From germano@dcci.unipi.it Thu Jul 10 01:51:01 1997 Received: from server1.dcci.unipi.it for germano@dcci.unipi.it by www.ccl.net (8.8.3/950822.1) id AAA26248; Thu, 10 Jul 1997 00:55:02 -0400 (EDT) Received: from hulk.icqem.pi.cnr.it by server1.dcci.unipi.it (SMI-8.6/SMI-SVR4) id GAA18317; Thu, 10 Jul 1997 06:55:09 +0200 Date: Thu, 10 Jul 1997 06:54:56 +0200 (MDT) From: Guido Germano X-Sender: guido@hulk.icqem.pi.cnr.it To: Computational Chemistry List , help@gaussian.com Subject: Gaussian bug? Message-ID: Organization: Dipartimento di Chimica e Chimica Industriale - Univ. di Pisa MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Find enclosed a Gaussian 94 input file with a simple Hartree-Fock run. On a SGI Indigo 2 (Gaussian 94 Rev. D.4) its first SCF reads SCF Done: E(RHF) = -1090.96251553 A.U. after 11 cycles while the SAME input file yields on an IBM (Rev. B.3) and a DEC (Rev. D.4) SCF Done: E(RHF) = -1086.47515931 A.U. after 3 cycles Isn't this strange? I apologize to CCL for asking a Gaussian question. Please answer to me; if something interesting turns out I will summarize to the list. Thanks in advance and regards. Guido Germano PhD student in Computational Chemistry Dipartimento di Chimica e Chimica Industriale e-mail germano@dcci.unipi.it Universita` di Pisa http://www.dcci.unipi.it/~germano Via Risorgimento 35 finger guido@hal.icqem.pi.cnr.it I-56126 Pisa phone +39-50-918.266, .295 or .239, fax .260 %chk=g94_pdtbuB #p LanL2DZ opt=(maxcyc=100,z-matrix) scf=direct scfcon=6 Pd(PHtBu2)3, simmetria C3h (H fosfinici vincolati sul piano dei P e del Pt) 0 1 Pd X 1 1. 15 1 R3 2 A3 1 3 R4 1 A4 2 T4 6 3 R5 1 A5 4 T5 6 5 R6 3 A6 1 T6 1 6 R7 5 A7 3 T7 1 6 R8 5 A8 3 T8 1 6 R9 5 A9 3 T9 6 5 R10 3 A10 1 T10 1 10 R11 5 A11 3 T11 1 10 R12 5 A12 3 T12 1 10 R13 5 A13 3 T13 6 5 R14 3 A14 1 T14 1 14 R15 5 A15 3 T15 1 14 R16 5 A16 3 T16 1 14 R17 5 A17 3 T17 6 3 R5 1 A5 4 -T5 6 18 R6 3 A6 1 -T6 1 19 R7 18 A7 3 -T7 1 19 R8 18 A8 3 -T8 1 19 R9 18 A9 3 -T9 6 18 R10 3 A10 1 -T10 1 23 R11 18 A11 3 -T11 1 23 R12 18 A12 3 -T12 1 23 R13 18 A13 3 -T13 6 18 R14 3 A14 1 -T14 1 27 R15 18 A15 3 -T15 1 27 R16 18 A16 3 -T16 1 27 R17 18 A17 3 -T17 15 1 R3 3 A31 2 T31 1 31 R4 1 A4 2 T4 6 31 R5 1 A5 32 T5 6 33 R6 31 A6 1 T6 1 34 R7 33 A7 31 T7 1 34 R8 33 A8 31 T8 1 34 R9 33 A9 31 T9 6 33 R10 31 A10 1 T10 1 38 R11 33 A11 31 T11 1 38 R12 33 A12 31 T12 1 38 R13 33 A13 31 T13 6 33 R14 31 A14 1 T14 1 42 R15 33 A15 31 T15 1 42 R16 33 A16 31 T16 1 42 R17 33 A17 31 T17 6 31 R5 1 A5 32 -T5 6 46 R6 31 A6 1 -T6 1 47 R7 46 A7 31 -T7 1 47 R8 46 A8 31 -T8 1 47 R9 46 A9 31 -T9 6 46 R10 31 A10 1 -T10 1 51 R11 46 A11 31 -T11 1 51 R12 46 A12 31 -T12 1 51 R13 46 A13 31 -T13 6 46 R14 31 A14 1 -T14 1 55 R15 46 A15 31 -T15 1 55 R16 46 A16 31 -T16 1 55 R17 46 A17 31 -T17 15 1 R3 31 A31 2 T31 1 59 R4 1 A4 2 T4 6 59 R5 1 A5 60 T5 6 61 R6 59 A6 1 T6 1 62 R7 61 A7 59 T7 1 62 R8 61 A8 59 T8 1 62 R9 61 A9 59 T9 6 61 R10 59 A10 1 T10 1 66 R11 61 A11 59 T11 1 66 R12 61 A12 59 T12 1 66 R13 61 A13 59 T13 6 61 R14 59 A14 1 T14 1 70 R15 61 A15 59 T15 1 70 R16 61 A16 59 T16 1 70 R17 61 A17 59 T17 6 59 R5 1 A5 60 -T5 6 74 R6 59 A6 1 -T6 1 75 R7 74 A7 59 -T7 1 75 R8 74 A8 59 -T8 1 75 R9 74 A9 59 -T9 6 74 R10 59 A10 1 -T10 1 79 R11 74 A11 59 -T11 1 79 R12 74 A12 59 -T12 1 79 R13 74 A13 59 -T13 6 74 R14 59 A14 1 -T14 1 83 R15 74 A15 59 -T15 1 83 R16 74 A16 59 -T16 1 83 R17 74 A17 59 -T17 R4 1.4301 R5 1.9516 R6 1.5476 R7 1.0866 R8 1.0847 R9 1.0803 R10 1.5420 R11 1.0872 R12 1.0814 R13 1.0822 R14 1.5434 R15 1.0874 R16 1.0845 R17 1.0799 A4 117.9675 A5 116.6035 A6 105.1153 A7 109.2675 A8 111.5364 A9 111.5275 A10 111.1365 A11 109.4080 A12 111.4958 A13 111.9739 A14 114.4580 A15 109.0936 A16 111.9495 A17 112.4040 T5 112.5302 T6 -49.9891 T7 178.4615 T8 -62.5660 T9 58.6286 T10 67.4662 T11 -167.8824 T12 -48.2547 T13 73.1407 T14 -167.8085 T15 167.2768 T16 48.2090 T17 -73.9480 R3 2.2800 A3 90.0000 A31 120.0000 T4 -90.0000 T31 -90.0000 From bennett@TheOffice.net Thu Jul 10 03:51:03 1997 Received: from arwen.unibe.ch for bennett@TheOffice.net by www.ccl.net (8.8.3/950822.1) id DAA27134; Thu, 10 Jul 1997 03:46:00 -0400 (EDT) Received: from sauron.unibe.ch by arwen with SMTP (PP); Thu, 10 Jul 1997 09:44:02 +0200 Received: from cluster1.unibe.ch. by sauron.unibe.ch (MX V4.2 AXP) with SMTP; Thu, 10 Jul 1997 09:42:57 MET Message-ID: Date: Thu, 10 Jul 97 09:46:00 +0300 From: "Frederick R. Bennett" Subject: G:Gaussian on a Mac ? To: CHEMISTRY@www.ccl.net X-Mailer: VersaTerm Link v1.1 I know that Gaussian Inc. hates this sort of thing but I will ask anyway. I am wondering whether anyone has G94 running on a PowerMac running one of the Linux operating systems (MKLinux or the non-Micro Kernal). Just as a matter of opinion, I think that Gaussian Inc. should seriously consider supporting this platform, as they do the various Unices running on Intel machines. The motorola PowerPC chips are leaving Intel Pentiums for dead at the moment and with the new generation motorola chips on the way out, fast system buses and new cacheing technology, Mac's or Mac clones should/can provide the hardware for some high power/cost ratio workstations for chemistry. =============================================================================== Namenet Address: Frederick R. Bennett Papernet Address: Department of Chemistry and Biochemistry Freiestrasse 3 CH-3012 Bern Switzerland Mouthnet Address: [41] (031) 631 4231 Faxnet Address [41] (031) 631 3994 Internet Address: bennett@TheOffice.net =============================================================================== From luca@lcfs.chim.UNIFI.IT Thu Jul 10 03:56:56 1997 Received: from cesit1.unifi.it for luca@lcfs.chim.UNIFI.IT by www.ccl.net (8.8.3/950822.1) id CAA26966; Thu, 10 Jul 1997 02:56:17 -0400 (EDT) Received: from lcfs.chim.unifi.it by CESIT1.UNIFI.IT (PMDF V5.0-4 #3688) id <01IL2DV7LR1C001PKF@CESIT1.UNIFI.IT> for chemistry@www.ccl.net; Thu, 10 Jul 1997 08:56:08 +0100 (MET) Received: by lcfs.chim.unifi.it (5.x/SMI-SVR4) id AA01563; Thu, 10 Jul 1997 09:01:32 +0100 Date: Thu, 10 Jul 1997 09:01:31 +0100 (WET DST) From: Luca Subject: 3D visualisation software - summary X-Sender: luca@lcfs To: chemistry@www.ccl.net Message-id: MIME-version: 1.0 Content-type: TEXT/PLAIN; charset=US-ASCII Content-transfer-encoding: 7BIT Dear CCL members, 10 days ago I posted a question about a 3D visualisation software I would like to use to get picture of electronic density and so on. The software should be able to draw isosurfaces. Here are the answers. I would like to thank all the people who