From toukie@zui.unizh.ch Mon Aug 12 03:16:58 1996 Received: from rzusuntk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.7.5/950822.1) id CAA12278; Mon, 12 Aug 1996 02:25:21 -0400 (EDT) Received: from rzurs3.unizh.ch by rzusuntk.unizh.ch (4.1/SMI-4.1.9) id AA28885; Mon, 12 Aug 96 08:25:14 +0200 Received: by rzurs3.unizh.ch (AIX 3.2/UCB 5.64/4.03) id AA06968; Mon, 12 Aug 1996 08:25:13 +0200 From: toukie@zui.unizh.ch (Hr Dr. S. Shapiro) Message-Id: <9608120625.AA06968@rzurs3.unizh.ch> Subject: Summary on deconvoluting software To: chemistry@www.ccl.net Date: Mon, 12 Aug 1996 08:25:12 +0200 (MEST) Cc: dhyams@eng.clemson.edu, toukie@zui.unizh.ch X-Mailer: ELM [version 2.4 PL25 PGP2] Content-Type: text Dear Colleagues; A few days ago I posted a query about PC programmes than can be used for deconvoluting spectra or chromatogrammes. Despite the season a number of useful replies were forthcoming, which I wish to summarise for the list. One respondent advised me of a programme written in FORTRAN77 named LGFIT2, which will deconvolute complex spectra into sets of overlapping Lorentzian or Gaussian bands, and which is downloadable from http:// www.kfa-juelich.de:80/ zam/CompServ/software/mathe/mathsrc/cpc/abmk.cpc; unfortunately, at the moment I myself can't download from the WWW. Moreover, I have neither the tools nor the skills to port a FORTRAN77 programme to DOS/Windows. However, if anybody out there would be willing to undertake such a challenging port and actually port and g port and actually suc- succeeds, I would very much like to hear from you later. r from you [3~ceeds, I would very much like to hear from you later. Another kind correspondent pointed out that the principle of superposition says that a chromatogramme or spectrum consisting of two overlapping peaks can be expressed as f(x) = A*exp((-a)*(x-xa)**2)) + B*exp((-b)*(x-xb)**2)) so it is "simply" a matter of calculating appropriate values for A, a, xa, B, b, and xb that will regenerate your spectrum or chromatogramme of interest. He added that it shouldn't be such a formidible task to do this by hand (well, I suppose not if you've hand a brain implant from Riemann) but that it can also be done rather simply using Excel or some similar spreadsheet programme. Again, unfortunately, I don't have ready access to Excel or related spreadsheet pro- grammes, and a couple of "quickie" attempts to arrive at the six parameters by hand weren't very fruitful. Finally, I did a WWW (Lycos) search for "curve fitting" and located a Win- dows shareware programme by Prof. Dr. Daniel Hyams of Clemson University that did the trick. Since the sum of two Gaussians is not included in the pro- gramme's repertoire of mathematical models, I simply added the aforementioned equation to "User's Models" and ran my data through it on a Pentium-90 MHz fit- ted with MS-DOS 6.2 + Windows for Workgroups 3.11 + 80 MB RAM. A minute or two after initiating the calculation out popped a set of six parameters which gene- rated a curve mathing my experimental one with a correlation coefficient r = 0.9999, which I think you will agree is reasonably acceptable. Since Prof. Dr. Hyams' programme is shareware (registration fee = US$35.