From wally@CompChem.com Fri Jan 5 01:15:41 1996 Received: from vp.netgate.net for wally@CompChem.com by www.ccl.net (8.6.10/950822.1) id BAA06434; Fri, 5 Jan 1996 01:05:00 -0500 Received: from p90 (d9.netgate.net [205.214.160.41]) by vp.netgate.net (8.6.12/8.6.9) with SMTP id WAA02945; Thu, 4 Jan 1996 22:21:43 -0800 Message-Id: <199601050621.WAA02945@vp.netgate.net> X-Sender: wally@ng.netgate.net X-Mailer: Windows Eudora Pro Version 2.1.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 04 Jan 1996 22:05:08 -0800 To: CHEMISTRY@www.ccl.net From: "Walter E. Reiher III" Subject: Re: CCL:Good Fortran Compiler for computational science on PC? Cc: Taisung Lee Related issues have been raised here before, so I'm responding to the list: At 09:18 PM 1/4/96 -0500, Taisung Lee wrote: > We are developing some quantum calculation codes. According to our >test, the performance of Intel Pentium-100 is around 1/2-1/5 of an >IBM/RS6000 3CT (the same CPU as 590). And, surely, Pentium is much much >cheaper. According the last issue of Byte magzine, the PentiumPro-200 >(P6), with SPECint92=~360, SPECFp92=~260), is as fast as IBM/RS6000 3CT. >But the problem comes, we don't any good Fortran90 compiler. We just >tried Microsoft Fortran PowerStation 4.0. It has very nice developer >interface and is quite easy to use. However, it only compiles small test >programs; for big 'real' programs, we just got a lot of ridiculous errors. >Afer two weeks work, we returned it. > > So, we want to know is there any computation chemist using PC as a >calculational power and can anyone suggest a good Fortran 90 compiler? > > If there is any good Fortran90 compiler, it seems to us that PC can >be a much cheaper choice for scientists. I've spent an inordinate amount of time over the past year and a half or so fiddling around with PC FORTRAN compilers, and the bottom line, IHMO, is that you'd better not count on them being like what you're accustomed to under UNIX. In general, PCs seem like a false economy to me. There are two issues here: the compiler and the operating system. You don't mention which OS you're using, but MS FPS only runs under NT or Win95. If you're running Win95, or DOS/Win, that's the first thing to get rid of. Windows NT is a reasonable OS; many say OS/2 is also. There are also UNIXes available for Intel CPUs. Just don't waste your time with a 16 bit OS like DOS or a hybrid 16/32 system like 95. Many 'big program' problems are related to trying to run in 16 bits or tricking a 16 bit OS into looking like a 32 bit one. How long has it been since we're tried doing this with UNIX? Years! Who needs to go back to _that_? On compilers, I've worked with three--Watcom, MS FORTRAN PowerStation 32 (predecessor to 4.0), and Absoft--and all of them have some problems for my applications, which involve mixed FORTRAN and C programming and interoperability with a MS Visual C++ graphics DLL. Watcom had loads of incompatibility problems and really poor tech support, but produces fast code when you can make it work. MS FPS also produces fast code and has a nice development environment, but has surprisingly poor interoperability with C. I'm continuing to use Absoft, who has excellent tech support and C interoperability but produces slow code on a Pentium and has some other quirks. Other compiler vendors I have not tried include Salford (a British company; expensive compiler but it must be a 'real' one since all of Chem-X builds under it), Microway NDP, and Lahey. BTW, I've only used these as FORTRAN 77's, not 90's. If you don't need to worry about working with C and calling DLLs, life will probably be easier for you. It seems to me that FORTRAN really isn't taken seriously by the compiler vendors--the emphasis is on C/C++. I was disappointed to learn this week that the FORTRAN on my 'reference' platform, the SGI, also isn't what it used to be. Some switches that I found valuable for finding bugs in old code on my old IRIX 5.2 system are missing on my new IRIX 6.1 system (e.g., -trapuv and -u). See the "SciTech Software for Science" catalog for a comprehensive list of FORTRAN compilers and other technical software tools. 