answered, it has been really useful. The list is divided in two parts, "freeware" and "to buy". FREEWARE -------------------------------------------------------------------------- From: Elmar Gerwalin Subject: 3d visualisation Hi Luca A good tool for quickly drawing plots, surfaces ... from data tables is GNUPLOT. It's available on nearly every platform (PC(DOS+WIN),UNIX,...) and easy to install. It's very fast, has good export capabilities (PS,printerfiles,gif,...), only the usage is a bit strange, but you can learn it quickly. Just try it ! Hope that helps BYe Elmar -------------------------------------------------------------------------- From: Julius Su Subject: Re: CCL:3D visualisation software Hello, You should check out the Visualization Toolkit at http://iuinfo.tuwien.ac.at:8000/htdocs/vtk/. It does everything you mention and is platform independent. I would like to add to this section the link to SciAn, which is a very powerful software but unfortunately it runs only if you have GL capability. People at http://www.scri.fsu.edu/~lyons/scian declare it working on SGI and RS6000. Regarding GNUPLOT, I tried the last version but I didn't find any way to get isosurfaces. TO BUY -------------------------------------------------------------------------- From: Peter Tebbutt Subject: plotting hi Luca, You could try easyPlot which is marketed by Spiral Software in the states or Cherwell Scientific elswhere (URL below). -------------------------------------------------------------------------- From: Greg Paris Subject: re: isosurface visualization... Although not developed originally with molecular data types, the package from IBM called Data Explorer is reasonably platform independent, and is a good general purpose visualizer package. It is not free, but is, in my estimation, a good buy. You may wish to examine IBM's web pages that describe this product...: http://www.almaden.ibm.com/dx/ Best wishes, Greg Paris -------------------------------------------------------------------------- From: Jeffrey Gosper Subject: Re: CCL:3D visualisation software Re_View3, which is under constuction, can do isosurfacing of data like this, although at present we have concentrated on atoms data and some form of surrounding cube data. I'm still devloping the data interface so an suggestions are welcome. NB: Test versions of Re_View3 are available to those who purchase a departmental licence for Re_View. -------------------------------------------------------------------------- From: Ton van Daelen Subject: CCL:3D visualisation software Dear Luca - MSI's software developer's kit does exactly what you want. It includes an API set to visualize iso-surfaces, molecular structure, trajectories, normal modes, plots/graphs, etc. It also allows you in a few steps to put an interface together to any computational chemistry code. For general information about this toolkit visit: http://www.msi.com/support/sdk/ for specific information on plotting iso-surfaces visit: http://www.msi.com/support/sdk/users/examples/iso/README.html Regards - Ton -------------------------------------------------------------------------- From: Martin Leboeuf Subject: Re: 3D visualisation software Luca, Take a look at VU : http://www.cerca.umontreal.ca/vu. ciao, martin -------------------------------------------------------------------------- VU is a freeware for academic institution and they are really nice. I still have to try this software (thanks, Martin). Of course one could add the well known Explorer, once integrated in the IRIX OS and now commercialized by NAG (see http://www.nag.co.uk, for instance), as well as other packages like MATHEMATICA, MAPLE, and so on. Thank you again, I hope somebody will find this list useful. Regards Luca Dr. Luca Pedocchi Laboratorio di Chimica Fisica delle Interfasi via Cavour, 82 - 50129 Firenze - ITALY http://lcfs.chim.unifi.it/solid/pedocchi e-mail luca@lcfs.chim.unifi.it phone +39-55-2757793 fax +39-55-219802 Non esistono uomini cattivi, se sono cucinati bene (Stefano Benni) From hinsen@lmspc1.ibs.fr Thu Jul 10 05:51:05 1997 Received: from ibs.ibs.fr for hinsen@lmspc1.ibs.fr by www.ccl.net (8.8.3/950822.1) id FAA27614; Thu, 10 Jul 1997 05:10:10 -0400 (EDT) Received: from lmspc1.ibs.fr (hinsen@lmspc1.ibs.fr [192.134.36.141]) by ibs.ibs.fr (8.6.12/8.6.12) with ESMTP id LAA29872; Thu, 10 Jul 1997 11:11:22 +0200 Received: (from hinsen@localhost) by lmspc1.ibs.fr (8.8.5/8.8.5) id LAA18066; Thu, 10 Jul 1997 11:10:08 +0200 Date: Thu, 10 Jul 1997 11:10:08 +0200 Message-Id: <199707100910.LAA18066@lmspc1.ibs.fr> From: Konrad Hinsen To: serge@qsar.chem.msu.su CC: chemistry@www.ccl.net In-reply-to: <199707071145.PAA07805@org.chem.msu.su> (serge@qsar.chem.msu.su) Subject: Re: CCL:Object-oriented means for computational chemistry programming > FORTRAN still remains the main programming language of computational > chemistry. But > I wonder if anybody knew about the programs where methods computational > chemistry and, in particular quantum mechanical (ab initio or > semiempirical), MM or QM/MM force field methods are developed by means of > object-oriented languages (C++ preferably). I know Hyperchem is announced Have a look at the Molecular Modelling Toolkit at http://starship.skyport.net/crew/hinsen/mmtk.html It's an object-oriented library for molecular modelling, implemented mostly in Python (which is also the "scripting" language for users) with time-critical parts (force field evaluation, minimization, MD) in C. No ab-initio or QM/MM yet, but that would be a nice addition... MMTK is free, so there's no reason not to try it. The choice of an interpreted high-level language (Python) may come as a surprise, but the majority of algorithms in molecular modelling are not at all CPU intensive, although people happen to talk much about the number crunching parts. Using Python speeds up development tremendously. Further advantages: - Python is a complete general-purpose programming language, not a simplified scripting language. Instead of writing scripts for a modelling program, you write Python programs using the MMTK library. There is no restriction to what you can do in your programs. - Free combination of modelling libraries with more general-purpose Python libraries. Want non-standard visualization? Use the VRML module. Want a quick histogram of some quantity? Use the statistics and plotting modules. Want to have a long simulation produce a continuous progress report on a Web page? Use the HTML module. Want to post your results automatically to