From lai@csb0.IPC.PKU.EDU.CN Wed Nov 12 02:32:33 1997 Received: from csb0.IPC.PKU.EDU.CN for lai@csb0.IPC.PKU.EDU.CN by www.ccl.net (8.8.3/950822.1) id CAA09443; Wed, 12 Nov 1997 02:19:18 -0500 (EST) Received: by csb0.IPC.PKU.EDU.CN (920330.SGI/940406.SGI.AUTO) for CHEMISTRY@www.ccl.net id AA05879; Wed, 12 Nov 97 14:19:00 -0800 Date: Wed, 12 Nov 1997 14:19:00 -0800 (PST) From: "Prof. Luhua LAI" To: CHEMISTRY@www.ccl.net Subject: Examples for Main Chain Flexible Docking Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers: We are studying main chain flexibility in protein-protein or protein-ligand docking. We would like to find some examples where protein main chain conformation changes significantly when binds with other molecule. Could someone give me a few examples? Thanks in advance. Luhua Lai ----------------------------------------- Luhua Lai Institute of Physical Chemistry & Department of Chemistry Peking University Beijing 100871 CHINA Phone: 86-10-62751490 Fax: 86-10-62751725 E-mail: lai@ipc.pku.edu.cn ----------------------------------------- From tamasgunda@tigris.klte.hu Wed Nov 12 05:32:34 1997 Received: from tigris.klte.hu for tamasgunda@tigris.klte.hu by www.ccl.net (8.8.3/950822.1) id FAA10152; Wed, 12 Nov 1997 05:08:38 -0500 (EST) Message-Id: <199711121008.FAA10152@www.ccl.net> Received: from anti02 (anti02.chem.klte.hu) by tigris.klte.hu (MX V4.1 VAX) with SMTP; Wed, 12 Nov 1997 08:56:07 +0100 Comments: Authenticated sender is From: "Tamas Gunda" To: chemistry@www.ccl.net Date: Wed, 12 Nov 1997 09:01:47 +1 MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7BIT Subject: medicinal chemistry Priority: normal X-mailer: Pegasus Mail for Windows (v2.42a) Dear CCL'ers, Maybe those who are dealing with drug research & development, could suggest me an alternative book for T. Nogrady's Medicinal Chemistry. This book has a biochemical point of view instead of the "classical" treatment of the subject, it contains ample informations about the different receptors, physicochemical principles of drug action, mode of action etc. Unfortunately, its last edition is already 10 years old. I am looking for a similar but newer book. Regards Tamas E. Gunda ************************************************************************ Dr Tamas E. Gunda phone: (+36-52) 316666 ext 2479 Research Group of Antibiotics fax : (+36-52) 310936 L. Kossuth University e-mail: tamasgunda@tigris.klte.hu POBox 36 H-4010 Debrecen Hungary ************************************************************************ From hinsen@lmspc1.ibs.fr Wed Nov 12 05:39:29 1997 Received: from ibs.ibs.fr for hinsen@lmspc1.ibs.fr by www.ccl.net (8.8.3/950822.1) id FAA10158; Wed, 12 Nov 1997 05:11:54 -0500 (EST) 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 LAA08224; Wed, 12 Nov 1997 11:10:58 +0100 Received: (from hinsen@localhost) by lmspc1.ibs.fr (8.8.5/8.8.5) id LAA07364; Wed, 12 Nov 1997 11:08:57 +0100 Date: Wed, 12 Nov 1997 11:08:57 +0100 Message-Id: <199711121008.LAA07364@lmspc1.ibs.fr> From: Konrad Hinsen To: shenkin@still3.chem.columbia.edu CC: chemistry@www.ccl.net In-reply-to: <9711111140.ZM3237@still3.chem.columbia.edu> (shenkin@still3.chem.columbia.edu) Subject: Re: CCL:Sequence Classes and CORBA Servers > We, on the other hand, as a (small) third-party vendor, cannot > with impunity build our distributed applications around CORBA, > because there's no guarantee that our customers will have the > technology up and running in-house. They would have to license > it, possibly from us -- but that would be a significant extra > expense for them and bookkeeping of pass-through expenses for us. Warning: I have no personal experience with this approach, it's just an idea... There is a free CORBA-like system developed at Xerox PARC, called ILU. It ought to be possible to develop software using either ILU or CORBA with little extra effort. Customers could then choose which solution they prefer. -- ------------------------------------------------------------------------------- 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 chipot@host7.lctn.u-nancy.fr Wed Nov 12 05:42:37 1997 Received: from host7.lctn.u-nancy.fr for chipot@host7.lctn.u-nancy.fr by www.ccl.net (8.8.3/950822.1) id FAA10169; Wed, 12 Nov 1997 05:20:28 -0500 (EST) From: Received: (from chipot@localhost) by host7.lctn.u-nancy.fr (AIX4.2/UCB 8.7/8.7) id LAA24818 for CHEMISTRY@www.ccl.net; Wed, 12 Nov 1997 11:10:56 +0100 (NFT) Message-Id: <199711121010.LAA24818@host7.lctn.u-nancy.fr> Subject: Computational Chemistry and the Living World To: CHEMISTRY@www.ccl.net Date: Wed, 12 Nov 1997 11:10:56 +0100 (NFT) X-Mailer: ELM [version 2.4 PL23] Content-Type: text European Conference on COMPUTATIONAL CHEMISTRY AND THE LIVING WORLD: FROM SEQUENCE TO FUNCTION. Chambery (French Alps), 20-24 April, 1998 Organised by the Physical Chemistry Division, French Chemical Society Bunsen-Gesellschafft fur Physikalische-Chemie, Faraday Division of the Royal Society of Chemistry, Division di Chimica Fisica (SCI), French Biophysical Society. International Scientific Committee: J.C. Smith (CEA-Saclay, Chairman); R. Botter (DCP Paris), secretary; J. Brickmann (TH Darmstadt); J.E. Dubois (U Paris VII); J. Garnier (INRA-Jouy); M. Karplus (U. Strasbourg); R. Lavery (IBPC, Paris); B. Maigret (U. Nancy); C. Chipot (U Nancy); G. Richards (U. Oxford); E. Soulie (CEA-Saclay); J. Tomasi (U. Pisa); C. Troyanowsky (DCP Paris). _______________________________________________________________________ THIS PAGE CONTAINS THE FOLLOWING INFORMATION: A) DESCRIPTION OF THE SCOPE OF THE MEETING B) PROGRAMME C) APPLICATION FORM A) DESCRIPTION OF THE SCOPE OF THE MEETING. _______________________________________ The results of the genome projects are expected to lead to a scientific revolution in the beginning of the next century. The complete gene se- quences of organisms of several different levels of development, in- cluding Homo sapiens, will be available. This enormous amount of gene- tic information will be in the form of nucleotide sequences. The infor- mation present in a gene sequence is translated in the cell into a protein sequence. This sequence determines the way the protein folds into a three-dimensional architecture which confers biological function (catalysis, recognition etc). The question arises as to how to exploit the genetic information as ef- fectively as possible. To do this will require an understanding of the processes of translation of the genetic information from sequence to structure and function. Both theory and experiment are expected to play major roles in obtaining this understanding. The meeting in Chambery will focus on the role of computational chemistry= in the activity that will be sparked by the genome results. How can numerical calculation help us to understand and exploit genome sequences? How can modelling and simulation help in understanding how amino-acid sequence is trans- lated into three-dimensional biological structure, the functional interactions of these structures and the effect of engineered modifica- tions? The meeting will be treating the following topics organised into three themes: Sequence analysis, Biomolecular structure and folding, and Biomolecular function. In the first theme the impact of genome sequencing projects will be as- sessed, genome organisation discussed and the access and direct exploi- tation of sequence data reviewed. Evolutionary analysis of sequences will be examined, together with the classification of sequences in terms of structure. The second theme concerns biomolecular folding and structure. On the experimental side X-ray crystallography and nuclear magnetic resonance spectroscopy are the major techniques capable of solving macromolecular structures at atomic resolution. However, for technical reasons, the rate at which new structures are being solved far lags behind the rate at which new gene sequences are being produced. Thus, there is a need for reliable theoretical/computational techniques capable of predicting protein structures from sequences. To do this requires an understanding of the principles by which proteins fold: the factors determining their thermodynamic stability and kinetic folding pathways. We will examine modelling of protein structure by homology and with energy functions, the `inverse folding' methods (from structure to sequence), and tech- niques for global energy optimization. Prion protein conformational flexibility will be addressed with reference to prion diseases as diseases of protein conformation. Nucleic acid sequence-structure rela- tionships will also be discussed, with special reference to the fine structure, bending and supercoiling of DNA, and the prediction of the structure and activity of tRNA. The third theme will be the functional interactions of biomolecules. The calculation of binding modes and reaction mechanisms will be exami- ned and methods for calculating free energy changes associated with bi- ological processes assessed. The modelling and simulation of ordered molecular systems such as protein-protein and protein-nucleic acid com- plexes, oligosaccharides and glycoproteins and membrane-based systems will be reviewed. Finally, dynamic