____/ |=| Bethesda, MD U.S.A. | \ / |=| ( Not an official statement or rvenable@deimos.cber.nih.gov | \ / |=| position of the FDA; for that, http://www.erols.com/rvenable \/ |=| see http://www.fda.gov ) From chemistry-request@www.ccl.net Sat Sep 19 17:04:07 1998 Received: from alchemy.chem.utoronto.ca (alchemy.chem.utoronto.ca [142.150.224.224]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id RAA13075 Sat, 19 Sep 1998 17:04:07 -0400 (EDT) Received: (from elewars@localhost) by alchemy.chem.utoronto.ca (8.7.4/8.7.3) id RAA02448 for chemistry@www.ccl.net; Sat, 19 Sep 1998 17:03:55 -0400 (EDT) Date: Sat, 19 Sep 1998 17:03:55 -0400 (EDT) From: "E. Lewars" Message-Id: <199809192103.RAA02448@alchemy.chem.utoronto.ca> To: chemistry@www.ccl.net Subject: HF ENERGY TO KJ: ANSWER 1998 Sept 19 Concerning the question: > 17-SEP-1998 01:12:30.27 >From: IN%"chaudash@aston.ac.uk" >To: IN%"chemistry@www.ccl.net" >Subj: CCL:Hartree Fock enegy > > >Hi ccl'ers >Could someone tell me /point me in the right direction as to where I >can find a reference as to conversion of Hartree Fock energy to >KJ/mol. A reference would also be much appreciated. >Many thanks >=============== [This is related to one asked July 30: Thurs July 30 Yury Voloshin asked How can one convert semiempirical energies, in kcal/mol, to hartrees, for comparison with ab initio values?] -- Answer: Chemistry studies energy _differences_, not energies. To convert ab initio "energies" (energy differencies) to kJ/mol (these are just single-point STO-3G energies on MM geometries, but they make the point): H H H CH3 Z ------- \ / \ / /|\ C==C C==C | / \ / \ (AM1) | CH3 CH3 CH3 H deltaE | | -154.23944 h -154.24286 h E -------- Z E deltaE = -154.23944 -(-154.24286) hartrees = 0.00342 h = 2626 x 0.00342 kJ/mol = 8.98 kJ/mol (or use 2625.50--I don't think it makes any difference) ( h x 627.510 gives kcal/mol) It's useful to note that 1 mh (millihartree) is about 3 kJ/mol (2.626), then you can see at a glance about how big a given energy difference is. E. Lewars ============================ From chemistry-request@www.ccl.net Sun Sep 20 10:57:07 1998 Received: from harfang.CC.UMontreal.CA (harfang.CC.UMontreal.CA [132.204.2.102]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA15074 Sun, 20 Sep 1998 10:57:06 -0400 (EDT) Received: from esi21.ESI.UMontreal.CA (esi21.ESI.UMontreal.CA [132.204.2.91]) by harfang.CC.UMontreal.CA (8.8.8/8.8.8) with ESMTP id KAA10533 for ; Sun, 20 Sep 1998 10:57:06 -0400 (EDT) Received: from localhost (proynov@localhost) by esi21.ESI.UMontreal.CA with SMTP id KAA14452 (8.8.7/IDA-1.6 for ); Sun, 20 Sep 1998 10:57:05 -0400 (EDT) X-Authentication-Warning: esi21.ESI.UMontreal.CA: proynov owned process doing -bs Date: Sun, 20 Sep 1998 10:57:05 -0400 (EDT) From: Proynov Emil X-Sender: proynov@esi21.ESI.UMontreal.CA To: chemistry@www.ccl.net Subject: erratum reference (Emil Proynov) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear netters, Some time ago I distributed an info about how to cite the Lap Ec functionals. The main reason was the erratum that must be attached from now on to the first reference mentioned in the info. This erratum was cited as "in press", now I present the final reference of it: The erratum concerns the following paper published in 1994: E.I. Proynov and D.R. Salahub, A Simple but Efficient Correlation Functional from a Pair Correlation Function, Phys.Rev. B49, 7874 (1994); To this reference the following erratum reference must be now attached:) Erratum: E.I Proynov, D.R. Salahub, Phys.Rev B57, 12616 (1998). The errors found are of a mistyped origin and do not affect the final results of the paper. Thanks for the attention, Emil From chemistry-request@www.ccl.net Sun Sep 20 13:53:05 1998 Received: from potato.harvard.edu (berriz@potato.harvard.edu [128.103.96.173]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id NAA15450 Sun, 20 Sep 1998 13:53:04 -0400 (EDT) Received: (from berriz@localhost) by potato.harvard.edu (8.8.7/8.8.7) id NAA28473; Sun, 20 Sep 1998 13:52:43 -0400 Date: Sun, 20 Sep 1998 13:52:43 -0400 Message-Id: <199809201752.NAA28473@potato.harvard.edu> From: Gabriel Berriz To: chemistry@www.ccl.net Subject: CASP vs. The Tower of Babel I study the statistical mechanics of protein folding using minimal computer models. I find that my specialty has a Tower of Babel (Babble?) problem, and perhaps the same is true of the whole field of computational protein studies, or even of all of computational chemistry. It has to do with checking and building on the results of others. I was an experimentalist in cellular immunology for a few years before switching to my current field, and I recall that trading reagents, libraries, strains, was quite common in that field. I often unpacked little vials shipped in dry ice, and bearing some precious mutant; typically, after some quick tests, I was up and running with the new stuff. Not much was required from the source of the samples (a couple of concentrations, buffers used, maybe some growth conditions here and there...). *Nothing* like this happens in my current field. I'm not sure why, but I have a few guesses. For one thing, programs are a pain to port across systems (portability of code is not a criterion for publication). More important, in most cases I don't want the program just to use as a black box. On the contrary, my interest in the program is usually in how it implements a model; I want not only to reproduce published results, but also to tweak the conditions, and to extend the experiments. This invariably requires that I understand enough of the code to hack away in it, and here's where I hit the biggest wall. It takes me too long to understand the code written by my *labmates*, let alone that written by some unknown graduate student 5 years ago half a world away. (Again, clarity of code is, for the most part, not a criterion for publication). So, typically I conclude that either I re-implement the idea from scratch, which is usually something I can't afford, or else I drop the matter altogether. (Incidentally, in the few cases I've tried to get source code from other labs, I've received such unequivocal, resounding, unapologetic refusals, that I must conclude my request was deemed to be bad manners.) It is, in my opinion, a very serious problem; it reduces the field to a collection of largely independent efforts, deprived of one of the greatest strengths of the scientific method, namely, the ability to test and build upon the work of others. I wonder if others feel similarly. I think this frustrating situation was what ultimately gave rise to the biennial structure prediction competition CASP (Critical Assessment of techniques for protein Structure Prediction), in which participants put their structure prediction programs through the fire test of predicting some recently solved protein structures prior to their publication. This skips over the problem of understanding the programs and the models devised by others by focusing on "objective results". Faced with this clear prize, the field has naturally responded by a adopting an increasingly heuristic attitude: whatever works, however ad hoc or poorly understood, throw it in there. If you loose, no one will care, and if you hit the CASP jackpot, then "there's no arguing with success!" Well, I guess that's *one* way to deal with our Tower of Babel problem, but I wonder where this leaves the science... I'm relatively new to this field, though, and I wonder what others with more experience feel about these issues. Best wishes, Gabriel Berriz Department of Chemistry and Chemical