Usenet? Use the NNTP module. (Note: *don't* do that unless you like flame wars!) - An object-oriented description at the user level is very appropriate for molecular modelling. A C++ program would not offer that automatically; it would be object-oriented internally, but creating a user-level access to that description would be a major effort. - Portable binary data formats. No more problems with getting big files from the supercomputer to your desktop workstation. > Is there any benchmarks where their characteristics are presented as > compared to FORTRAN programs? Is there any sufficient difference in the > speed of computation? That is as much a question about compilers than about languages and programs. Recent issues of Computers in Physics have had several reports on C++ vs. Fortran for numerical efficiency. -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@ibs.ibs.fr Laboratoire de Dynamique Moleculaire | Tel.: +33-4.76.88.99.28 Institut de Biologie Structurale | Fax: +33-4.76.88.54.94 41, av. des Martyrs | Deutsch/Esperanto/English/ 38027 Grenoble Cedex 1, France | Nederlands/Francais ------------------------------------------------------------------------------- From guillem@dewar.uib.es Thu Jul 10 05:57:29 1997 Received: from dewar.uib.es for guillem@dewar.uib.es by www.ccl.net (8.8.3/950822.1) id FAA27658; Thu, 10 Jul 1997 05:22:31 -0400 (EDT) Received: by dewar.uib.es; id AA25553; Thu, 10 Jul 1997 11:21:42 +0200 Sender: guillem@dewar.uib.es Message-Id: <33C4A9A6.41C6@dewar.uib.es> Date: Thu, 10 Jul 1997 11:21:42 +0200 From: "Guillem A. Sunyer" Organization: Departament de Quimica, Universitat de les Illes Balears X-Mailer: Mozilla 3.0 (X11; I; OSF1 V3.2 alpha) Mime-Version: 1.0 To: Computational Chemistry List Subject: SUMMARY:G94 basis set for hydrogen transfer reactions Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Netters, Below you will find all the mssg I've received regarding ab initio H-transfer reactions and related basis set. Many thanks to: Milan Hodoscek, Lorne M. Fell and Ernest Chamot. My original post was: "Dear Netters, I would like to know some references regarding ab initio studies of hydrogen transfer reactions, in order to see which basis set are most suitables for such studies, and if the basis set election are a key point in such calculations. Many thanks in advance, Guillermo" ... and the mssg: ---------------------------------------------------------------- Subject: Hydrogen transfer Date: Tue, 8 Jul 1997 16:26:19 +0200 (METDST) From: Milan Hodoscek To: guillem@dewar.uib.es See for example: M. Hodoscek, D. Hadzi, Proton Transfer in the HCOOH . CH_3NH_2 Complex. Ab Initio Study With Various Basis Sets and Reaction Fields, (Theochem), 198, (1989), 461-473. ---------------------------------------------------------------- Subject: Re: CCL:G:G94 basis set for hydrogen transfer reactions Date: Tue, 8 Jul 1997 09:55:08 -0400 (EDT) From: "Lorne M. Fell" To: "Guillem A. Sunyer" Hello, I would be very interested to see what replies you receive. Will you summarize to the list? We have used various basis sets to optimize structures of radical cation hydrogen transfers, D95** seems to be one of the best, although cc-pVDZ (could be tried, I am unaware of sudies using this basis set), 6-31G* and 6-31G** have certainly been used extensively. Thank you, Lorne ============================================================================ Lorne M. Fell Department of Chemistry McMaster University a quote " Hamilton, Ont., Canada phone (905) 525-9140 x.23146 email: felllm@mcmail.cis.mcmaster.ca ============================================================================ ---------------------------------------------------------------- Subject: Re: CCL:G:G94 basis set for hydrogen transfer reactions Date: Tue, 8 Jul 97 10:30:32 +0100 From: "Ernest Chamot" To: "Guillem A. Sunyer" Dear Guillermo, You asked about: >. . . some references regarding ab initio studies of >hydrogen transfer reactions, in order to see which basis set are most >suitables for such studies, and if the basis set election are a key >point in such calculations. The most recent work I am aware of is by Dr. Branko Jursic at the University of New Orleans. In a pair of posters at last years ACS meeting, he had preprints of papers submitted to: Int. J. Quantum Chem., "The Computation Potential Energy Surface for H2 + OH -> H2O + H with Ab initio and Density Functional Theory Methods" and, J. Chem. Soc. Faraday Trans., "Computational Study of the CH4 + OH -> CH3 + H2O Reaction with ab Initio and Density Functional Theory Methods" I assume these are out in print, but don't have the issue and page number handy. They both compare several basis sets and levels of correlation. In my experience, CORRELATION has been the "key point" to include in H-transfer reaction calculations. There is also an older paper from the Truhlar group addressing a detail of a H(D) transfer reaction: J. Amer. Chem. Soc., 115, 7806-17 (1993), "Direct Dynamics Calculation of the Kinetic Isotope Effect for an Organic Hydrogen-Transfer Reaction, Including Corner-Cutting Tunneling in 21 Dimensions" I hope this helps. EC --- Ernest Chamot Chamot Labs, Inc. 530 E. Hillside Rd. Naperville, Illinois 60540 (630)637-1559 echamot@chamotlabs.com http://www.chamotlabs.com/cl ---------------------------------------------------------------- -- Dr Guillermo A. Suner; Dep. de Quimica, UNIVERSITAT DE LES ILLES BALEARS E-07071-Palma de Mallorca, SPAIN. E-mail: guillem@dewar.uib.es Tel: + 34 71 173498 Fax: + 34 71 173426 WWW URL: http://www.uib.es/depart/dqu/dquo/suner.html From hayden@chemcomp.com Thu Jul 10 12:06:14 1997 Received: from bobino.sefmedia.com for hayden@chemcomp.com by www.ccl.net (8.8.3/950822.1) id KAA29490; Thu, 10 Jul 1997 10:51:50 -0400 (EDT) Received: from [205.236.86.174] by bobino.sefmedia.com (NTMail 3.02.13) with ESMTP id ta005921 for ; Thu, 10 Jul 1997 10:52:02 -0400 Message-Id: <1.5.4.16.19970710103930.410723d6@mail.chemcomp.com> X-Sender: hayden@mail.chemcomp.com X-Mailer: Windows Eudora Light Version 1.5.4 (16) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@www.ccl.net From: "William A. Hayden" Subject: Apple MacIntosh Platform Feedback Date: Thu, 10 Jul 1997 10:52:02 -0400 CHEMICAL COMPUTING GROUP is currently surveying scientists in order to obtain their feedback on usage of the Apple Mac in research. The purpose is to help us gauge the feasibility of porting our chemical computing software, MOE - Molecular Operating Environment, to the Mac. If you are interested