processes in biological function will be examined, from fast, picosecond events to slower, domain motions and allosteric phenomena. The meeting will be over five days and will consist of long lectures (45 mins), short lectures (15 mins), poster sessions and informal dis- cussion. Research into the chemistry of biological macromolecules requires close cooperation between theorists and experimentalists. In the present meeting we hope to attract scientists from both fields. We will invite a number of leading experimentalists to give lectures, and hope to emphasize the broad complementarity between theory and experi- ment in the lectures rather than specialized discussion of theoretical methodology. The meeting is expected to be of interest to researchers in all bran- ches of computational chemistry, as well as structural and molecular biologists and biochemists. The consequences for industry of success in the endeavours discussed above are enormous, and this has been rea- lised in several drug companies that have set up integrated computa- tional/experimental groups on sequence-structure-function relation- ships. A famous example of 'rational' structure-based drug design is the very recent successful development of HIV Protease inhibitors for the treatment of AIDS. Industrial researchers working on this and other problems will also be invited to speak. B) PROVISIONAL PROGRAMME _____________________ MONDAY APRIL 20th _________________ 8.45-9.15 Welcome. THEME 1: SEQUENCES. 9.15-10.00 Jean-Michel Claverie 10.00-10.30 Pause+Exhibition. 10.30-11.15 A. Danchin. 11.00-12.15 Three short talks 14.00-14.45 Cyrus Chothia (Cambridge) 14.45-15.45 Three short talks. 15.45-16.15 Break. 16.15-17.15 Oral Poster presentations. 17.15-18.15 Poster session. TUESDAY 21 APRIL ________________ THEME 2: FOLDING AND STRUCTURE. 9.00- 9.45 Mannfred Sippl (Graz) 9.45-10.45 Three short talks 10.45-11.30 Pause+Exhibition. 11.30-12.15 Michael Hecht (Princeton) 14.00-14.45 Eugene Shakhnovitch (Harvard) 14.45-15.45 Three short talks. 15.45-16.15 Break. 16.15-17.15 Oral poster presentations. 17.15-18.15 Poster session. WEDNESDAY 22 APRIL __________________ 9.00- 9.45 Wilfred van Gunsteren (Zurich) 9.45-10.30 Pause+Exhibition. 10.30-11.15 Three short talks. Afternoon free * SKI TRIP * WINE TRIP THURSDAY 23 APRIL _________________ 9.00- 9.45 Chris Dobson (Oxford) 9.45-10.30 Pause+Exhibition. 10.30-11.30 Three short talks. 11.15-12.15 Eric Westhof (Strasbourg) THEME 3: BIOMOLECULAR INTERACTIONS AND FUNCTION. 14.00-14.45 David Chandler (Berkeley) 14.45-16.00 Pause+Exhibition. 15.30-16.30 Three short talks. FRIDAY 24 APRIL _______________ 9.00- 9.45 Harel Weinstein (New York) 9.45-10.30 Pause+Exhibition. 10.30-11.30 Three short talks. 11.30-12.15 Klaus Schulten (Illinois) Afternoon - To be announced. C) PRELIMINARY REGISTRATION FORM _____________________________ Please send this form by REGULAR MAIL to the following address: M. Rene Botter, Computational Chemistry and the Living World, Laboratoire de Chimie Physique, 11 rue P. et M. Curie, 75005 PARIS France. The deadline for submitting abstracts has been postponed to January 10-th 1998 ..................................................................>8... Name: ______________________________________________________________ Address: ___________________________________________________________ ____________________________________________________________________ ____________________________________________________________________ Telephone: _________________________________________________________ Fax: _______________________________________________________________ E-mail: _____________________________________________________________ _____ I WISH/DO NOT WISH TO PRESENT A POSTER. _____ I WISH/DO NOT WISH TO MAKE AN ORAL PRESENTATION. ..................................................................>8... _______________________________________________________________________ Chris Chipot Laboratoire de Chimie Theorique Phone: (33) 3-83-91-25-96 U.R.A. C.N.R.S. No 510 Fax: (33) 3-83-91-25-30 Universite Henri Poincare - Nancy I B.P. 239 54506 Vandoeuvre-les-Nancy Cedex E-mail: chipot@lctn.u-nancy.fr `The light shines through the darkness and the darkness has not overcome it' _______________________________________________________________________ From GAJOS@WCHUWR.CHEM.UNI.WROC.PL Wed Nov 12 06:32:34 1997 Received: from indigo2 for GAJOS@WCHUWR.CHEM.UNI.WROC.PL by www.ccl.net (8.8.3/950822.1) id FAA10302; Wed, 12 Nov 1997 05:42:01 -0500 (EST) Received: from wchuwr.chem.uni.wroc.pl by indigo2 via SMTP (940816.SGI.8.6.9/930416.SGI) for id LAA02105; Wed, 12 Nov 1997 11:41:20 -0100 Received: from ICHUWR/SMTPQueue by wchuwr.chem.uni.wroc.pl (Mercury 1.11); Wed, 12 Nov 97 11:41:12 +0100 Received: from Mailqueue by ICHUWR (Mercury 1.11); Wed, 12 Nov 97 11:40:59 +0100 From: "Grzegorz Gajewski" Organization: University of Wroclaw (Chemistry) To: chemistry@www.ccl.net Date: Wed, 12 Nov 1997 11:40:50 GMT+2 Subject: pseudopotential Priority: normal X-mailer: Pegasus Mail v3.1 (R1) Message-ID: <35B1965BE4@wchuwr.chem.uni.wroc.pl> I'm interested in Barthelet's pseudopotencial (core and valence orbitals) for Bi.Please give me references or parameters. Thank for all help! From chaudash@helios.aston.ac.uk Wed Nov 12 09:32:43 1997 Received: from hermes.aston.ac.uk for chaudash@helios.aston.ac.uk by www.ccl.net (8.8.3/950822.1) id JAA11066; Wed, 12 Nov 1997 09:18:35 -0500 (EST) Message-Id: <199711121418.JAA11066@www.ccl.net> Received: from Pharm33.aston.ac.uk by hermes.aston.ac.uk with SMTP (PP); Wed, 12 Nov 1997 14:22:04 +0000 Comments: Authenticated sender is From: chaudash@aston.ac.uk Organization: aston.ac.uk To: chemistry@www.ccl.net Date: Wed, 12 Nov 1997 14:26:59 +0000 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: Aluminium and computational chemistry Reply-to: chaudash@aston.ac.uk Priority: normal In-reply-to: <199711121008.FAA10152@www.ccl.net> X-mailer: Pegasus Mail for Windows (v2.54) Dear all, A while back I wrote asking if anyone was doing any computational chemistry, in particular with PM3. I know that I received several interesting replies, however the email system at the university went down, consequently have lost all the replies, hence I would be most grateful if you would write again with your thoughts and advice. Sorry to be a pain. From FLOWER_DR@charnwood.gb.astra.com Wed Nov 12 09:59:05 1997 Received: from mail-gw-1.astra.com for FLOWER_DR@charnwood.gb.astra.com by www.ccl.net (8.8.3/950822.1) id JAA11087; Wed, 12 Nov 1997 09:29:20 -0500 (EST) Received: from gatekeeper.astra.com by mail-gw-1.astra.com (5.65v3.2/1.1.10.5/30Jun97-0418PM) id AA23078; Wed, 12 Nov 1997 15:33:33 +0100 Received: by gatekeeper.astra.com; (5.65v4.0/1.3/10May95) id AA11020; Wed, 12 Nov 1997 15:29:38 +0100 Message-Id: From: "Flower, Darren" To: "'chemistry@www.ccl.net'" Subject: Revised Meeting Date: Wed, 12 Nov 1997 13:54:16 +0100 X-Mailer: Microsoft Exchange Server Internet Mail Connector Version 4.0.995.52 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Molecular Modelling Group Royal Society of Chemistry : Industrial Section ONE DAY SYMPOSIUM Molecular Modelling for Industry : The Training Issues Thursday, 4 December 1997 Scientific Societies Lecture Theatre New Burlington Place, Piccadilly, London Molecular modelling is now widely used in the pharmaceutical, chemical and electronic industries. Its success depends to a large extent on how well integrated the modelling is with an on going experimental programme. Are the experimentalists and modellers adequately trained to ask relevant questions to each other - for the benefit of both? Where and what type of training they can get? How to get access to molecular modelling when no facilities exist in-house? These are some of the questions to be debated at this meeting. We have speakers from industry to talk on what they expect from Molecular Modelling and the efforts that they have made. In the afternoon, the speakers will describe the kind of training that they have provided both within the industry and in the academia. In the Panel Discussion, the audience will have an opportunity to assess and suggest any improvements, if necessary. AGENDA 10.00 Coffee & Registration 10.25 Welcome & Introduction 10.30 Prof Graham Richards (U. of Oxford & Oxford Molecular) 11.00 Dr Joe Howard (Applied Extrusion Technologies Ltd.) 11.30 Dr Kevin Ray (Horsell) 12.00 Prof Rod Hubbard (U of York) 12.30 Lunch & Posters 14.15 Prof Nick Quirke (U. of Wales, Bangor) 14.45 Prof Dominic Tildesley (U. of Southampton) 15.15 Dr Mike Stapleton (MSI) 15.45 Dr Elizabeth Colbourn (OXMAT) 16.15 PANEL DISCUSSION 17.00 CLOSE Registration Fee: RSC & Modelling Group Members GBP 30.00, Others GBP 40.00 Contact: Dr John Kendrick, ICI Wilton, Middlesborough TS90 8JE Phone: 01642-437994 Fax: 01642-432244 E-mail: john_kendrick@ici.com From shenkin@still3.chem.columbia.edu Wed Nov 12 10:32:37 1997 Received: from mailrelay1.cc.columbia.edu for shenkin@still3.chem.columbia.edu by www.ccl.net (8.8.3/950822.1) id KAA11444; Wed, 12 Nov 1997 10:09:08 -0500 (EST) Received: from still3.chem.columbia.edu (still3.chem.columbia.edu [128.59.112.36]) by mailrelay1.cc.columbia.edu (8.8.5/8.8.5) with SMTP id KAA14156 for <@smtp.columbia.edu:chemistry@www.ccl.net>; Wed, 12 Nov 1997 10:09:05 -0500 (EST) Received: by still3.chem.columbia.edu (950413.SGI.8.6.12/930416.SGI.AUTO) for chemistry@www.ccl.net id KAA08182; Wed, 12 Nov 1997 10:09:02 -0500 From: "Peter Shenkin" Message-Id: <9711121009.ZM8180@still3.chem.columbia.edu> Date: Wed, 12 Nov 1997 10:09:02 -0500 In-Reply-To: Konrad Hinsen "Re: CCL:Sequence Classes and CORBA Servers" (Nov 12, 11:08am) References: <199711121008.LAA07364@lmspc1.ibs.fr> X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: chemistry@www.ccl.net Subject: Re: CCL:Sequence Classes and CORBA Servers Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii On Nov 12, 11:08am, Konrad Hinsen wrote: > Subject: Re: CCL:Sequence Classes and CORBA Servers > > We, on the other hand, as a (small) third-party vendor, cannot > > with impunity build our distributed applications around CORBA, > > because there's no guarantee that our customers will have the > > technology up and running in-house. They would have to license > > it, possibly from us -- but that would be a significant extra > > expense for them and bookkeeping of pass-through expenses for us. ... > There is a free CORBA-like system developed at Xerox PARC, called > ILU. Yes, I'm aware of ILU. But this still doesn't answer the question how suppliers of third-party software will be able to utilize CORBA classes devised by some consortium, in the absense of a guarantee that all their customers will have bought into CORBA. -P. -- ****************** Sir Isaiah Berlin, 1909 - 1997, RIP ******************** * Peter S. Shenkin; Chemistry, Columbia U.; 3000 Broadway, Mail Code 3153 * ** NY, NY 10027; shenkin@columbia.edu; (212)854-5143; FAX: 678-9039 *** *MacroModel WWW page: http://www.columbia.edu/cu/chemistry/mmod/mmod.html * From Graham.Cameron@EBI.AC.UK Wed Nov 12 11:32:38 1997 Received: from alpha1.ebi.ac.uk for Graham.Cameron@EBI.AC.UK by www.ccl.net (8.8.3/950822.1) id LAA11707; Wed, 12 Nov 1997 11:02:08 -0500 (EST) Received: from Mars.ebi.ac.uk (mars.ebi.ac.uk [193.62.196.73]) by alpha1.ebi.ac.uk (8.8.7/8.8.7) with ESMTP id QAA00470 for ; Wed, 12 Nov 1997 16:01:52 GMT Received: from ebi.ac.uk by ebi.ac.uk (PMDF V4.3-9 #2491) id <01IPXEZXO29S94MZEH@ebi.ac.uk>; Wed, 12 Nov 1997 16:01:55 +0100 Date: Wed, 12 Nov 1997 15:57:26 +0100 From: Graham Cameron Subject: Life Sciences, OMG, Standards etc. To: biowidgets-consortium@fruitfly.bdgp.berkeley.edu, javachem@wag.caltech.edu, bioobjects@ebi.ac.uk, chemistry@www.ccl.net Cc: cameron@ebi.ac.uk Message-id: <01IPXF69U8BO94MZEH@ebi.ac.uk> MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Dear Colleagues, The tone of the discussion on Object Technology, CORBA, Standards and the OMG leads me to think that there is some misunderstanding of recent developments in establishing the OMG DSIG for life sciences research and about the EBI position and intentions. I attempt here to clarify the EBI position (which may or may not coincide with the OMG philosophy). Apologies if you are one one of the mailing lists peripheral to this discussion. I promise to shut up after this message! 1. This is not a crusade - no-one is going to *impose* standards. Even were it desirable it would not be possible. Standards which come out of the process will be adopted if they turn out to be useful. 2. Any future CORBA-based services of the EBI will not supplant existing traditional data delivery methods - except in the unlikely event that the demand for the old methods dwindles to near zero. 3. The process of defining standards within OMG is (a) open, and (b) non-authoritarian. Anyone can be involved in both proposing and evaluating standards, and standards are chosen from proposals by organisations willing to implement them. 4. The question of whether we believe that Object Technology in general, and CORBA in particular will lend themselves technically and socially to application in the life sciences is an open one. We feel that it is best if those who are committed to giving it a try attempt to work to standards; and the OMG process, while at first sight rather complex, does seem a good way to define workable standards. 5. NCBI would be best to speak for themselves. They were represented at the first meeting, but since they have no immediate committment to CORBA it may not be so high on their list of priorities. 6. We at the EBI supply about 60 biological databases (two or three of the major ones are collaborations with NCBI and/or the DNA Databank of Japan), but this is still a fraction of all life sciences information. On object technology and CORBA We have experience of both at the EBI, and we are convinced of the utility of this technology, even if only internally. Already the approach is doing real work for us. We are committed to offering CORBA services, but will continue with our other services. We plan these developments because we believe that they will turn out to be really useful, but we have no desire or need to drag the unwilling down this path. A number of collaborators and developers are keen to work with us on this, and as our collective experience builds, the picture will clarify. For us there is little downside to even a negative community response to this approach - it offers so much for our internal purposes as to be worthwhile anyway. So, for heaven's sake don't let us be cultist about this. It's a method that works in our hands, and it may create opportunities for others. Graham. -- Graham Cameron Head of Services EMBL Outstation - the European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton CB10 1SD Cambridge UK phone: +44 (0) 1223 494467 (direct) +44 (0) 1223 494649 (secretary) fax: +44 (0) 1223 494468 email: cameron@ebi.ac.uk -- From kotelyan@plmsc.psu.edu Wed Nov 12 11:36:17 1997 Received: from plmsc.psu.edu for kotelyan@plmsc.psu.edu by www.ccl.net (8.8.3/950822.1) id LAA11726; Wed, 12 Nov 1997 11:05:51 -0500 (EST) Received: (from kotelyan@localhost) by plmsc.psu.edu (8.8.2/8.8.2) id LAA25430; Wed, 12 Nov 1997 11:05:52 -0500 (EST) Date: Wed, 12 Nov 1997 11:05:50 -0500 (EST) From: Mike Kotelyanskii To: CHEMISTRY@www.ccl.net Subject: CCL:Inorganic crystal structures SUMMARY Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII A while ago I posted a request about the possible source of the inorganic crystal structure data Thanks to everybody who replied. Sorry, it took a while to put together a summary, here is my original posting and replies. Unfortunately I cannot comment on the on-line resources, as most of those sources are not free and I did not have an access to them. I found what I needed in Wyckoff's handbook in our library, thanks to Michael S Sennett. Original message: Is anybody aware of the database, or other source of the crystal structures (lattice symmetry groups, lattice parameters, moduli??) of the inorganic compounds like SiC, aluminium, zinc and other oxides, particularly, III-V groups elements and compounds, Thank you Michael ------> Replies: A few references are as follows: W.B. Pearson, The Crystal Chemistry and Physics of Metals and Alloys, (Wiley-Interscience, New York, 1972). P. Villars and L.D. Calvert, Pearson's Handbook of Crystallographic Data for Intermetallic Phases, 2nd Edition (ASM International, Materials Park, Ohio, 1991). R.W.G. Wyckoff, Crystal Structures, Vol. 1 (John Wiley & Sons, New York, London, 1963). (Other volumes and later editions have been published). Thomas A. Adler Albany Research Center, Department of Energy 1450 Queen Avenue, SW Albany OR 97321-2198 E-mail: adler@alrc.doe.gov (541) 967-5853 -------------------------------------------------------------------------- From: sennettm@world.std.com (Michael S Sennett) See Wyckoff's "Crystal Structures" in your library. ------------------------------------------------------------------------ Mike, There is a company "Scientific Information Services, Inc." which has something called the Inorganic Crystal Structure Database (ICSD). The number is 914-834-8864 & the contact person I have down is Patricia Guenkel. I have no connection with the company, and have not ordered the program yet, but the literature I have suggests that the ICSD might be what you are looking for. Hope this helps. Tom Cundari =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+ Tom Cundari Department of Chemistry Associate Professor The University of Memphis e-mail:tcundari@cc.memphis.edu Memphis, TN 38152-6060 phone: 901-678-2629 FAX: 901-678-3447 http://www.chem.memphis.edu/umchem.html **** U of Memphis is conducting a search for an Assistant Professor of Computational Chemistry, contact me by email for details **** =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+ From: chaudash@aston.ac.uk Have you tried QUEST available from the Cambridge Structural Database -------------------------------------------------------------------------- Mike: While not very modern, the best compendium of these crystal structures that I know of is the series of annual books called "Structure Reports". This is a summary of X-ray and neutron diffraction studies. As far as I know, this information is not in