-), I hesitate to provide the FTP site from which I downloaded it. For details, I suggest that you contact Prof. Dr. Hyams personally at dhyams@eng.clemson.edu. With kindest regards, S. Shapiro ZH toukie@zui.unizh.ch From owner-chemistry@ccl.net Mon Aug 12 06:17:02 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.5/950822.1) id FAA15906; Mon, 12 Aug 1996 05:24:07 -0400 (EDT) Received: from tifrvax.tifr.res.in for RANJAN@tifrvax.tifr.res.in by bedrock.ccl.net (8.7.5/950822.1) id FAA15148; Mon, 12 Aug 1996 05:24:00 -0400 (EDT) Received: from tifrvax.tifr.res.in by tifrvax.tifr.res.in (PMDF #12198) id <01I86XMX2NBK000387@tifrvax.tifr.res.in>; Mon, 12 Aug 1996 14:54 +0530 Date: Mon, 12 Aug 1996 14:54 +0530 From: Ranjan Das Subject: Re: CCL:basic fluorescence information To: chemistry@ccl.net Message-id: <01I86XMX2NBK000387@tifrvax.tifr.res.in> X-VMS-To: IN%"chemistry@ccl.net" Benzoquinones do not fluoresce. Their ISC rate is exceedingly high and they go to triplet state with quantum efficiency of almost unity. Ranjan Das Tata Institute of Fundamental Research Bombay 400005. From owner-chemistry@ccl.net Mon Aug 12 09:17:05 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.5/950822.1) id JAA16979; Mon, 12 Aug 1996 09:05:44 -0400 (EDT) Received: from tiger.chem.uw.edu.pl for janr@tiger.chem.uw.edu.pl by bedrock.ccl.net (8.7.5/950822.1) id JAA16333; Mon, 12 Aug 1996 09:05:39 -0400 (EDT) Received: by tiger.chem.uw.edu.pl (AIX 3.2/UCB 5.64/4.03) id AA19791; Mon, 12 Aug 1996 15:02:46 +0200 Date: Mon, 12 Aug 1996 15:02:46 +0200 From: janr@tiger.chem.uw.edu.pl (Jan Radomski) Message-Id: <9608121302.AA19791@tiger.chem.uw.edu.pl> To: chemistry@ccl.net Subject: Q: hands-on experience with some new Tripos' products? Cc: janr@tiger.chem.uw.edu.pl Dear Netters, I'd like to get any info about pros & cons, hands-on etc. on the following new products from Tripos: [1] Advanced CoMFA; [2] Hdisq; [3] DiverseSolutions; [4] clogP. I'll summarise for the net. TIA & best regards, Jan Radomski From vvw@dialup.oar.net Mon Aug 12 09:26:30 1996 Received: from dialup.oar.net for vvw@dialup.oar.net by www.ccl.net (8.7.5/950822.1) id IAA16745; Mon, 12 Aug 1996 08:24:50 -0400 (EDT) Received: for vvw@dialup.oar.net by dialup.oar.net (8.6.10/931123.1402) id IAA10018; Mon, 12 Aug 1996 08:21:40 -0400 Date: Mon, 12 Aug 1996 08:21:38 -0400 (EDT) From: Vernon Walatka To: chemistry@www.ccl.net Subject: Smiles Code: Thank you Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I want to thank everyone who responded to my request for information about Smiles code. The WWW references were very helpful as well as the original paper by David Weininger. I was able to get the information that I needed. Thank you. Vernon Walatka Quantum Chemical Cincinnati, Ohio USA From ASZY%PLPUAM11.BITNET@phem3.acs.ohio-state.edu Mon Aug 12 09:31:39 1996 Received: from phem3 for ASZY%PLPUAM11.BITNET@phem3.acs.ohio-state.edu by www.ccl.net (8.7.5/950822.1) id IAA16749; Mon, 12 Aug 1996 08:25:48 -0400 (EDT) Received: from PLPUAM11.AMU.EDU.PL (MAILER@PLPUAM11) by phem3.acs.ohio-state.edu (PMDF V4.2-13 #5888) id <01I86K2U7Z1S8WVYQS@phem3.acs.ohio-state.edu>; Mon, 12 Aug 1996 08:25:44 EDT Received: from PLPUAM11 (ASZY) by PLPUAM11.AMU.EDU.PL (Mailer R2.07) with BSMTP id 2547; Mon, 12 Aug 96 14:25:08 CET Date: Mon, 12 Aug 1996 14:16:53 +0100 (CET) From: "A.Szyczewski" Subject: QSAR program To: chemistry@www.ccl.net Message-id: <01I86K2U7Z1U8WVYQS@phem3.acs.ohio-state.edu> X-Envelope-to: chemistry@www.ccl.net Content-transfer-encoding: 7BIT Dear Netters, I look for the program for QSAR (quantitative structure - activity relation- ship) calculations for PC - Pentium (the best, shareware version) Who could help me in this matter. E-mails could you send directly to me. Thank in advance. Andrzej Dr.Andrzej Szyczewski Institute of Physics A.Mickiewicz University Umultowska 85 61-614 Poznan/Poland e-mail: aszy@plpuam11.amu.edu.pl, aszy@phys.amu.edu.pl