in participating in the survey (it will only take a couple of minutes on the phone or if you like, email) please email us at: hayden@chemcomp.com with your phone number and email. To find out more about MOE, please visit our web site at: http://www.chemcomp.com Thank you, Bill Hayden Vice President CHEMICAL COMPUTING GROUP hayden@chemcomp.com 514 393 1055 - phone 514 874 9538 - fax From jmbriggs@chemcca10.ucsd.edu Thu Jul 10 12:15:24 1997 Received: from mailbox1.ucsd.edu for jmbriggs@chemcca10.ucsd.edu by www.ccl.net (8.8.3/950822.1) id LAA29674; Thu, 10 Jul 1997 11:34:39 -0400 (EDT) Received: from chemcca10.ucsd.edu (chemcca10.ucsd.edu [132.239.68.250]) by mailbox1.ucsd.edu (8.8.5/8.6.9) with SMTP id IAA29025 for <@ucsd.ucsd.edu:CHEMISTRY@www.ccl.net>; Thu, 10 Jul 1997 08:33:40 -0700 (PDT) Received: by chemcca10.ucsd.edu (950511.SGI.8.6.12.PATCH526/931108.SGI.ANONFTP) id IAA29437; Thu, 10 Jul 1997 08:33:30 -0700 From: jmbriggs@chemcca10.ucsd.edu (Jim Briggs) Message-Id: <199707101533.IAA29437@chemcca10.ucsd.edu> Subject: NAS Colloquium announcement To: CHEMISTRY@www.ccl.net Date: Thu, 10 Jul 1997 08:33:30 -0700 (PDT) Cc: mpotter@chemcca10.ucsd.edu (Mike Potter), vhelms@chemcca10.ucsd.edu (Volkhard Helms), jmbriggs@chemcca10.ucsd.edu (Jim Briggs) Reply-To: jmbriggs@ucsd.ucsd.edu Organization: University of California, San Diego X-URL: http://chemcca10.ucsd.edu/~jmbriggs/ X-Mailer: ELM [version 2.4 PL25] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit *********************************************************************** NATIONAL ACADEMY OF SCIENCES COLLOQUIUM ON COMPUTATIONAL BIOMOLECULAR SCIENCE 11-13 September 1997 Beckman Center of the National Academies of Sciences and Engineering Irvine, California Dear Colleague, We are pleased to invite you to attend the NAS "Colloquium on Computational Biomolecular Science," to be held in Irvine, California, September 11-13, 1997. The Colloquium is intended to stimulate interdisciplinary discussion across the areas of biomolecular structure, function, and evolution, and to point to ways in which computation can help to explore the interfaces among these areas. Attendance will be limited to about 200 participants. A diverse group of speakers will provide points of departure for the discussion, but ample time will be allowed for general and informal elaboration. The speakers will include Peer Bork (EMBL, Heidelberg) Wen-Hsiung Li (Univ. Texas, Houston) Douglas Brutlag (Stanford) Alexey Murzin (MRC, Cambridge) William Eaton (NIH) Jose Onuchic (UCSD) Ron Elber (Hebrew Univ) Gregory Petsko (Brandeis) Hans Frauenfelder (Los Alamos) Robert Sauer (MIT) Elizabeth Getzoff (Scripps Research Harold Scheraga (Cornell) Institute) Klaus Schulten (Illinois) Philip Green (Univ. Washington) Rebecca Wade (EMBL, Heidelberg) Angela Gronenborn (NIH) Arieh Warshel (USC) Michael Levitt (Stanford) The meeting is planned to extend from the late afternoon of September 11 (registration and a light dinner/reception), through September 13, so that participants can depart early on September 14. The meeting will be held at the Academy's conference center in Irvine. If you would like to join us for this Colloquium, please send the attached registration form and your registration fee of $200 (which includes the cost of all meals for 11-13 September) as soon as possible to Dr. Edward Patte at the address indicated on the form. Please feel free to duplicate the form and extend the invitation to any students or colleagues you feel would contribute to this discussion. A block of rooms has been reserved at the hotel for the Colloquium. Please contact National Academies Travel (NAT) rather than calling the hotel directly, to make your reservations. Main reservations: 800-801-6696 or 202-298-9046 Receptionist: 202-298-1637 Fax: 202-338-2366 When contacting NAT, please refer to event name - Computational Biomolecular Science event code - BE02066 event date - September 11-13, 1997 hotel name - Hyatt Newporter Resort 1107 Jamboree Rd. Newport Beach, CA 92660 Please reserve your room before August 15, because the rooms will be released shortly after this date. We hope that you will be able to join us for this unusual Colloquium. Russell Doolittle (rdoolittle@ucsd.edu) J. Andrew McCammon (jmccammon@ucsd.edu) Peter G. Wolynes (wolynes@aries.scs.uiuc.edu) --------------------------------- cut here --------------------------------------- NATIONAL ACADEMY OF SCIENCES COLLOQUIUM "COMPUTATIONAL BIOMOLECULAR SCIENCE" REGISTRATION FORM Please complete and return this form to: Dr. Edward Patte NAS-146 National Academy of Sciences 2101 Constitution Avenue, NW Washington, DC 20418 FAX CREDIT CARD PAYMENTS ONLY: (202) 334-2153 Name________________________________________________________ Title_______________________________________________________ Company Name________________________________________________ Address_____________________________________________________ ____________________________________________________________ ____________________________________________________________ Phone_______________________________________________________ Email_______________________________________________________ Arrival Date___________________ Time________________________ Departure Date_________________ Time________________________ Registration fee of $200 (nonrefundable) includes all meals during meeting: ____ Registration check in U.S. dollars payable to "National Academy of Sciences" ___ Credit Card registration payable to "National Academy of Sciences" Charge to: ___Visa ___MasterCard ___American Express Card number_____________________________________ Expires_________ Signature_______________________________________ Date____________ My special dietary needs are as follows:_______________________________ _______________________________________________________________________ _______________________________________________________________________ *********************************************************************** -- Jim Briggs, Ph.D. Department of Pharmacology University of California, San Diego La Jolla, CA 92093-0365 Phone: (619)534-0956 FAX: (619)534-7042 e-mail: JMBriggs@UCSD.EDU WWW: http://chemcca10.ucsd.edu/~jmbriggs/ From kneth@chem.ruc.dk Wed Jul 9 05:50:51 1997 Received: from koala.ruc.dk for kneth@chem.ruc.dk by www.ccl.net (8.8.3/950822.1) id FAA20397; Wed, 9 Jul 1997 05:39:45 -0400 (EDT) Received: from localhost (kneth@localhost) by koala.ruc.dk (8.8.5/8.8.5) with SMTP id LAA12851; Wed, 9 Jul 1997 11:38:22 +0200 Date: Wed, 9 Jul 1997 11:38:22 +0200 (CEST) From: Kenneth Geisshirt X-Sender: kneth@koala.ruc.dk To: "B. Kallies" cc: chemistry@www.ccl.net Subject: Re: CCL:Definition of van Hove function (MD) In-Reply-To: <9707070715.AA22026@serv.chem.uni-potsdam.de> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi all, > I'm wondering if anyone knows the definition of the van Hove function. The van Hove correlation function is defined as: N N 1 / --- --- / \ G(r, t) = --- < > > |(delta(r'+r-r(i,t))*delta(r-r(j,0))dr' > N \ --- --- / / i=1 j=1 where delta is Dirac's delta function and the bracket is the (ensemble) average. > Any information would be helpful. Thanks in advance. Reference: Theory of Simple Liquids by J.P. Hansen and I.R McDonald. Best wishes Kenneth +-------------------------------------------------------------+ | Kenneth Geisshirt Ph.D.