any electronic database, so brute-force searching through these books has often been my most fruitful technique. I would appreciate hearing about other, more searchable, databases that you might learn about. Best wishes, Brian J. Teppen teppen@srel.edu Advanced Analytical Center for Environmental Sciences Savannah River Ecology Laboratory University of Georgia Drawer E Aiken, SC 29802 phone:803-725-8157 fax:803-725-3309 -------------------------------------------------------------------------- From: "Cathy Thompson" The "Inorganic Crystal Structure Database" (ICSD) is a very good source of information. It is released in CD format by the Gmelin institute and the Fachinformationszentrum Karlsruhe and contains crystal structure information and bibliographic data. I hope this helps. Greetings Catharine Thompson ----------------------------------------------------------------------- Dear Mike: The site has altered a bit since I last looked at it. Just go to the the host URL: http:/www.fiz-karlsruhe.de/ and look under CD-ROM products. You will find a couple of links to ICSD there. Leslie ============================================================== (Prof.) Leslie Glasser Dept. of Chemistry E-mail: glasser@aurum.chem.wits.ac.za Univ. of Witwatersrand Tel: Intl + 27 11 716-2070 P. O. WITS 2050 Fax: Intl + 27 11 339-7967 South Africa Home Pages: University http://sunsite.wits.ac.za Chemistry http://www.chem.wits.ac.za ====================================================================== ------------------------------------------------------------------------------- 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 http://www.plmsc.psu.edu/~kotelyan University Park, PA 16802, USA -------------------------------------------------------------------------------- From states@gpc.ibc.wustl.edu Wed Nov 12 12:32:38 1997 Received: from wugate.wustl.edu for states@gpc.ibc.wustl.edu by www.ccl.net (8.8.3/950822.1) id LAA11985; Wed, 12 Nov 1997 11:54:10 -0500 (EST) Received: from gpc.ibc.wustl.edu (gpc.ibc.wustl.edu [128.252.45.1]) by wugate.wustl.edu (8.8.5/8.8.5) with SMTP id KAA01744 for ; Wed, 12 Nov 1997 10:54:10 -0600 (CST) Received: from sos.wustl.edu by gpc.ibc.wustl.edu (SMI-8.6/SMI-SVR4) id KAA27929; Wed, 12 Nov 1997 10:54:09 -0600 Received: by sos.ibc.wustl.edu with Internet Mail Service (5.0.1458.49) id ; Wed, 12 Nov 1997 10:52:53 -0600 Message-ID: From: "David J. States" To: Gerald.Loeffler@univie.ac.at, bioWidgets Consortium , Java in Chemistry Mailing List , BioObjects Mailing List , Computational Chemistry List Subject: RE: Sequence Classes and CORBA Servers Date: Wed, 12 Nov 1997 10:52:48 -0600 X-Priority: 3 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.0.1458.49) Content-Type: text/plain > 1) Are there any "standard" C++, Java or IDL specifications for classes that > represent > a) DNA sequences, > b) RNA sequences, > c) Protein sequences, > d) Pairwise and multiple sequence alignments? > > 2) What's the relation of the above sequence class specifications to existing > flat-file sequence formats (EMBL, GenBank, PIR, SwissProt, ...)? > > 3) Are there any CORBA servers available now ... The NCBI does deliver sequence in ASN.1 format from their web site. While ASN.1 is not CORBA, the NCBI bio-seq definitions are robust and have been stable for a number of years. The mapping from ASN.1 to CORBA is not as smooth as it might be because many (the vast majority) of the fields in the ASN.1 definitions are optional and not used in any particular entry. I don't know what plans NCBI has with regard to CORBA, but it would be worth asking them. Alternatively, a JAVA class that loaded NCBI objects would be nice to have. David States Institute for Biomedical Computing Washington University From rvenable@deimos.cber.nih.gov Wed Nov 12 14:32:37 1997 Received: from deimos.cber.nih.gov for rvenable@deimos.cber.nih.gov by www.ccl.net (8.8.3/950822.1) id OAA12721; Wed, 12 Nov 1997 14:24:45 -0500 (EST) Received: from localhost by deimos.cber.nih.gov with SMTP (1.37.109.14/16.2) id AA058802174; Wed, 12 Nov 1997 14:16:14 -0500 Date: Wed, 12 Nov 1997 14:16:14 -0500 (EST) From: Rick Venable To: Josi Santiago Duca Cc: CCL Subject: Re: CCL:average structures In-Reply-To: <3468EE20.F9C42D58@tigger.cc.uic.edu> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Tue, 11 Nov 1997, Josi Santiago Duca wrote: > I'd like to know which is (are) the criteria to found an average > structure once a molecular dynamics is run out on a flexible system (for > instance, a polyethylene chain with 50 ethylene units) starting the MD > from different seed numbers. If the chain is flexible, a lot of > different conformations of similar energies can be reached depending on > their initial random velocities, after e.g. 50 ps. and keeping the > kinetic energy constant. Is there any "usual" convention about finding > an average structure of this set of corformations? I think "average" structures can be real trouble, since they don't represent any *real* structure. An example is the case of a torsion that may be changing between 2 states; averaging gives an intermediate torsion that may be on a torsional barrier, and is clearly not representative of a dominant conformation. Instead, I like to use what I've termed a "typical" structure; it's a real structure from the trajectory that most resembles (from an RMSD criterion) the average structure. It avoids the prblem of creating unlikely conformations as a consequence of averaging. -- 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://nmr1.cber.nih.gov/ \/ |=| see http://www.fda.gov ) From elewars@alchemy.chem.utoronto.ca Wed Nov 12 16:32:40 1997 Received: from alchemy.chem.utoronto.ca for elewars@alchemy.chem.utoronto.ca by www.ccl.net (8.8.3/950822.1) id QAA13428; Wed, 12 Nov 1997 16:22:52 -0500 (EST) Received: (from elewars@localhost) by alchemy.chem.utoronto.ca (8.7.4/8.7.3) id QAA19897 for chemistry@www.ccl.net; Wed, 12 Nov 1997 16:22:51 -0500 (EST) Date: Wed, 12 Nov 1997 16:22:51 -0500 (EST) From: "E. Lewars" Message-Id: <199711122122.QAA19897@alchemy.chem.utoronto.ca> To: chemistry@www.ccl.net Subject: EHM TODAY--OPINIONS Wed, 1997 Nov 12 >From E. Lewars To: CCL Subj: Extended Hueckel Today--opinions Hello, What do people out there in netland think of the *current* status of the extended Hueckel method that was popularized by Roald Hoffmann, starting ca. 1963? It was, I think, the first generally applicable method, in the sense that it was not limited to planar pi electron arrays and could in principle perform geometry optimizations. Is it the general view that it is essentially obsolete, having been displaced by more sophisticated methods like MNDO and its decendants AM1 and PM3? Does it have some advantages over AM1 and PM3? Thanks E. Lewars ================ From fparnold@balihai.uchicago.edu Wed Nov 12 17:32:40 1997 Received: from balihai.uchicago.edu for fparnold@balihai.uchicago.edu by www.ccl.net (8.8.3/950822.1) id RAA14121; Wed, 12 Nov 1997 17:29:15 -0500 (EST) Received: from localhost by balihai.uchicago.edu via SMTP (950413.SGI.8.6.12/931108.SGI.ANONFTP) for id QAA09618; Wed, 12 Nov 1997 16:29:15 -0600 Date: Wed, 12 Nov 1997 16:29:15 -0600 (CST) From: "Fred P. Arnold" To: Computational Chemistry List Subject: EHM Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Personally, I find it still valuable, since it's generally consistent, includes support for elements that PM3, etc, don't, and has been generalized to the solid-state. It's also conceptually simple, serves as a good tool for a first pass at a problem, and is cheap to run, allowing qualitative results to be obtained for large systems in minimal time. If the limitations are taught first, it serves as an excellent tool for teaching basic modeling to students without overwhelming them in the technical details of ab-initio (or even better semi-empirical) methods. My preference, due to an interest in transition-metal systems, is to use Fenske-Hall, but that method is regrettably much less available, and has not been generalized to periodic systems. Frederick P. Arnold, Jr. The University of Chicago: Advanced Research Systems Where the End of the World Began. 