Biology Harvard University berriz@potato.harvard.edu For best results, replace the word potato by chasma in my address. From chemistry-request@www.ccl.net Mon Sep 21 02:58:06 1998 Received: from medchem.dfh.dk (medchem.dfh.dk [130.225.177.15]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id CAA17018 Mon, 21 Sep 1998 02:58:05 -0400 (EDT) Received: from [130.225.177.59] (compmac2 [130.225.177.59]) by medchem.dfh.dk (950413.SGI.8.6.12/950213.SGI.AUTOCF) via ESMTP id IAA11522 for ; Mon, 21 Sep 1998 08:58:04 +0200 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Mon, 21 Sep 1998 08:58:02 +0200 To: CHEMISTRY@www.ccl.net From: Per-Ola Norrby Subject: Recent Babel versions Hi, Does anybody out there know if the conversion program Babel is still being developed/supported? I have version 1.6 (but only the source for 1.3). The version I have does not include the babel routines developed by Schrodinger Inc. for interfacing with Jaguar (I only have those in 1.3), and it cannot read the new Gaussian98 output, among other things. I'm grateful for any info. If there is interest, I'll summarize. Per-Ola Norrby ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ * Per-Ola Norrby, Associate Professor * The Royal Danish School of Pharmacy, Dept. of Med. Chem. * Universitetsparken 2, DK 2100 Copenhagen, Denmark * tel. +45-35376777-506, +45-35370850 fax +45-35372209 * Internet: peon@medchem.dfh.dk, http://compchem.dfh.dk/ From chemistry-request@www.ccl.net Mon Sep 21 03:12:26 1998 Received: from medchem.dfh.dk (medchem.dfh.dk [130.225.177.15]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id DAA17119 Mon, 21 Sep 1998 03:12:25 -0400 (EDT) Received: from [130.225.177.59] (compmac2 [130.225.177.59]) by medchem.dfh.dk (950413.SGI.8.6.12/950213.SGI.AUTOCF) via ESMTP id JAA11675; Mon, 21 Sep 1998 09:11:03 +0200 Message-Id: In-Reply-To: <35FFFC8F.6F59@uno.edu> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Mon, 21 Sep 1998 09:11:01 +0200 From: Per-Ola Norrby Subject: Re: CCL:Re: Parameterization To: chemistry@www.ccl.net Howard Alper wrote: ..... > Specifically, I am interested in parameterizing Nitromethane. >While any information regarding a set of parameters (bond, angle, >torsion, out-of-plane,charges,van der Waals, etc) would be welcome, >we are interested in generating the neccesary parameters, and in a form >suitable for use in CHARMM.... ..... Dear Howard, We just published a method for parameterization, specifically implemented for MacroModel, but we put a lot of effort into making the routines general enough so that you should be able to use it in a similar manner with any MM program running under Unix. Anything force field specific is handled by Unix scripts, you only need to be able to handle Unix to modify the method for the force field you are interested in. The method is described in J. Comput. Chem., 1998, 19, 1146-1166. I'll share the routines (note! they are NOT user-friendly, and you definitely need the article to make sense of them). Send me an email if you're interested. The stuff I'm distributing right now is a year old, I'm right in the middle of putting together an updated version, should be ready in a couple of weeks.' Best regards, Per-Ola Norrby ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ * Per-Ola Norrby, Associate Professor * The Royal Danish School of Pharmacy, Dept. of Med. Chem. * Universitetsparken 2, DK 2100 Copenhagen, Denmark * tel. +45-35376777-506, +45-35370850 fax +45-35372209 * Internet: peon@medchem.dfh.dk, http://compchem.dfh.dk/ From chemistry-request@www.ccl.net Mon Sep 21 03:27:12 1998 Received: from syntem.eerie.fr (syntem.eerie.fr [146.19.248.