-student | | Dept. of Life Sciences and Chemistry Roskilde University | +-------------------------------------------------------------+ | E-mail: kneth@chem.ruc.dk Phone: +45 4675 7711, ext 2785 | +-------------------------------------------------------------+ From ccl@www.ccl.net Wed Jul 9 12:50:57 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id MAA21795; Wed, 9 Jul 1997 12:00:20 -0400 (EDT) Received: from gtc05f for reddy@gensia.com by bedrock.ccl.net (8.8.6/950822.1) id LAA20086; Wed, 9 Jul 1997 11:57:43 -0400 (EDT) Received: from genny (genny.res.gensia.com) by gtc05f (5.x/SMI-SVR4) id AA20616; Wed, 9 Jul 1997 08:58:42 -0700 Received: by genny (940816.SGI.8.6.9/930416.SGI.AUTO) id MAA22620; Wed, 9 Jul 1997 12:19:47 GMT Date: Wed, 9 Jul 1997 05:19:46 +48000 From: Rami Reddy To: CHEMISTRY@ccl.net Subject: Re: CCL:Re: CCL:FEP binding energy In-Reply-To: Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On 7 Jul 1997, Arne Elofsson wrote: > Soaring Bear writes: > > > Greetings: > > > > > > I have noticed that published studies of FEP energy calculations > > of inhibitor binding are largely on a pairwise basis, comparing > > small numbers of inhibitors (presumably due to computational cost). > > I am interested in locating studies which have compared at least > > a dozen. I would appreciate any references. Also, any > > examples with structure based affinity calculation (especially > > linear response approximation)? > > > Dear Dr. Bear, Reddy et al evaluated a large set of related analogs using computer-assisted drug design methods that combine molecular mechanics, dynamics, FEP calculations, inhibitor design, synthesis, biochemical testing, and crystallographic structure determination of the protein-inhibitor complexes. The calculated relative binding free energies were successfully incorporated into the design of novel HIV1 protese inhibitors. This study involved a large set of molecules whose relative binding affinities were predicted using FEP method prior to synthesis, and were later confirmed by experimental measurements. Reddy et al. J. Med. Chem. 37 (1994), 1145-1152 If you have any questions or comments please let know. M. Rami Reddy Metabasis Therapeutics, Inc Email: reddy@gensia.com From ccl@www.ccl.net Wed Jul 9 12:51:12 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id MAA21962; Wed, 9 Jul 1997 12:23:10 -0400 (EDT) Received: from indigo14.carb.nist.gov for gilson@indigo14.carb.nist.gov by bedrock.ccl.net (8.8.6/950822.1) id MAA20775; Wed, 9 Jul 1997 12:23:08 -0400 (EDT) Received: (from gilson@localhost) by indigo14.carb.nist.gov (8.7.5/8.7.3) id MAA29342; Wed, 9 Jul 1997 12:23:08 -0400 (EDT) Date: Wed, 9 Jul 1997 12:23:08 -0400 (EDT) Message-Id: <199707091623.MAA29342@indigo14.carb.nist.gov> From: "Dr. Mike Gilson" To: chemistry@ccl.net Subject: Database for Molecular Binding and Recognition Dear Colleagues, We are interested in creating a publicly accessible database containing information on noncovalent binding affinities, with an emphasis on biomolecules. Such a database could be useful in a range of applications, including drug-discovery and the development of computational models for predicting affinities. We hope to establish a stable, expanding resource that will be helpful to many scientists over a period of years. This is a complex and somewhat ill-defined task, however. It is necessary to define the scope of the data to be included, to implement the database effectively, and to establish mechanisms for filling and maintaining it. Before taking these steps, we would like to learn of any similar efforts in the scientific community in order to avoid duplication of effort. We also would like to consult with people interested in using the database, whether as depositors or users of the data. Finally, we would like to be sure that the utility of this database will justify the effort of creating it. This message, then, is to solicit your advice and suggestions on these topics. In order to permit a general exchange of views, we have established a web-site that will allow comments and subsequent discussion to be posted publicly. The URL is http://db3.sdsc.edu/DbNcB/. We would very much appreciate your participation. With best regards, Phil Bourne Mike Gilson San Diego Supercomputer Center Center for Advanced Research in Biotechnology gilson@indigo14.carb.nist.gov Nick Hodge Craig Wilcox Computer-Aided Drug Design Group Department of Chemistry The DuPont Merck Pharmaceutical Company University of Pittsburgh From ccl@www.ccl.net Wed Jul 9 15:45:59 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id PAA22996; Wed, 9 Jul 1997 15:02:22 -0400 (EDT) Received: from relay1.scripps.edu for pelleque@scripps.edu by bedrock.ccl.net (8.8.6/950822.1) id PAA27803; Wed, 9 Jul 1997 15:02:21 -0400 (EDT) Received: from scfv.scripps.edu (scfv.scripps.edu [137.131.240.32]) by relay1.scripps.edu (8.8.5/TSRI-1.5) with SMTP id MAA20360 for ; Wed, 9 Jul 1997 12:02:18 -0700 (PDT) Received: by scfv.scripps.edu (5.x/SMI-SVR4) id AA05165; Wed, 9 Jul 1997 12:02:18 -0700 Date: Wed, 9 Jul 1997 12:02:18 -0700 From: pelleque@scripps.edu (Jean-Luc Pellequer) Message-Id: <9707091902.AA05165@scfv.scripps.edu> To: chemistry@ccl.net Subject: Gaussian 94 optimization X-Sun-Charset: US-ASCII Hi, I am a beginner with Gaussian 94 and would like to know if it is possible to partialy optimize geometry using only cartesian coordinates. Thank you very much, Jean-Luc Pellequer pelleque@scripps.edu From ccl@www.ccl.net Wed Jul 9 15:46:05 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id PAA23009; Wed, 9 Jul 1997 15:05:35 -0400 (EDT) Received: from voimax.voima.jkl.fi for eloranta@voimax.voima.jkl.fi