5640 S. Ellis Ave Chicago, IL 60637 From chymo@xmu.edu.cn Wed Nov 12 20:32:43 1997 Received: from xmu.edu.cn for chymo@xmu.edu.cn by www.ccl.net (8.8.3/950822.1) id UAA20992; Wed, 12 Nov 1997 20:31:57 -0500 (EST) Received: by xmu.edu.cn (SMI-8.6/SMI-SVR4) id JAA12206; Thu, 13 Nov 1997 09:32:30 +0800 Date: Thu, 13 Nov 1997 09:32:30 +0800 From: chymo@xmu.edu.cn (mo yi rong) Message-Id: <199711130132.JAA12206@xmu.edu.cn> To: chemistry@www.ccl.net Cc: chymo@xmu.edu.cn Subject: Nuclear Magnetic Resonance Dear All: Regarding the calculation of Nuclear Magnetic Resonance (NMR) in Gaussian94, I want to know whether the unitary transformation, which keeps th total energy unchanged, will alter the NMR output. In other words, if the MOs are orthogonal but not the eigenfunctions of the Fock opeartor, are the NMR data based on these MOs realiable and meaningful? Thanx and have a good day, Yirong Mo chymo@xmu.edu.cn From lavelle@mbi.ucla.edu Sat Nov 8 22:31:50 1997 Received: from rho.ben2.ucla.edu for lavelle@mbi.ucla.edu by www.ccl.net (8.8.3/950822.1) id WAA18591; Sat, 8 Nov 1997 22:02:09 -0500 (EST) Received: from ewald.mbi.ucla.edu (ewald.mbi.ucla.edu [128.97.39.21]) by rho.ben2.ucla.edu (8.8.5/8.8.5) with SMTP id TAA67758; Sat, 8 Nov 1997 19:02:10 -0800 Received: from red5.mbi.ucla.edu by ewald.mbi.ucla.edu (5.65v3.2/1.1.10.5/09Oct97-1217PM) id AA30874; Sat, 8 Nov 1997 19:02:10 -0800 Message-Id: <3.0.32.19971108190512.00a2a3d0@mbi.ucla.edu> X-Sender: lavelle@mbi.ucla.edu X-Mailer: Windows Eudora Pro Version 3.0 (32) Date: Sat, 08 Nov 1997 19:05:12 -0800 To: hyperchem@hyper.com, chemistry@www.ccl.net From: Laurence Lavelle Subject: Improving ab initio computational speed Mime-Version: 1.0 Content-Type: text/enriched; charset="us-ascii" Two possible ways to speed up ab initio calculations are: 1) Use a bases set with fewer bases functions first. Then, after convergence, use a bases set with more bases functions. Repeat this process until convergence is obtained with the (largest) bases set that was originally intended. 2) Use the largest bases set with a higher 2e integral cuttoff point (e.g. 10^-7 Hartree) and after convergence decrease the 2e integral cuttoff point. Repeat until convergence is obtained with the originally intended 2e integral cuttoff point (e.g. 10^-11 Hartree). Do either of these approaches have potential downfalls. Is one approach better than the other? Thanks Laurence Lavelle
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" Laurence Lavelle, Ph.D. University of California Los Angeles Molecular Biology Institute, and Department of Chemistry & Biochemistry Laboratory of Structural Biology & Molecular Medicine Los Angeles, CA 90095-1570, USA Email:LAVELLE@MBI.UCLA.EDU Phone (Lab): (310) 206-8270 Phone (Office): (310) 825-2083 Fax: (310) 267-1957 http://www.doe-mbi.ucla.edu/people/lavelle/lavelle.html """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" It will be a great day when schools have all the money they need, and the military has bake day sales. In nature's infinite book of secrecy A little I can read.
From toukie@zui.unizh.ch Sun Nov 9 07:31:57 1997 Received: from zzmkgtw.zzmk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.8.3/950822.1) id HAA19711; Sun, 9 Nov 1997 07:24:14 -0500 (EST) Received: by zzmkgtw.zzmk.unizh.ch; (5.65v3.2/1.3/10May95) id AA04592; Sun, 9 Nov 1997 13:24:00 +0100 Message-Id: <3.0.3.32.19971109132643.00688474@highdent> X-Sender: toukie@highdent (Unverified) X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.3 (32) Date: Sun, 09 Nov 1997 13:26:43 +0100 To: chemistry@www.ccl.net From: "Hr. Dr. S. Shapiro" Subject: sec-butylphenols Cc: toukie@zui.unizh.ch Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear Colleagues; In connection with some calculations I am conducting on sec-butylphenols, I was able to find in the literature that (R)-o-sec-butylphenol is laevorotatory (sodium D-line) and that (S)-o-sec-butylphenol is dextrotatory. However, I could not find any information relating to the absolution configurations of m- or p-sec-butylphenols and their corresponding optical rotations. If anyone has access to such information, or would care to share their thoughts, ideas, or calculations on the possible correspondence between absolute configurations of the m- and p-sec-butylphenols and their optical rotations, I would be very glad to hear from you. Thanks in advance to all responders, S. Shapiro toukie@zui.unizh.ch From toukie@zui.unizh.ch Sun Nov 9 08:31:56 1997 Received: from zzmkgtw.zzmk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.8.3/950822.1) id IAA19798; Sun, 9 Nov 1997 08:06:15 -0500 (EST) Received: by zzmkgtw.zzmk.unizh.ch; (5.65v3.2/1.3/10May95) id AA01639; Sun, 9 Nov 1997 14:05:58 +0100 Message-Id: <3.0.3.32.19971109140842.00687d00@highdent> X-Sender: toukie@highdent (Unverified) X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.3 (32) Date: Sun, 09 Nov 1997 14:08:42 +0100 To: chemistry@www.ccl.net From: "Hr. Dr. S. Shapiro" Subject: Seeking GA regress. anal. software Cc: toukie@zui.unizh.ch Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear Colleagues; I am seeking software that will run on a PC fitted with Win95 (i.e., DOS, Win 3.x, Win95) that can perform a "best subsets" regression analysis using a genetic algorithm. The number of indepedent variables can range from 5 up to 100, depending upon the nature of the analysis. Thanks in advance to all responders. Sincerely, S. Shapiro toukie@zui.unizh.ch From toukie@zui.unizh.ch Sun Nov 9 08:32:00 1997 Received: from zzmkgtw.zzmk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.8.3/950822.1) id HAA19765; Sun, 9 Nov 1997 07:52:21 -0500 (EST) Received: by zzmkgtw.zzmk.unizh.ch; (5.65v3.2/1.3/10May95) id AA05789; Sun, 9 Nov 1997 13:52:20 +0100 Message-Id: <3.0.3.32.19971109135504.00688474@highdent> X-Sender: toukie@highdent (Unverified) X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.3 (32) Date: Sun, 09 Nov 1997 13:55:04 +0100 To: chemistry@www.ccl.net From: "Hr. Dr. S. Shapiro" Subject: Biomembrane orderliness/disorderliness Cc: toukie@zui.unizh.ch Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear Colleagues; I am seeking recent reviews and original articles dealing with the state of "orderliness" or "disorderliness" of biomembranes and how small moelcular weight compounds interact with the membrane per se (as opposed to, for example, ligand interactions with discrete receptors in or on the membrane) to either enhance or reduce that membrane's state of orderliness. I would especially value publications dealing with real biomembranes, particularly bacterial membranes; but reports covering artificial membranes are also very welcome. Thanks in advance to all responders. Sincerely, S. Shapiro toukie@zui.unizh.ch From turner@ocisgi28.unizh.ch Mon Nov 10 03:33:14 1997 Received: from ocisgi28.unizh.ch for turner@ocisgi28.unizh.ch by www.ccl.net (8.8.3/950822.1) id DAA22375; Mon, 10 Nov 1997 03:30:55 -0500 (EST) Received: from ocisgi28.unizh.ch (localhost [127.0.0.1]) by ocisgi28.unizh.ch (950413.SGI.8.6.12/950213.SGI.AUTOCF) via ESMTP id JAA12275 for ; Mon, 10 Nov 1997 09:30:42 +0100 Sender: turner@ocisgi28.unizh.ch Message-ID: <3466C631.510F5D1C@ocisgi28.unizh.ch> Date: Mon, 10 Nov 1997 09:30:41 +0100 From: Alexander J Turner Organization: OCI - University of Zurich X-Mailer: Mozilla 4.03 [en] (X11; I; IRIX 6.3 IP32) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: C++ summary Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi! Thanks for all the info on C++. I enclose a summary covering several books. Best wishes Alex ############################################################################ Well, I can tell you what I used to learn C++ without any previous knowledge of C (but with experience with other programming languages): C++ Programming 101 by Greg Perry, published by SAMS Publishing. This is pretty much all I read, and I have been writing my own molecular dynamics code in C++ ever since then, so it must be pretty good. This book is at an introductory level, though, so depending on what you're looking for it may not be sufficient. Hope this helps. =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Naoko Akiya nakiya@engin.umich.edu University of Michigan Dept. of Chemical Engineering phone (313) 764-7121 Ann Arbor, MI 48109-2136 fax (313) 763-0459 =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= You might want to look at Scientific and Engineering C++ by J. Barton and L. Nachman. Addison-Wesley Publishing Co., ISBN # 0-201-53393-6 =================================================================== Enrico O. Purisima Biotechnology Research Institute e-mail: rico@bri.nrc.ca National Research Council of Canada phone : (514) 496-6343 6100 Royalmount Avenue fax : (514) 496-5143 Montreal, Quebec H4P 2R2 CANADA =================================================================== "cpluscplus.mal" 155 lines, 5453 characters > cat Suspended > jobs [1] - Suspended (tty input) rsh ocisgi15 /usr/programs/gv/gv [2] + Suspended cat > kill %2 > cat cpluscplus.mal Well, I can tell you what I used to learn C++ without any previous knowledge of C (but with experience with other programming languages): C++ Programming 101 by Greg Perry, published by SAMS Publishing. This is pretty much all I read, and I have been writing my own molecular dynamics code in C++ ever since then, so it must be pretty good. This book is at an introductory level, though, so depending on what you're looking for it may not be sufficient. Hope this helps. =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Naoko Akiya nakiya@engin.umich.edu University of Michigan Dept. of Chemical Engineering phone (313) 764-7121 Ann Arbor, MI 48109-2136 fax (313) 763-0459 =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= You might want to look at Scientific and Engineering C++ by J. Barton and L. Nachman. Addison-Wesley Publishing Co., ISBN # 0-201-53393-6 =================================================================== Enrico O. Purisima Biotechnology Research Institute e-mail: rico@bri.nrc.ca National Research Council of Canada phone : (514) 496-6343 6100 Royalmount Avenue fax : (514) 496-5143 Montreal, Quebec H4P 