fax: (++4861) 217-991 From sennettm@world.std.com Mon Aug 12 10:17:15 1996 Received: from europe.std.com for sennettm@world.std.com by www.ccl.net (8.7.5/950822.1) id JAA17332; Mon, 12 Aug 1996 09:52:31 -0400 (EDT) Received: from world.std.com by europe.std.com (8.7.5/BZS-8-1.0) id JAA01432; Mon, 12 Aug 1996 09:52:25 -0400 (EDT) Received: by world.std.com (5.65c/Spike-2.0) id AA02278; Mon, 12 Aug 1996 09:48:22 -0400 Date: Mon, 12 Aug 1996 09:48:22 -0400 From: sennettm@world.std.com (Michael S Sennett) Message-Id: <199608121348.AA02278@world.std.com> To: chemistry@www.ccl.net Subject: 2nd CALL/ACS, SF/AUG 15 DEADLINE SECOND CALL FOR PAPERS FOR THE SPRING 1997 ACS MTG. IN SAN FRANCISCO DIVISION: COMP *** PLEASE NOTE THE 15 AUGUST 1996 DEADLINE FOR TITLE SUBMISSION *** CALL FOR PAPERS American Chemical Society 213th National Meeting Division of Computational Chemistry (COMP) April 13-17, 1997, San Francisco, CA SIMULATIONS OF INORGANIC AND ORGANOMETALLIC MATERIALS Papers are solicited for the above symposium. Due to a relocation of the organizer during the past several months, would-be presenters may have encountered difficulty in contacting me, and I apologize for the inconvenience. This symposium was conceived as a forum for the discussion of issues related to the modeling of materials other than organic polymers. At this time I am requesting input of titles/subjects of proposed presentations. Topics include (but are not limited to) simulation of metals, metal alloys, ceramics, hybrid or composite materials. Simulation of surface and interphase phenomena including small molecule binding and catalysis would, I think, also be appropriate to this symposium. It is necessary to have the initial input NO LATER than 15 August 1996 for planning purposes. Abstracts are required by October 25th 1996. Abstract forms can be obtained from ACS by calling 1-800-227-5558 (press 9-4-0); via the web at http://ww.acs.org/memgen/meetings/abstract.htm; or by writing to ACS, 1155 Sixteenth Street, NW, Washington, D.C. 20036. RESPOND BY 15 AUG. 1996 to: Dr. Michael Sennett Abiomed R&D Inc. 24 Cherry Hill Drive Danvers, MA 01923 tel. 508-777-5410 x724 fax 508-774-6641 email: sennettm@world.std.com *********************************** From bakasov@ictp.trieste.it Mon Aug 12 11:17:07 1996 Received: from ictpsp6.ictp.trieste.it for bakasov@ictp.trieste.it by www.ccl.net (8.7.5/950822.1) id KAA17568; Mon, 12 Aug 1996 10:17:33 -0400 (EDT) Received: (from bakasov@localhost) by ictpsp6.ictp.trieste.it (8.6.9/8.6.9) id QAA05441; Mon, 12 Aug 1996 16:14:50 +0200 Date: Mon, 12 Aug 1996 16:14:49 +0200 (MET DST) From: Bakasov Ayaz To: chemistry@www.ccl.net Subject: 3d-integration, interpolation, differentiation Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters, your enourmous integral knowledge must provide the right answer to the following: There is a really urgent need to pick up a reliable version of a FORTRAN code which is capable of making 3d-integration, as well as codes which can do 3d-interpolation and differentiation for smooth enough functions. There is NO need in extreme efficiency, it must have normal efficiency but be reliable enough. A freeware is needed, ftp-able, or obtainable from authors, or otherwise. May be GNU has something?! Any one knows? The functions I am working with are quite smooth: these are basically an electrostatic potential in molecule or some related function. Besides, if any one knows free FORTRAN code, which is specialized on the 3d-integration, interpolation and differentiation for 3d-Gaussian