by bedrock.ccl.net (8.8.6/950822.1) id PAA27898; Wed, 9 Jul 1997 15:05:33 -0400 (EDT) Received: (from eloranta@localhost) by voimax.voima.jkl.fi (8.8.5/8.8.5) id WAA06171 for chemistry@ccl.net; Wed, 9 Jul 1997 22:05:42 +0300 From: Jussi Eloranta Message-Id: <199707091905.WAA06171@voimax.voima.jkl.fi> Subject: Summary of SC-IPCM query To: chemistry@ccl.net Date: Wed, 9 Jul 1997 22:05:42 +0300 (EET DST) Content-Type: text Dear netters, Sometime ago I posted a query about references for the SC-IPCM method. Here is the summary of the replies I got - thanks to all who replied. It appears that currently there is no paper describing the SC-IPCM method exactly, altough the references for the IPCM method reveal most of the practical information. Regards, Jussi Eloranta ---- CUT ---- My original posting: Does anyone know references for the SCI-PCM solvent model as implemented in Gaussian 94? The Gaussian manual gives four references which all are under preparation and I was not able to find out if these have been published now. "Exploring Chemistry with Electronic Structure Methods (2nd ed.)" also points to one of these unpublished articles. Also a pointer to good review article on the solvent models would be very helpful. Answers: -------------------------------------- landin@mednet.gu.se wrote: An extensive review on solvation methods has been written by Tomasi et.al. [1] , if merely an overview is desired consult instead Cramer & Truhlar [2] . 1. Tomasi, J. and M. Persico, Molecular Interactions in Solution: An Overview of Methods Based on Continuous Distributions of the Solvent. Chem. Rev., 1994. 94(7): p. 2027-2094. 2. Cramer, C.J. and D.G. Truhlar, Development and Biological Applications of Quantum Mechanical Continuum Solvation Models, in Quantitative Treatments of Solute/Solvent Interactions, P. Politzer and J.S. Murray, Editors. Vol. 1. 1994, Elsevier Science B. V.: Amsterdam. p. 9-54. --------------------------- mbdtsnm@mchhpf.ch.man.ac.uk wrote: as far as i know there have still been no 'published' accounts of the sci-pcm methods - though i assume that the theory will be very similar to the "IPCM" method which has has a couple of published references.(i don't have them handy but can get them if necessary - they should be easy enough to locate). Just out of interest i think there is a paper coming out in the Aug. 15th edition of J.Chem.Phys. from the lab of J. Tomasi which sets out a new definition of teh cavity surface in the PCM model ( i think that it will be more akin to a connolley type surface with concave parts.) -------------------------- arilahti@ra.abo.fi wrote (loosely translated text): I performed a literature search about SCIPCM about two weeks ago but it appears that the publication is still in preparation. The situation is rather strange because people are working with the model but no one can look at the method more closely. People tend to use the Gaussian manual or the "exploring chemistry with electronic structure methods" as a reference for the method. ------------------------------ albeiro@chemindy.sci.fau.edu wrote: Please check out JACS, 1996, 118, 5408 and the references cited on the methodolgy section. ----- CUT ------- From kotelyan@plmsc.psu.edu Wed Jul 9 17:50:56 1997 Received: from plmsc.psu.edu for kotelyan@plmsc.psu.edu by www.ccl.net (8.8.3/950822.1) id RAA24703; Wed, 9 Jul 1997 17:48:12 -0400 (EDT) Received: (from kotelyan@localhost) by plmsc.psu.edu (8.8.2/8.8.2) id RAA16977; Wed, 9 Jul 1997 17:47:57 -0400 (EDT) Date: Wed, 9 Jul 1997 17:47:56 -0400 (EDT) From: Mike Kotelyanskii To: "B. Kallies" cc: chemistry@www.ccl.net Subject: Re: CCL:Definition of van Hove function (MD) In-Reply-To: <9707070715.AA22026@serv.chem.uni-potsdam.de> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Very nice discussion of the Van Hove Function can be found in the book by J.Higgins and Benoit "Neutron Scattering from Polymers" (Title may not be very accurate, but it sounds like that) If I am not mistaken Allen & Tildesley's "Computer Simulation of Liquids" has it too Hope it helps Mike ------------------------------------------------------------------------------- Michael J. Kotelyanskii Phone (814) 863 43 81 Polymer Science Program FAX (814) 865 29 17 Department of Materials Science and Engineering kotelyan@plmsc.psu.edu Pennsylvania State University University Park, PA 16802, USA -------------------------------------------------------------------------------- On Mon, 7 Jul 1997, B. Kallies wrote: > > > > Dear Colleagues, > > I'm wondering if anyone knows the definition of the van Hove function. I > know that it is used to describe time-space correlation in MD simulations of > solutions in order to calculate relaxation times of ordered structures like > solvent shells. > > Any information would be helpful. Thanks in advance. > > > ----------------------------------------------------- > Dr. Bernd Kallies > Institut fuer Physikalische und Theoretische Chemie > Universitaet Potsdam > Am Neuen Palais 10 > 14469 Potsdam > GERMANY > e-mail: kallies@serv.chem.uni-potsdam.de > WWW : http://www.chem.uni-potsdam.de/~kallies/kallies.htm > Tel : [+49] (0)331 / 977-1313 > Fax : [+49] (0)331 / 977-1315 > ----------------------------------------------------- > > > > --- > 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 LONGO@NPD.UFPE.BR Thu Jul 10 16:06:42 1997 Received: from NPD1.NPD.UFPE.BR for LONGO@NPD.UFPE.BR by www.ccl.net (8.8.3/950822.1) id PAA01318; Thu, 10 Jul 1997 15:44:23 -0400 (EDT) From: Received: from NPD.UFPE.BR by NPD.UFPE.BR (PMDF V5.1-4 #20469) id <01IL2U3K2M060003H8@NPD.UFPE.BR> for chemistry@www.ccl.net; Thu, 10 Jul 1997 16:43:39 GMT-3 Date: Thu, 10 Jul 1997 16:43:39 +0000 Subject: NaY Structure To: chemistry@www.ccl.net Message-id: <01IL2U3K2M080003H8@NPD.UFPE.BR> X-VMS-To: IN%"chemistry@www.ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Hi CCLers, I'd appreciate if anyone could send me the coordinates (xyz, pdb, etc.) for the NaY zeolites with any Si/Al ratio. I'll make them available. Thanks a lot. Ricardo Longo DQF - UFPE longo@npd.ufpe.br Recife, PE - Brazil From fgonzale@lauca.usach.cl Thu Jul 10 18:06:15 1997 Received: from ralun.usach.cl for fgonzale@lauca.usach.cl by www.ccl.net (8.8.3/950822.1) id SAA02886; Thu, 10 Jul 1997 18:03:14 -0400 (EDT) Received: from lauca.usach.cl (lauca.usach.cl [158.170.64.28]) by ralun.usach.cl (8.6.11/8.6.9) with ESMTP id SAA24223 for ; Thu, 10 Jul 1997 18:12:24 -0500 Received: (from fgonzale@localhost) by lauca.usach.cl (8.6.12/8.6.12) id SAA02656; Thu, 10 Jul 1997 18:06:49 -0400 Date: Thu, 10 Jul 1997 18:06:48 -0400 (CST) From: Fdo Danilo Gonzalez Nilo To: chemistry@www.ccl.net Subject: G94 on LINUX/Win95 Message-ID: MIME-Version: 1.0 Content-Type: MULTIPART/MIXED; BOUNDARY="LAA23189.868551052/ralun.usach.cl" Content-ID: This message is in MIME format. The first part should be readable text, while the remaining parts are likely unreadable without MIME-aware tools. Send mail to mime@docserver.cac.washington.edu for more info. --LAA23189.868551052/ralun.usach.cl Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Content-ID: Hi All! I'm looking for any information about performance of calculations with G94 in the OS LINUX and Win95. Anybody have any experience on this system?, time CPU comparison between this two OS. Thanks a Lot! ************************************************************************* Fernando Danilo Gonzalez N. Universidad de Santiago de Chile Facultad de Quimica y Biologia Casilla 40, Correo 33, Santiago, Chile fono: 681 2575 E-mail : fgonzale@lauca.usach.cl fax : (562) 681 2108 danilo@quimbio.usach.cl URL : http://quimbio.usach.cl/~danilo/ *************************************************************************x --LAA23189.868551052/ralun.usach.cl-- From mn1@helix.nih.gov Thu Jul 10 18:12:45 1997 Received: from helix.nih.gov for mn1@helix.nih.gov by www.ccl.net (8.8.3/950822.1) id RAA02856; Thu, 10 Jul 1997 17:54:35 -0400 (EDT) Received: (from mn1@localhost) by helix.nih.gov (8.8.5/8.8.5) id RAA07432; Thu, 10 Jul 1997 17:54:37 -0400 (EDT) Date: Thu, 10 Jul 1997 17:54:37 -0400 (EDT) From: "M. Nicklaus" Message-Id: <199707102154.RAA07432@helix.nih.gov> To: CHEMISTRY@www.ccl.net Subject: Re: G:Gaussian on a Mac ? ---Or Other Platforms Cc: mn1@helix.nih.gov Hi, On Thu, 10 Jul 97, "Frederick R. Bennett" I know that Gaussian Inc. hates this sort of thing but I will ask anyway. I > am wondering whether anyone has G94 running on a PowerMac running one of the > Linux operating systems (MKLinux or the non-Micro Kernal). > > Just as a matter of opinion, I think that Gaussian Inc. should seriously > consider supporting this platform, as they do the various Unices running on > Intel machines. The motorola PowerPC chips are leaving Intel Pentiums for > dead at the moment and with the new generation motorola chips on the way > out, fast system buses and new cacheing technology, Mac's or Mac clones > should/can provide the hardware for some high power/cost ratio workstations > for chemistry. Since this can has been opened, let me chip in with a remark and a question. 1. I agree with Frederick R. Bennett in that Gaussian Inc. should support more of the new fast, and *cheap*, platforms such as PowerPC systems running Linux. I'd like to expand this request to include Alpha CPU systems running axp Linux. These chips are even faster than the PowerPC's. We've benchmarked them with other software. 500 MHz machines (non-DEC) can be had for $5,000-6,000. The 600 MHz 21164 chip based systems are basically shipping (albeit expensive, ~$11k), and the 800 MHz CPUs are in the pipeline. 2. We've tried to compile G94, Rev. E.1 for such a 21164 500 MHz Alpha based system, running RedHat Linux 4.1, kernel v. 2.0.27 --- unfortunately, unsuccessfully so far. We've experienced problems with f2c, gcc, as well as the linker. So therefore my question: Has anyone been able to get G94 to run on this platform? If yes, how? I'll summarize for the list if I get useful responses. Marc ------------------------------------------------------------------------ Marc C. Nicklaus National Institutes of Health E-mail: mn1@helix.nih.gov Bldg 37, Rm 5B29 Phone: (301) 402-3111 BETHESDA, MD 20892-4255 USA Fax: (301) 496-5839 http://www.nci.nih.gov/intra/lmch/MCNBIO.HTM Laboratory of Medicinal Chemistry, National Cancer Institute, & Lab. of Structural Biology, Div. of Computer Research and Technology ------------------------------------------------------------------------ From support@mathtrek.com Thu Jul 10 19:06:16 1997 Received: from granite.sentex.net for support@mathtrek.com by www.ccl.net (8.8.3/950822.1) id TAA03089; Thu, 10 Jul 1997 19:03:21 -0400 (EDT) Received: from p10a.lithium.sentex.ca (p10a.lithium.sentex.ca [207.245.212.171]) by granite.sentex.net (8.8.5/8.6.9) with SMTP id TAA20105; Thu, 10 Jul 1997 19:12:35 -0400 (EDT) Message-Id: <3.0.16.19970710190111.2a5fcde4@mathtrek.com> X-Sender: mathtrek@mathtrek.com X-Mailer: Windows Eudora Pro Version 3.0 (16) Date: Thu, 10 Jul 1997 19:01:14 -0400 To: chemistry-request@www.ccl.net, Konrad Hinsen , serge@qsar.chem.msu.su From: "W. R. Smith" Subject: Re: CCL:Object-oriented means for computational chemistry programming Cc: chemistry@www.ccl.net Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Hello, Who says FORTRAN cannot be "object-oriented"? How about Windows FORTRAN .DLL's, or other types of FORTRAN libraries? Please enlighten me if I'm off-base, but it seems to me that the entire "object-oriented thing" is simply a modern version of what we used to call a "subroutine" in FORTRAN. The only difference is that one must adopt an accepted convention to define the ways in which the "object" \equiv "subroutine" communicates with the outside world. At 11:10 AM 7/10/97 +0200, Konrad Hinsen wrote: >> FORTRAN still remains the main programming language of computational >> chemistry. But >> I wonder if anybody knew about the programs where methods computational >> chemistry and, in particular quantum mechanical (ab initio or >> semiempirical), MM or QM/MM force field methods are developed by means of >> object-oriented languages (C++ preferably). I know Hyperchem is announced > -- W. R. Smith, PhD, P. Eng., Senior Scientist, Mathtrek Systems -- 3-304 Stone Road West, Suite 165, Guelph, Ontario CANADA N1G 4W4 EMail: support@mathtrek.com Tel:519-763-1356,FAX:519-763-4525 --------------------- http://www.mathtrek.com --------------------- -Mathtrek Systems - Home of EQS4WIN Chemical Equilibrium Software - From frenz@fs.cc.ocha.ac.jp Thu Jul 10 22:06:16 1997 Received: from fs.cc.ocha.ac.jp for frenz@fs.cc.ocha.ac.jp by www.ccl.net (8.8.3/950822.1) id VAA03583; Thu, 10 Jul 1997 21:29:06 -0400 (EDT) Received: from mozart ([133.65.49.251]) by fs.cc.ocha.ac.jp (5.x/OchaFs-R1.0.0) id AA19225; Fri, 11 Jul 1997 10:21:44 +0900 Date: Fri, 11 Jul 1997 10:21:44 +0900 Message-Id: <9707110121.AA19225@fs.cc.ocha.ac.jp> X-Sender: frenz@fs.cc.ocha.ac.jp X-Mailer: Windows Eudora Light Version 1.5.