2R2 CANADA =================================================================== I used B.Stroustrup, "The C++ Programming Language", 2nd Ed., Addison-Wesley 1991 (it's the classic by the inventor of the language) and G.Buzzi-Ferraris, "From Fortran to C++: An Introduction to Oject-Oriented Programming Applied to Numerical Problems", Addison-Wesley 1991 or later 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 Professor Turner: There is an *excellent* book on C++ that I would recommend highly: "Practical C++ Programming" by Steve Oualline O'Reilly & Associates, Inc. 1995 (list price is 32.95 U.S. dollars) In general, computer books published by O'Reilly tend to be extremely well-written and user-friendly. Good luck! --Jack Hammer Graduate Student, Yale University Dear Dr.Turner, There is a lot of C++ tutorial on the net. You can find a list of them at http://www.yahoo.com/Computers_and_Internet/Programming_Languages/C_and_C__/ http://www.strangecreations.com/library/c/index.htm Hope this help. Yours, Somsak Tonmunphean. Hi I stumbled upon this WWW site which is quite a useful resource for C, C++, and Java. http://www.mit.edu:8001/afs/athena.mit.edu/user/t/h/thomasc/Public/ prog/index.html I still ended up buying a book though. (I'm not at my desk right now, so I can't remember which one.) Regards Rod ------------------------------------------------- R. M. Macrae Muon Science Laboratory Institute of Physical and Chemical Research (RIKEN) e-mail: macrae@rikaxp.riken.go.jp (normal) and : macrae@rikmtl.riken.go.jp (MIME-encoded) Tel : (81) 484 62 1111 ext 3336 Fax : (81) 484 62 4648 ------------------------------------------------- Stroutstrup's original book (the C++ programming language) is not bad for people who already know programmin in general - it teaches C++ without first teaching you what a variable is. There is a book called "Scientific and Engineering C++" (or a similar title), published by Addison-Wesley, which is of a more advanced nature (not necessarily a very good introduction, although it claims to be), but aims at the correct audience. It's probably easier to learn C++ with some well-written and meaningful code at hand. -- ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Hi Alex, the same question I asked half a year ago. I got the following answer : John J. Barton, Lee R. Nackman Scientific and Engineering C++ An Introduction with Advanced Techniques and Examples Addison Wesley Longman, Inc., 1994, Reprint March 1997 ISBN 0-201-53393-6 I think, it is really good. From the preface : "We expect the book to be useful to three (overlapping) groups : (1) Engineers and scientists who are experienced programmers in FORTRAN or C, (2) Professional programmers experienced in C or C++ lloking for a new systematic discussion of object-oriented programming in C++, and (3) C++ programmers interested in advanced examples useful as a basis for scientific and engineering programming." Hope this helps, Ciao Heinz -- Dr. Heinz Schiffer Phone ++49-69-305-2330 Hoechst Research & Technology Fax ++49-69-305-81162 Scientific Computing, G864 Email schiffer@h1tw0036.hoechst.com 65926 Frankfurt am Main Schiffer@CRT.hoechst.com ------------------------------------------------------------------- | Dr. Alexander J Turner | | | Universitaet Zuerich |Tel.: (41)-1-6354239 | | Organisch-Chemisches Institut|Fax: (41)-1-6356812 | | Winterthurerstrasse 190 | | | CH-8057 Zuerich |E-Mail: turner@ocisgi28.unizh.ch | | Switzerland | | ------------------------------------------------------------------- From rivelino@ufba.br Mon Nov 10 08:32:08 1997 Received: from lencois.ufba.br for rivelino@ufba.br by www.ccl.net (8.8.3/950822.1) id IAA23174; Mon, 10 Nov 1997 08:25:38 -0500 (EST) Received: from localhost by lencois.ufba.br (AIX 4.1/UCB 5.64/4.03) id AA26392; Mon, 10 Nov 1997 10:22:54 -0300 Date: Mon, 10 Nov 1997 10:22:53 -0300 (GRNLNDST) From: Roberto Rivelino de Melo Moreno To: chemistry@www.ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Here are the answers about Li2 molecule data: ********************************************************************* I would look in Huber and Herzberg, "Constants of Diatomic Molecules". They have data. The book was published in 1979 so there may be newer references. The book contains data for 5 observed electronic states. Martin L. Sage Syracuse University ********************************************************************* Hello: In general, "K. P. Huber, and G. Herzberg, Molecular Spectra and Molecular Structure, Vol. IV., Constants of Diatomic Molecules, (Van Nostrand, Toronto, 1979)." is an extremely useful book. It is a compilation (and critical evaluation) of practically all known spectroscopic data for all diatomics UP TO 1979. For Li2, D_0=1.04(6) ; R_e=2.6729 Angstrom; and omega_e=351.4 cm-1. The latter is not from HH, it is from: D.D. Konalow and M. L. Olson, J. Chem. Phys. 71, 450 (1979). When I don't find the info on the diatomic I want, I try: M. D. Morse, Chem. Rev. 86, 1049-1109 (1986) [transition-metal dimers] or make an author search (mostly in J. Chem. Phys.) for articles having as co-author either: M. D. Morse or B. Simard or A. J. Merer or R. W. Field or C.W. Bauschlicher; I'm sure this is very incomplete list, but it's often a good starting point for the diatomics that I am interested in (transition metals). Cheers, Rene Fournier. *************************************************************************** Did you check Huber and Herzberg? The full title is something like "Constants of Diatomic Molecules" and it is volume 4 in the Herzberg set of classics. ************************************************************************** May be in : V. Bonacic-Koutecky, P. Fantucci and J. Koutecky, Chem. Rev. , 91, 1035 (1991). They deal wit Li clusters and possibly refer to experimental data. (I Cannot remember exactly) Hope it helps Pascal ***************************************************************************** If you do a web search on Li clusters, some references will come up. Irene Newhouse **************************************************************************** Sear Sir Probably, you can find some fererences in {Ab initio potential energy surface and vibrational energies of Li-over 3.} {Chemical Physics Letters, APR 25 1997 v 269 n1/2} Timothy G Shinkevich Postgraduate student of Laboratory of Spectrochemistry of Chemical dep. of St.Petersburg State University *************************************************************************** I think there are references for electron affinity and UV spectra of diatomic molecules in the CRC Handbook of Chemistry and Physics. *************************************************************************** Thanks all. From mattacf@mcmail.CIS.McMaster.CA Tue Nov 11 00:32:17 1997 Received: from mcmail.CIS.McMaster.CA for mattacf@mcmail.CIS.McMaster.CA by www.ccl.net (8.8.3/950822.1) id XAA00137; Mon, 10 Nov 1997 23:34:20 -0500 (EST) Received: from localhost (mattacf@localhost) by mcmail.CIS.McMaster.CA (8.8.5/8.8.5) with SMTP id XAA04660; Mon, 10 Nov 1997 23:34:15 -0500 (EST) Date: Mon, 10 Nov 1997 23:34:15 -0500 (EST) From: "C.F. Matta" To: chemistry@www.ccl.net cc: gene@q-chem.com, jim@wavefun.com, SusanBoyd@chiroscience.com, davidm@chiroscience.com, Krys.Radacki@ac.RWTH-Aachen.DE, MOL@Lundbeck.com, willsd@appstate.edu, LAVELLE@MBI.UCLA.EDU, kruger@che.und.ac.za, jmartell@lyon.edu, jparikh@ari.net Subject: Hyperchem Hardware (REPLIES) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Colleagues, I appreciate very much your response to my question. I thank all those who took the time to enlight me with their experience: Dr. Eugene Fleischmann, Dr. John Parikh, Dr. Jim Parisi, Dr. Suzan Boyd, Dr. Krys Radacki, Dr. Morten Langgrd, Dr. Steve Williams, Dr. Jaime Martell, Dr. Laurence Lavelle, Dr. Gert Kruger. Thank you all for your help. The following is a listing of the individual replies: REPLIES: ======= Dear Prof. Matta, You may wish to consider purchasing Q-Chem to perform your ab initio calculations. Without getting into too much detail, much more information about our many features may be obtained from our wegsite at: http://www.q-chem.com. We are able to integrate smoothly with the HyperChem interface, yet we provide an ab initio program that extends the power and capability of HyperChem. If you are interested, please let me know. Sincerely, Eugene Fleischmann - +--------------------------------------------------------------------+ | Eugene D. Fleischmann, Ph.D. http://www.q-chem.com | | Director of Sales | | Q-Chem, Inc. voice: (609) 896-3942 | | 317 Whipple St. FAX: (609) 896-1244 | | Pittsburgh, PA 15218 email: gene@q-chem.com | +--------------------------------------------------------------------+ ************************************************************* Dear Dr. Matta, Go for the maximum you can afford. John Parikh AHSystems Group 5401 Lakeford Lane, Suite L-1 Bowie, MD 20720 Phone (301) 352-0896 Fax (301) 352-0199 Web Site: http://www2.ari.net/ahsystems/wwwhome.htm *************************************************** Dr. Matta, I saw your note on the CCL and thought you might want to take a look at PC Spartan. PC Spartan is a great molecular