functions - that would be simply great! Summary will be posted - no doubt. Sincerely, Ayaz Bakasov. ***************************************************** actually, I use the address aiba@ir.phys.chem.ethz.ch most often, but due to some mysterious reasons the ccl-emailer rejects my postings from that address, and I decided to give this address a try :-) ***************************************************** From owner-chemistry@ccl.net Mon Aug 12 12:17:12 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.5/950822.1) id LAA18179; Mon, 12 Aug 1996 11:37:36 -0400 (EDT) Received: from rune.biokemi.su.se for arne@rune.biokemi.su.se by bedrock.ccl.net (8.7.5/950822.1) id LAA19154; Mon, 12 Aug 1996 11:37:27 -0400 (EDT) Received: (from arne@localhost) by rune.biokemi.su.se (8.7/8.7) id RAA06929; Mon, 12 Aug 1996 17:36:17 +0200 (MDT) To: CHEMISTRY@ccl.net Subject: Prediction servers and predictions From: Arne Elofsson Date: 12 Aug 1996 17:36:17 +0200 Message-ID: Lines: 37 X-Mailer: Gnus v5.2.37/XEmacs 19.14 Dear netters I will teach a course in "Theoretical DNA and Protein analysis" and as more and more of the tools get available over the WWW I will focus on using the WWW to analyze the sequence/protein you are interested in. The students will work on a small set of selected sequence and use the WWW to try to find out as much as possible about these proteins. In a way it is similar to what Tim Hubbard and Anna Tramontano did but on a much smaller scale. We will use this course as a test of different servers that are available over the net. A summary evaluating the different servers will be published on the net. SO I would rally appreciate 1) Any server that you want the students to use and test. (If you have a small, easy to use and fast program that you want ous to test we can provide a WWW interface for the server) 2) Any comprehensive list of servers and others related links. 3) Any protein sequence that you want the students to work on. 4) Anything else you can think I have use of. thank you a lot I will summarize respons and put up a WWW page with all received information. arne -- ----------------------------------------------------------------- From: Arne Elofsson Email: arne@rune.biokemi.su.se Tel:+46(0)8-161553 WWW: http://www.biokemi.su.se/~arne/ From duanx@Picard.ml.wpafb.af.mil Mon Aug 12 15:17:08 1996 Received: from riker.ml.wpafb.af.mil for duanx@Picard.ml.wpafb.af.mil by www.ccl.net (8.7.5/950822.1) id OAA19407; Mon, 12 Aug 1996 14:29:58 -0400 (EDT) Received: from picard.ml.wpafb.af.mil by riker.ml.wpafb.af.mil (5.65/Ultrix3.0-C) id AA04044; Mon, 12 Aug 1996 14:30:00 -0400 Received: by Picard.ml.wpafb.af.mil (4.1/version) id AA17759; Mon, 12 Aug 96 14:29:56 EDT Date: Mon, 12 Aug 1996 14:29:56 -0400 (EDT) From: Xiaofeng Duan To: CHEMISTRY@www.ccl.net Subject: Extended Huckel code Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, everyone! I was wondering where I can find codes that can do Extended Huckel calculations on the unix machine. We have Hyperchem which can do so, but it is on PCs. **************************************** Xiaofeng Duan WL/MLBP, Bldg. 654 2941 P St. Ste. 1 Wright-Patterson AFB, OH 45433 duanx@Picard.ml.wpafb.af.mil **************************************** From d3g359@fido.pnl.gov Mon Aug 12 18:17:12 1996 Received: from pnl.gov for d3g359@fido.pnl.gov by www.ccl.net (8.7.5/950822.1) id RAA20152; Mon, 12 Aug 1996 17:47:57 -0400 (EDT) Received: from fido.pnl.gov by pnl.gov (PMDF V4.3-13 #6012) id <01I86XEP00M88Y6O0U@pnl.gov>; Mon, 12 Aug 1996 14:47:55 -0700 (PDT) Received: by