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id DAA17148 Mon, 21 Sep 1998 03:27:11 -0400 (EDT) Received: from roger.eerie.fr by syntem.eerie.fr via SMTP (951211.SGI.8.6.12.PATCH1502/940406.SGI.AUTO) for id JAA22063; Mon, 21 Sep 1998 09:27:51 +0200 Date: Mon, 21 Sep 1998 09:27:51 +0200 Message-Id: <199809210727.JAA22063@syntem.eerie.fr> X-Sender: roger@syntem.eerie.fr Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" To: CHEMISTRY@www.ccl.net From: rlahana@syntem.eerie.fr (Roger Lahana) Subject: Universal Applications of Molecular Modeling X-Mailer: Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by www.ccl.net id DAA17149 Dear colleagues, This is to announce a symposium named "Universal Applications of Molecular Modeling". The meeting will take place in Marseilles, France (7-10 June, 1999). The program outline, further details, and pre-registration forms are available on the conference Web site: http://www.uamm.fst.u-3mrs.fr The aim of this meeting is to gather scientists from various domains, such as polymer science, reactivity, catalysis, biology and many more in order to demonstrate that applications of molecular modelling are universal, from chemistry to biology. All these disciplines share the classical tools involved in molecular modelling (quantum chemistry, molecular dynamics, QSAR/QSPR). The meeting will also cover new methods and, more importantly, novel strategies in research. The official language of the meeting will be English. A specific session will be reserved to young scientists. This is to give the opportunity to young scientists to present their work to an experienced audience in an international meeting. An award will be attributed to the most interesting lecture(s), which will be published in an international molecular modelling journal. Applicants should propose a summary of their contribution to the Scientific Committee (see details below) before March 15, 1999. Scientific Committee: Graham RICHARDS (Chairman) Chairman of Chemistry - New Chemistry Laboratory Oxford University (UK) Han VAN DE WATERBEEMD Pfizer Central Research - Sandwich (UK) Jean Louis RIVAIL Laboratoire de Chimie Théorique Université Henry Poincaré, Nancy (FRANCE) Bernard LEVY Laboratoire de Physico-Chimie des Rayonnements Université Paris-Sud - Orsay (FRANCE) Pierre Alain CARRUPT Ecole de Pharmacie - Institut de Chimie Therapeutique Université de Lausanne (SWITZERLAND) Tony REES Department of Biology and Biochemistry University of BATH (UK) Joseph BICERANO The Dow Chemical Company M. E. Pruitt Research Center Midland Michigan (USA) Michel DUPUIS Pacific Northwest National Laboratory Environmental Molecular Sciences Laboratory Richland (USA) Organising Committee: Roger LAHANA Synt:em Parc Scientifique G. BESSE, Nîmes (FRANCE) Véronique LAZZERI Laboratoire de Stéréochimie Universite d'Aix-Marseille (FRANCE) Frédéric FOTIADU ENSSPICAM Université d'Aix-Marseille (FRANCE) Michel RAJZMANN Université d'Aix-Marseille (FRANCE) All email correspondence should be sent to: lazzeri@vmesa12u-3mrs.fr We hope you will be able to contribute to this meeting. Best wishes, Roger Lahana (on behalf of the organizing committee) **************************************************************** Dr Roger Lahana Synt:em Vice-President R&D Parc Scientifique G.Besse Molecular Modeling 30000 Nimes email: rlahana@syntem.eerie.fr France Tel: +33 (0)466 048 666 Fax: +33 (0)466 048 667 **************************************************************** http://www.syntem.com **************************************************************** From chemistry-request@www.ccl.net Mon Sep 21 09:38:19 1998 Received: from xx1.icas.ac.cn (root@[159.226.64.181]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id JAA22033 Mon, 21 Sep 1998 09:38:14 -0400 (EDT) Received: from zhangxd ([192.168.2.32]) by xx1.icas.ac.cn (8.8.7/8.8.7) with SMTP id JAA05138; Fri, 22 Sep 1995 09:04:51 GMT Message-ID: <000d01bde565$0fb7c000$2002a8c0@zhangxd.xx1.icas.ac.cn> From: "zhangxd" To: "Computational Chemistry List" Subject: one question Date: Mon, 21 Sep 1998 21:38:01 +0800 MIME-Version: 1.0 Content-Type: text/plain; charset="US-ASCII" 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 hi, Dear netters: when I run gs94, there is one question as followings. 