modeling program similar to Hyperchem, with exceptional graphics and computational tools including a fast ab initio enginge. And it only costs $449. PC Spartan and MacSpartan are both subsets of our flagship program, Spartan 5.0 for UNIX. All our software has been designed with the same easy to use interface, making it ideal for for teaching purposes as well as research. Additionally, our programs are not interfaces to other computational backends. All computational methods are included within the program. All our software is completely seamless -- one program at one price. FEATURES: PC Spartan and MacSpartan include: 1. A Graphical User Interface that includes BUILDERS for: A. Organic Molecules B. Polypeptides C. Transition States 2. Calculations using the following methodologies: A. Molecular Mechanics (SYBYL) B. Semi-Empirical (AM1) C. Ab Initio Hartree-Fock (3-21G and 6-31G* basis sets) 3. Displays: A. Structure B. Molecular Orbitals, electron densities, electrostatic potentials C. Vibration Animation We also offer an enhanced version of PC Spartan and MacSpartan. These programs, PC Spartan Plus and MacSpartan Plus, are identical to their predecessors, except they include our inorganic "expert" molecule builder, enhanced import and export capabilities, and the PM3/PM3(tm) semi-empiricalmethod. This is an exciting feature. We are the only company to offer semi-empirical parameters for transition metals. PLATFORM: PC Spartan requires a 486 or Pentium system with much the same configuration. PC Spartan requires Windows 95/NT. All appropriate screens are supported, but the minimum for practical use is 13". For optimal performance, I recommend at least 32 MB of RAM and a fast Pentium processor. US/NAFTA PRICES: Academic Price MacSpartan/PC Spartan: $299 Academic Price MacSpartan Plus/PC Spartan Plus: $449 You can place orders by contacting us at macsales@wavefun.com or 714/660-6101 (voice) 714/955-2118 (fax). -- Jimbo Jim Parisi US Marketing Manager ----------------------------------------------------------------- WAVEFUNCTION, INC. Phone: 714-955-2120 18401 Von Karman, Suite 370 FAX: 714-955-2118 Irvine, CA e-mail: jim@wavefun.com 92612 USA WEB: http://www.wavefun.com ************************************************************* From: "Boyd, Susan" Thank you for your email. I am currently on maternity leave, but will be checking my email periodically (but probably not daily!) until I return, which is expected to be early in 1998. If your request is urgent, please contact David Manallack (davidm@chiroscience.com) who will be able to contact me directly. Thanks a lot! Susan Boyd ************************************************************* Shortly i can answer: HC for SGI. On PC (only pentium) i've tried to calculate on 631G+ molecule with 7 heavy and 8 hydrogens atoms and it takes to much time (days) and HD-space (hundrets Kb). Now am useing Gaussian on SGI and 11-heavy 11-hydrogen atoms molekule need to optimised geometry 13 h (without symmetry) or 2.5 (C-5v symmetry). Krzys Radacki _________________________---------------------------------------------------- ------------------------- e-mail: Krys.Radacki@ac.RWTH-Aachen.DE --- ************************************************************* It is very difficult question to answer. My first comment will be something like - don't even think about it. At least I think you should forget about HyperChem for this kind of jobs. HyperChem is a very nice program, but unfortunately extremely slow for ab initio work. This is mainly due to an inefficient optimization algorithm. You should also be aware that HyperChem only regards the energy gradient as optimization criteria. You are saying HyperChem 05 (I guess that it should be 5.0), which means that you are talking about a WIN95/WIN-NT PC platform. Then you should go for a 300MHz Pentium II, with the maximum ram it can hold (about a 1 Gb). A fast SCSI disk system may also be considered if the calculation needs to swap (HyperChem swaps a lot). My guess is that your calculation could be done within a week on such a system, but maybe we are talking about months. If we are talking about speed and PC's, I will strongly recommend that you buy Gaussian 94w instead. G94w is at least 10 times faster than HyperChem and it has a much safer optimization algorithm and criteria. It should be possible to carry out your calculation on a PC, but it is definitely more suitable for a high end UNIX system. Hope this helps Best regards Morten "[iso-8859-1] Morten Langgrd" ************************************************************** Why don't you use gaussian94 for windows? The 32 bit (win95, NT) version is much cheaper, much more complete in its electronic structure capabilities, and much faster than hyperchem. For your contemplated ~600 or os basis functions it would be crazy NOT to do this with a direct scf method which hyperchem does not have. You will likely need several gigs of disk just for the integral file that hyperchem will write, and there is NO disk controller that can compete with direct scf for getting these integrals into the fock matrix. Steve Steve Williams F F F Chemistry \ / \ / Appalachian State University Al Al Boone, NC 28608 / \ / \ USA F F F willsd@appstate.edu ************************************************************* Are you sure Hyperchem is capable of this. You might also want to check out Q-Chem (www.q-chem.com), Jaguar (www.psgvb.com) and Gaussian (www.gaussian.com). Gaussian has the most capabilities, the other two are specifically designed to be faster for larger systems. >What sort of CPU, RAM, virtual memory, and HD space should I aim at if I'd >like such a job to converge within a few days? As much as you can afford. My minimum suggestion would be 128 MB RAM, 4 GB disk. Best wishes Jaime Jaime Martell, Ph.D. P.O. Box 2317 Camille and Henry Dreyfus Fellow Batesville, AR 72503-2317 Biology and Chemistry Division Phone: 870-698-4688 Lyon College Fax: 870-698-4622 *************************************************************** Hi C.F, Your question does not state which OS, and if you intend to use other software at the same time as HyperChem. I will assume (and recommend) that you are using NT Workstation and no other (large) software. HyperChem 5.02 is the fastest HyperCube offers for ab initio calculations. There are however, faster ab initio packages. HyperChem has options within ab initio that greatly reduce the RAM and virtual memory requirements. So 64MB of RAM and 200MB virtual memory would be fine for your calculations. To give you an example of what I mean by greatly reduced memory requirements with respect to the 2e-integrals: For a system with 731 (=m) basis functions. Not using direct SCF (more memory, less CPU time): # 2e- integrals = 3.5 x 10^10 and memory required = 571 GB But using direct SCF (less memory, more CPU time): The # 2e- integrals = m^2 log m = 1.5 MB So clearly you would use direct SCF. However I should also inform you that: The original required memory was 571 GB which on using the (much more) computationally intensive direct SCF was reduced to ~1.5 MB (depending on the 2e- integral cutoff point) and finally HC actually limits the total 2e- integral storage to 256KB of RAM, and if it is larger than 256KB it writes to HD. Although I have asked HyperCube why the 256KB RAM limitation, I have had no reply. So you don't need lots of RAM and virtual memory, what you need is fast RAM. terms of HD's I recommend a fast (7200-10000RPM), large (~8GB, because you always need storage space) with 0.5 to 1MB buffer. Or start with one 4GB (similar specs) and add another HD when you need it. Here comes the bad news. If you want these jobs (70 atoms, using 6311++G** with ~650 basis functions) to converge in two days there is no PC (with HyperChem) available to do it. Which means you need a large capital expenditure to buy some non-Intel/AMD/Cyrix unix/NT machine (e.g. Digital Alpha 600MHz workstation, etc). However things would be different if HyperChem was a multi-threaded application. All the major vendors produce multi-CPU machines (NCR, HP, SGI, Digital, etc.) not to mention that one can order a multitude of inexpensive multi-CPU clones. In addition the strongest HyperChem user base is the PC or PC-workstation/server with MS-Windows as the OS. Windows NT (Workstation & Server) is one of the few OS's that utilizes multi-CPU hardware. Some of your options are: Spend 5 to 10 times more on a non-Intel unix/NT machine. Wait for HyperCube to release a multi-threaded version of HyperChem. **Buy a PC with a Pentium II, 300MHz processor with 512KB to 1MB L2 cache and wait twice as long for the results. **Best option. Laurence Lavelle Laurence Lavelle, Ph.D. University of California Los Angeles Molecular Biology Institute, and Department of Chemistry & Biochemistry Laboratory of Structural Biology & Molecular Medicine Los Angeles, CA 90095-1570, USA Email:LAVELLE@MBI.UCLA.EDU Phone (Lab): (310) 206-8270 Phone (Office): (310) 825-2083 Fax: (310) 267-1957 http://www.doe-mbi.ucla.edu/people/lavelle/lavelle.html """"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" ************************************************************** Dear