fido.pnl.gov (951211.SGI.8.6.12.PATCH1042/951211.SGI.AUTO) for CHEMISTRY@www.ccl.net id OAA05245; Mon, 12 Aug 1996 14:43:47 -0700 Date: Mon, 12 Aug 1996 14:43:47 -0700 From: d3g359@fido.pnl.gov (John Nicholas) Subject: Chemistry in C++ To: CHEMISTRY@www.ccl.net Message-id: <199608122143.OAA05245@fido.pnl.gov> Content-transfer-encoding: 7BIT Hi, I'd like to know about public domain chemistry codes written in C++. Thanks in advance. John ------------------------------------------------------------------------------ John Nicholas Office: (509) 375-6559 Senior Research Scientist FAX: (509) 375-6631 Environmental Molecular Sciences Laboratory Pacific Northwest National Laboratory Mailstop K1-96 Richland, WA 99352 ------------------------------------------------------------------------------ From kneth@serf2.Colorado.EDU Mon Aug 12 20:17:08 1996 Received: from serf2.Colorado.EDU for kneth@serf2.Colorado.EDU by www.ccl.net (8.7.5/950822.1) id TAA20466; Mon, 12 Aug 1996 19:39:55 -0400 (EDT) Received: from localhost by serf2.Colorado.EDU via SMTP (920330.SGI/911001.SGI) for chemistry@www.ccl.net id AA03254; Mon, 12 Aug 96 17:39:26 -0600 Date: Mon, 12 Aug 1996 17:39:16 -0600 (MDT) From: Kenneth Geisshirt To: chemistry@www.ccl.net Subject: Re: Chemistry in C++ In-Reply-To: <199608122143.OAA05245@fido.pnl.gov> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Mon, 12 Aug 1996, John Nicholas wrote: > Hi, I'd like to know about public domain chemistry codes > written in C++. Some of the utilities which come with GroMacs are written is C++. But it is not a PD program. But some of the basic numeric algorithms have been written in C++ (like matrix manipulations) - see the list of freeware numerical code in C/C++. But what about chemistry code in Java? How has some examples of that? Kenneth +-----------------------------------------------------------------+ | Kenneth Geisshirt Ph.D.-student | | Department of Life Sciences and Chemistry, Roskilde University | | Currently at: University of Colorado at Boulder | +-----------------------------------------------------------------+ | E-mail: kneth@fatou.ruc.dk | | Homepage: http://virgil.ruc.dk/~KNETH | +-----------------------------------------------------------------+ | Old chemists don't die - they just reach equilibrium | +-----------------------------------------------------------------+ From nick@chem.ucla.edu Mon Aug 12 23:17:08 1996 Received: from xenon.chem.ucla.edu for nick@chem.ucla.edu by www.ccl.net (8.7.5/950822.1) id WAA20886; Mon, 12 Aug 1996 22:26:13 -0400 (EDT) Received: from 128.97.34.195 (corvus.chem.ucla.edu [128.97.34.195]) by xenon.chem.ucla.edu (8.6.9/8.6.9) with SMTP id TAA03948 for ; Mon, 12 Aug 1996 19:31:02 -0700 Message-Id: <199608130231.TAA03948@xenon.chem.ucla.edu> Date: 12 Aug 1996 19:30:46 U From: " nick.c " Subject: Re: CCL:Chemistry in C++ To: "CHEMISTRY@www.ccl.net" X-Mailer: Mail*Link PT/Internet 1.5.1 > Hi, I'd like to know about public domain chemistry codes > written in C++. This might not be what you want, but if you are looking for example chemistry code I'd recommend checking out RasMol/RasMac. The code is copyright by Roger Sayle (ras32425@ggr.co.uk)--so definitely not PD. Also, it's in std C rather than using the oop aspects of C++ but it is valuable reference code. It can be accessed at: Luck, -------------------= Nicholas C. DeMello, Ph.D. =-------------------- Internet: nick@chem.ucla.edu _/ _/ _/ _/_/_/ _/ _/ AOL: codeweaver _/_/ _/ _/ _/ _/ _/_/_/ CIS: 71232,766 _/ _/_/ _/ _/ _/ _/ http://www.chem.ucla.edu/~nick/ _/ _/ _/_/_/ _/ _/