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: From: Franz Renz Subject: CCL:Summary: Which method is better for a rather big molecule. Hi, Thanks for the advice. Here's the summary. Hi, All, I want to optimize the conformations of some big molecules, for example, N-methyl-N-octadecylanaline. I think RHF or DFT methods are not suitable for this kind big system. Also, some semi-empirical methods are not accurate enough for such calculations. Which method can do this kind work? Thank you very much! Y. FAN =================================================== FAN, Yubo Department of Chemistry Fudan University Shanghai, 200433 P. R. China Voice(86-21)65492222-4294 =================================================== Hello, Your molecule is not as big as you think. Have you tried the RIS method to find the minimum potential energy conformation ? My friends once studied the polybenzozaxine dimer using this method, and it worked very well. But you have to write the code or find a package containing RIS module. Good luck. On Mon, 16 Jun 1997, [CN-GB] ~{76S}2(~} wrote: A classic way of handling a molecule of this size is to break it down to logical pieces. Perhaps do at least two optimizations 1) N-ethyl-N-methylanaline, 2) N-dimethyl-N-alkylamine. Personally, I don't know of any other way. -- Luke Anthony Burke tel:609-225-6158 (-6142) Professor and Chair, fax:609-225-6506 Department of Chemistry e-mail: Rutgers University burke@camden.rutgers.edu Camden, NJ 08102, USA http://camchem.rutgers.edu/~burke I think the best way is to do a DFT calculation, starting with B3LYP/4-31G DFT is a good method for large molecules. bye, *-----*-----*-----*-----*-----*-----*-----* / / / Anselmo Elcana de Oliveira / * Cidade Universitaria Zeferino Vaz * / IQ - UNICAMP CEP 13083-970 \ / Campinas, SP - Brasil \ * elcana@iqm.unicamp.br * / http://chope.iqm.unicamp.br \ / \ * To err is human, * / To really foul up requires the root password \ / \ *-----*-----*-----*-----*-----*-----*-----*-----*-----*-----* You may use RHF with small basis sets. However, it still depends how many memory your computer has. ================================================================= Dr. Buyong Ma buyong@ibmnla.chem.uga.edu Computational Center for Molecular Structure and Design Department of Chemistry University of Georgia Athens, Georgia 30602 USA Voice (706) 542-2044 ================================================================= On Mon, 16 Jun 1997, [CN-GB] ~{76S}2(~} wrote: Optimize? You did not indicate what you wish to optimize but I shall assume that you are looking for the global minimum, i.e. the conformation with the minimum energy. This is a non-trivial task and you want to use classical methods to search conformational space for candidates. I use molecular dynamics at 1000 K or 2000 K. I have also used Crippen's distance geometry algorithm. Jeff Blaney has written a nice implementation of distance geometry which is available through QCPE. Once you have sampled conformational space, you need to minimize each structure using molecular mechanics and then sort the structures as to energy. If you want a good ab initio energy, you then want to apply quantum-mechanical methods to the best structures identified by the classical approach. You won't be able to do the entire problem quantum mechanically. Millions of structures are involved. ___ _ | 1 | _ \= / / \ \ =/ >---------< ( @ @ ) -------oOOo----(_)----oOOo-------------------------------------- Franz RENZ O C H A N O M I Z U University Faculty of Science, Department of Chemistry (Dr. Dipl.-Ing.) 2-1-1, Otsuka, Bunkyo-ku, Tokyo 112, JAPAN JSPS-Fellow) Tel.:+81-3-5978-5291, Fax.: +81-3-5978-5898 E-mail: frenz@fbch.tuwien.ac.at .oooO ( ) Oooo. ----------\ (----( )------------------------------------------ \_) ) / (_/ From taisung@chem.duke.edu Thu Jul 10 22:13:02 1997 Received: from chem.duke.edu for taisung@chem.duke.edu by www.ccl.net (8.8.3/950822.1) id VAA03448; Thu, 10 Jul 1997 21:12:59 -0400 (EDT) Received: from debye.chem.duke.edu (debye.chem.duke.edu [152.3.169.112]) by chem.duke.edu (8.7.4/Duke-1.1) with ESMTP id VAA10015; Thu, 10 Jul 1997 21:13:02 -0400 (EDT) Received: (taisung@localhost) by debye.chem.duke.edu (8.7.4/Duke-1.1) id VAA26265; Thu, 10 Jul 1997 21:13:01 -0400 (EDT) Date: Thu, 10 Jul 1997 21:13:00 -0400 (EDT) From: Taisung Lee X-Sender: taisung@debye To: "W. R. Smith" cc: chemistry-request@www.ccl.net, chemistry@www.ccl.net Subject: Re: CCL:Object-oriented means for computational chemistry programming In-Reply-To: <3.0.16.19970710190111.2a5fcde4@mathtrek.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Correct me if I am wrong. Object-oriented is a style of programming. FORTRAN can do almost anything that an object-oriented language can do. However, it doesn't mean it can be object-oriented. The reason to use object-oriented languages is to simplify the task of programming. For example, FORTRAN77 can not define a private subroutine. Each subroutine is global. Thus you need to check every subroutine name before you write a new one. Experts reading CCL should be able to provide more simple examples. About .DLL libraries in Windows, they are objects, but not full-function objects. In FORTRAN there is no way to construct or destruct a subroutine in the run-time. You can not make many copies of one subroutine. There is no virtual function/overload function calls in FORTRAN. Certainly you can not define templates for subroutine.... If you have learned C++, you will find how different it is from FROTRAN. As I know, it is more difficult for those who already know FORTRAN to learn C++ than those who don't have any programming experience. Just because they are totally different worlds. In my opinion, most of program packages for computational chemistry are very difficult to modify when the program is big. The main reason is they are written in FORTRAN. The source code of MS-Windows NT is more than 1,000,000 lines. I don't believe anyboday on the earth has the ability to write a working FORTRAN program with 1,000,000 lines. Taisung Lee Research Associate Dept. of Chemistry Duke University > Hello, > > Who says FORTRAN cannot be "object-oriented"? How about Windows > FORTRAN .DLL's, or other types of FORTRAN libraries? Please enlighten me > if I'm off-base, but it seems to me that the entire "object-oriented thing" > is simply a modern version of what we used to call a "subroutine" in > FORTRAN. The only difference is that one must adopt an accepted convention > to define the ways in which the "object" \equiv "subroutine" communicates > with the outside world. >