709 basis functions 2127 primitive gaussians 437 alpha electrons 436 beta electrons nuclear repulsion energy 29939.3458312225 Hartrees. One-electron integrals computed using PRISM. The smallest eigenvalue of the overlap matrix is 1.567E-01 CNDO Guess failed. Using Huckel. DenBas #5 allocation failure: iend,mxcore= 3042519 2859064 Error termination via Lnk1e in e:\gs94\l401.exe. Job cpu time: 0 days 3 hours 25 minutes 17.0 seconds. File lengths (MBytes): RWF= 35 Int= 0 D2E= 0 Chk= 1 Scr= 1 Could you tell me what happened? Thax in advance. With best regards, Zhang, Xiao dong From chemistry-request@www.ccl.net Mon Sep 21 09:39:09 1998 Received: from max4.rrze.uni-erlangen.de (root@max4.rrze.uni-erlangen.de [131.188.71.16]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id JAA22235 Mon, 21 Sep 1998 09:39:04 -0400 (EDT) Received: from apollo1.pharmazie.uni-erlangen.de by max4.rrze.uni-erlangen.de; Mon, 21 Sep 1998 15:38:59 +0200 Received: from APOLLO1/SpoolDir by apollo1.pharmazie.uni-erlangen.de (Mercury 1.21); 21 Sep 98 15:36:40 +1 Received: from SpoolDir by APOLLO1 (Mercury 1.30); 21 Sep 98 15:36:37 +1 From: "Dr. Wolfgang Utz" Organization: LS fuer Pharmazie und LM-Chemie To: CHEMISTRY@www.ccl.net Date: Mon, 21 Sep 1998 15:36:32 MET MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: Snapshot Utility under NT 4.0 X-Confirm-Reading-To: "Dr. Wolfgang Utz" X-pmrqc: 1 Priority: normal Message-ID: <1BCB406FC8@apollo1.pharmazie.uni-erlangen.de> Dear Netters, I am looking for a snapshot utility for WindowsNT4.0 on Intel. It should be able to do the same task as snapshot or capture on SGI (drawing a frame and get the screen within the frame as any graphics format). Thank you in advance for your answer. Yours Wolfgang Utz *********************************************************************** Dr. Wolfgang Utz Institut fuer Pharmazie u. LM-Chemie Universitaet Erlangen-Nuernberg Schuhstr. 19 91052 Erlangen Tel. 09131/854100 Fax 09131/852585 E-mail:utz@pharmazie.uni-erlangen.de *********************************************************************** From chemistry-request@www.ccl.net Mon Sep 21 14:33:24 1998 Received: from ifi.unicamp.br (lua.ifi.unicamp.br [143.106.6.13]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id OAA10077 Mon, 21 Sep 1998 14:33:18 -0400 (EDT) Received: (from daemon@localhost) by ifi.unicamp.br (8.8.8/8.8.8) id PAA25196; Mon, 21 Sep 1998 15:32:04 -0300 (BSC) Received: from slater.ifi.unicamp.br(143.106.72.136), claiming to be "ifi.unicamp.br" via SMTP by lua.ifi.unicamp.br, id smtpdaayBaa; Mon Sep 21 15:31:58 1998 Message-ID: <36069DEB.B4A65628@ifi.unicamp.br> Date: Mon, 21 Sep 1998 15:41:48 -0300 From: "Márcio Cyrillo" X-Mailer: Mozilla 4.05 [en] (Win95; I) MIME-Version: 1.0 To: CHEMISTRY@www.ccl.net Subject: Restraining dihedrals using HyperChem Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear HyperChemists, I would like to ask you something that I think is very strange about HyperChem Geometry Optimization (GO) calculations. Actually I had already asked this before but the latter support man from HyperCube (Dr. Stravrev) did not want or did not know how to answer to my question. I think its about time to clear this issue! I hope someone can help me. The problem is: we read in HyperChem manual that for GO optimizations we can restraint a variable (bond length, angle or dihedral) using a restraing constant that adds a force field to the hamiltonian of the system so that a potential like that of a spring can "hold" the variable to a specific supplied value. This "Hook" constant, default value equals 60, is set up depending on the problem, but in the manual they tell us that it cannot be as big as we want because we would then add a nonlinear term that would perturbate the original hamiltonian producing artificial results. I have the following questions: - For molecular mechanics I understand this procedure of adding a quadratic potential to the hamiltonian to restrain a variable, but it seems to me as being meaningless to apply the same procedure to a semi-empirical hamiltonian. Am I wrong? - In mopac we can easily accomplish the restraint of a variable - changing a digit from 1 to 0 in the z-matrix scheme. Why did not HyperChem use the same algorithm? With MOPAC it works fine, which is pretty different in HyperChem where it almost impossible to, in fact, restrain the variable to the desired value. Everyone that has used my program HyperSpin (www.ifi.unicamp.br) before, knows what I mean. Talking about HyperSpin, I am going to release a new version soon but I am also working on a interface that will do quite the same work but using old and good MOPAC6. I am looking forward to hearing from you soon, best regards, Marcio. -- Marcio Cyrillo - http://www.ifi.unicamp.br/~cyrillo email: cyrillo@ifi.unicamp.br or mcyrillo@yahoo.com ICQ: 14059279 Graduate Student State University of Campinas (UNICAMP), SP, Brazil Applied Physics Department - DFA/IFGW room 51, phone +55 19 788 5364, fax +55 19 788 5376 From chemistry-request@www.ccl.net Mon Sep 21 16:03:56 1998 Received: from rzusuntk.unizh.ch (rzumail2.unizh.ch [130.60.128.10]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id QAA10685 Mon, 21 Sep 1998 16:03:55 -0400 (EDT) Received: [from rzusgi.unizh.ch (chburger@rzusgif.unizh.ch [130.60.68.19]) by rzusuntk.unizh.ch (8.8.5/SMI-5.25) with SMTP id WAA02800 for ; Mon, 21 Sep 1998 22:03:53 +0200 (MET DST)] Date: Mon, 21 Sep 1998 22:03:53 +0200 (MDT) From: "Dr. Peter Burger" To: CHEMISTRY@www.ccl.net Subject: CCL: Parallel Gaussian98 on Linux? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLer's just stumbled over the fact that Gaussian98 supposedly runs in parallel on Intel/Linux boxes. Is there anybody out who can shed a light on how it is done (MPI?) and performance and related issues? Best regards Peter ....................... Peter Burger Anorg.-Chem. Institut Universitaet Zuerich 8057 Zuerich chburger@aci.unizh.ch From chemistry-request@www.ccl.net Mon Sep 21 16:13:28 1998 Received: from sumter.awod.com ([208.140.99.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id QAA10755 Mon, 21 Sep 1998 16:13:27 -0400 (EDT) Received: from [208.140.96.202] (chs0202.awod.com [208.140.96.202]) by sumter.awod.com (8.8.7/8.8.8) with SMTP id QAA02989; Mon, 21 Sep 1998 16:13:15 -0400 (EDT) (envelope-from netsci@awod.com) X-Sender: arichon@208.140.99.1 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Mon, 21 Sep 1998 16:12:15 +0100 To: chemistry@www.ccl.net From: netsci@awod.com (Network Science) Subject: The 1999 Charleston Conference Awards Network Science Corporation, the host of The Charleston Conference announces the creation of the Network Science Student Stipend Award. Advanced graduate students and post doctoral fellows are invited to submit an abstract for the poster presentation at the 1999 Conference. The focus of the poster session is new techniques which can be applied to drug discovery. Two students will receive awards that include waiver of the conference registration fee along with a stipend to defray travel expenses to the March 15 - 17 meeting. Details are available as part of the conference announcement at http://www.netsci.org/Resources/Meetings/charleston99.html or by e-mailing editors@netsci.org With best regards, The NetSci Editors