colleque, I can not answer your question although I would like to share some of our experience with you. I would not use Hyperchem for abinitio calculations for the simple reason one can not impose symmetry to your structure. This option is available in a program like Gaussian (other as well) which saves alot on computor time. Hyperchem would be unpractical using abinitio calculations of structures with some symmetry. Best wishes Gert Kruger __________________________________________________________ Dr HG Kruger, Dept Chemistry, University of Natal, PO Box 18091, Dalbridge 4014, Durban, South Afica Tel +27-31-2602181 Fax +27-31-2603091 Email kruger@che.und.ac.za ************************************************************* END OF RESPONSES ************************************************************* THE SUBMITTED QUESTION WAS: ============================ Date: Wed, 5 Nov 1997 09:49:09 -0500 (EST) From: "C.F. Matta" To: chemistry@www.ccl.net Subject: Hypechem Hardware Resources Hi everybody, I am planning to upgrade a machine with the intension to purchase Hyperchem 05. I am interested to obtain highly accurate ab initio wavefunctions medium-sized organic molecules (C,O,N,H) at a RHF 6-311++G**//6-31+G* level of theory). Such molecules would have approx 70 atoms (including H), and using 6311++G** we are talking perhaps of 650 basis functions and perhaps some 1200 primitives. What sort of CPU, RAM, virtual memory, and HD space should I aim at if I'd like such a job to converge within a few days? Thank you very much. C.Matta McMaster University, McMaster University, Hamilton, Ontario, Canada. From bkraus@best.com Tue Nov 11 13:50:09 1997 Received: from proxy4.ba.best.com for bkraus@best.com by www.ccl.net (8.8.3/950822.1) id NAA03888; Tue, 11 Nov 1997 13:03:30 -0500 (EST) Received: from Best.best.com (bkraus.vip.best.com [204.156.137.4]) by proxy4.ba.best.com (8.8.7/8.8.BEST) with SMTP id JAA00442; Tue, 11 Nov 1997 09:57:54 -0800 (PST) From: "Bill Kraus" To: "Konrad Hinsen" , Cc: , , , , , Subject: Re: CCL:Sequence Classes and CORBA Servers Date: Tue, 11 Nov 1997 09:54:56 -0800 Message-ID: <01bceeca$eb975820$04899ccc@Best.best.com> 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 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 >Jeroen Coppieters writes: > >> OO has been around for a long time (and has been thought to undergrads for >> ages). Many developers of scientific software (both academic and >> commercial) are well educated in OO. On the other hand many life science >> researchers have been thinking about objects, long before OO became >> fashionable. > >Konrad Hinsen writes: >Maybe other branches of life sciences are more up to date, but in the >field I am familiar with (protein modelling), I couldn't name any >widely used tool based on OO technology, much less any published >OO interface used by more than one software supplier. Yes, there >are OO libraries etc. for certain applications, but they are used >only by a handful of people. > >> world. I agree that innovative work happens in academic groups and small >> companies. But that does not mean that a standard interface for common >> objects would restrain that research. There is a core of entities, that > >It might prove insufficient and would then not be used at all. > I must add my support to what Konrad is saying. As a commercial software developer who has written bioinformatics apps (e.g. MacVector, AssemblyLIGN) as well as others (e.g. Adobe PageMill), and as someone who has been architecting systems using OO technology for the last ten years (even doing time at the ill-fated Taligent effort), using OO technology is no guarantee. In fact, it's been my experience that there is a significant risk to standardizing object interfaces - the resulting APIs can either be too constraining or so generalized as to be useless. Although Jeroen states that many developers of scientific software may be "well educated in OO", the proof is in the pudding - many of the systems I've seen may have been OO, but were not well architected (e.g. suffered >from lack of transitive closure, used multiple inheritance inappropriately), and as a result could not be easily extended. Standards are a good thing, but the standardization must come at a level where it creates opportunities, not restricts them. From ccl@www.ccl.net Mon Nov 10 15:32:13 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id OAA25059; Mon, 10 Nov 1997 14:44:24 -0500 (EST) Received: from origin.gig.usda.gov for srheller@gig.usda.gov by bedrock.ccl.net (8.8.6/950822.1) id OAA22593; Mon, 10 Nov 1997 14:44:23 -0500 (EST) Received: by origin.gig.usda.gov (5.x/SMI-SVR4) id AA20902; Mon, 10 Nov 1997 14:33:28 -0500 Date: Mon, 10 Nov 1997 14:33:27 -0500 (EST) From: "Stephen R. Heller" To: jcicshelp , chemistry@ccl.net, chminf-l@iubvm.ucs.indiana.edu, orgchem@extreme.chem.rpi.edu Subject: sofwtare for review Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Status: RO Content-Length: 1992 10 November, 1997 Subject: Computer Software for Review As the Software Review Editor for the ACS Journal of Chemical Information and Computer Science (JCICS) I often get software for review in the journal. I have one (1) new software products. I am looking for a person who is willing to review this software product. In return for the review which is published in JCICS you get to keep the software or database. The review should be completed in 1-3 months. The length of the review is 4-10 double spaced typed pages. Sample reviews can be found in most of the recent issues of JCICS. Please try to give me some (short) reason to choose you over another person. I have tried this approach for about the past five years and it is working reasonably well. (REMINDER: For those who haven't finished your reviews of software sent months and months ago, this last sentence does not apply to you!) As a result, I am continuing this new method to find reviewers using this e-mail/user group system. I reserve the right to abandon this if it is a problem, or inappropriate. I will not notify people if I have found a reviewer. If you don't hear from me within a few days I have chosen someone else to review the particular package. As I get many, many, (too many) replies to this message, please do not respond after 12 November 1997 (Wednesday), as I am sure the software will be gone by then. I can be reached on Internet (SRHELLER@GIG.USDA.GOV). PLEASE BE SURE TO INCLUDE AN STREET ADDRESS, PHONE, and FAX NUMBER!!! (I usually send the software by Federal Express.) Without this information I WILL NOT consider your request. Steve Heller The package I now have is: 1. Life Science Workbench 1.0/Data Analysis Toolkit for Windows95/NT or Macintosh from MDL. Steve Heller, NIST Bldg. 221, Room A111 Gaithersburg, MD 20899 USA Phone: 301-975-3338 or 2204 FAX: 301-975-3670 E-mail: srheller@gig.usda.gov WWW: www.hellers.com/~steve From arthur@csb0.IPC.PKU.EDU.CN Wed Nov 12 23:32:42 1997 Received: from csb0.IPC.PKU.EDU.CN for arthur@csb0.IPC.PKU.EDU.CN by www.ccl.net (8.8.3/950822.1) id XAA22742; Wed, 12 Nov 1997 23:25:24 -0500 (EST) Received: by csb0.IPC.PKU.EDU.CN (920330.SGI/940406.SGI.AUTO) for chemistry@www.ccl.net id AA10330; Thu, 13 Nov 97 12:25:09 -0800 Date: Thu, 13 Nov 1997 12:25:08 -0800 (PST) From: Wang Arthur To: CCL mailing list Subject: logP and solubility for Amino Acids and peptides Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLer We are currently on a project of de novo protein design. A set of scales which describe the hydrophobicities of the natural amino acids is what we badly need. So, would you please kindly provide any clue for the following issues: (1) Any paper describing such a set of scales (2) LogP values for the 20 natural amino acids and oligopeptides (up to buta- or pentapeptides). (3) Solubilities for these amino acids and oligopeptides. I will surely put back the summary. Meanwhile, please receive my best wishes. Arthur _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ Arthur Wang Doctoral Candidate _/ _/ Molecular Design Lab _/ _/ Institute of Physical Chemistry, Peking University _/ _/ Beijing 100871, P.R.China _/ _/ _/ _/ E-mail: arthur@ipc.pku.edu.cn _/ _/ Tel: 86-10-62751490 Fax: 86-10-62751725 _/ _/ WWW: http://www.ipc.pku.edu.cn/moldes/arthur/home.html _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ From tmmec@fcindy5.NCIFCRF.GOV Wed Nov 12 23:36:13 1997 Received: from ncisun1-nf0.ncifcrf.gov for tmmec@fcindy5.NCIFCRF.GOV by www.ccl.net (8.8.3/950822.1) id WAA22542; Wed, 12 Nov 1997 22:56:35 -0500 (EST) Received: from fcindy5.NCIFCRF.GOV (fcindy5.NCIFCRF.GOV [129.43.50.12]) by ncisun1-nf0.ncifcrf.gov (8.8.7/8.7.3) with SMTP id WAA20865 for <@fcs280s.NCIFCRF.GOV:chemistry@www.ccl.net>; Wed, 12 Nov 1997 22:56:14 -0500 (EST) Received: by fcindy5.NCIFCRF.GOV (950413.SGI.8.6.12/911001.SGI) for chemistry@www.ccl.net id WAA01714; Wed, 12 Nov 1997 22:56:56 -0500 Date: Wed, 12 Nov 1997 22:56:56 -0500 From: tmmec@fcindy5.NCIFCRF.GOV (tmmec) Message-Id: <199711130356.WAA01714@fcindy5.NCIFCRF.GOV> To: chemistry@www.ccl.net Subject: TMMEC - NEW PAPERS Dear List Administrator. 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