800-622-3345, http://www.scitechint.com/scitech/. I'm not affiliated with them. Hope this helps...good luck. I'd be interested in hearing the experiences of others. Wally ======================================================================== Walter E. Reiher III, Ph.D. Wally@CompChem.com CompChem Innovations P.O. Box 61056 voice 408-720-0240 Sunnyvale, CA 94088 fax 408-720-0378 From owner-chemistry@ccl.net Fri Jan 5 01:30:41 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id BAA06777; Fri, 5 Jan 1996 01:29:03 -0500 Received: from occam.gh.wits.ac.za for craig@occam.gh.wits.ac.za by bedrock.ccl.net (8.7.1/950822.1) id BAA14799; Fri, 5 Jan 1996 01:28:55 -0500 (EST) Received: (from craig@localhost) by occam.gh.wits.ac.za (8.6.12/8.6.9) id IAA23769; Fri, 5 Jan 1996 08:28:45 +0200 Date: Fri, 5 Jan 1996 08:28:45 +0200 (GMT+0200) From: Craig Taverner X-Sender: craig@occam.gh.wits.ac.za To: Taisung Lee cc: chemistry@ccl.net Subject: Re: CCL:Good Fortran Compiler for computational science on PC? In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII > So, we want to know is there any computation chemist using PC as a > calculational power and can anyone suggest a good Fortran 90 compiler? > > If there is any good Fortran90 compiler, it seems to us that PC can > be a much cheaper choice for scientists. We use PC's as computational tools extensively in crystallography, but we run them all (the computational ones that is) under LINUX for which f77 is freely available (g77 and f2c), and we also have the NAG f90 compiler, which so far seems to compile fine with true fortran 90 programs, but has proved to be somewhat tricky with fortran 77 programs. Unfortunately I have not used it nearly enough to give you any performance spec.'s or say whether it can cope with very large programs, but I should certainly expect it to be able to. So far our experience with using Linux instead of Dos/windows has definitely demonstrated it to be more appropriate for computational work. Contact NAG at: NAG Ltd NAG Inc tel +44 (0)1865 311744 +1 708 971 2345 fax +44 (0)1865 311755 +1 708 971 2346 post NAG Response Centre NAG Response Center NAG Ltd NAG Inc Wilkinson House 1400 Opus Place Jordan Hill Road Suite 200 OXFORD Downers Grove United Kingdom IL 60515-5702 OX2 8DR USA email infodesk@nag.co.uk infodesk@nag.com www http://www.nag.co.uk gopher NAME=NAG Gopher Server, Type=1, Port=70, Path=1/, Host=www.nag.co.uk This is straight from their magazine, verbatum. I hope it's not overboard. Cheers, Craig "If God had meant us to be naked, we would have been born that way." Craig Taverner Structural Chemistry, University of the Witwatersrand, South Africa From owner-chemistry@ccl.net Fri Jan 5 04:30:44 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id EAA08479; Fri, 5 Jan 1996 04:23:23 -0500 Received: from inetnif.niftyserve.or.jp for JDA03546@niftyserve.or.jp by bedrock.ccl.net (8.7.1/950822.1) id EAA16071; Fri, 5 Jan 1996 04:23:18 -0500 (EST) Received: by inetnif.niftyserve.or.jp (8.6.9+2.4W/3.3W8-950117-Mail-Gateway) id SAA02964; Fri, 5 Jan 1996 18:24:44 +0900 Message-Id: <199601050924.SAA02964@inetnif.niftyserve.or.jp> Date: Fri, 05 Jan 1996 18:18:00 +0900 From: "JDA03546@niftyse" Subject: Standard Basis Set for Lanthanides To: chemistry@ccl.net Dear CCL'ers, This might have been asked here many times but does anyone know the standard (I mean well established) basis set for lanthanide atoms with effective core potential (which I prefer since I don't want to do any relativistic corrections)? LANL2MB/DZ of gaussian 94 doesn't seem to support them. Thank you. ** JDA03546@niftyserve.or.jp/Kazuo Teraishi <01/05 16:44> ** From owner-chemistry@ccl.net Fri Jan 5 04:37:22 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id EAA08489; Fri, 5 Jan 1996 04:23:45 -0500 Received: from inetnif.niftyserve.or.jp for JDA03546@niftyserve.or.jp by bedrock.ccl.net (8.7.1/950822.1) id EAA16078; Fri, 5 Jan 1996 04:23:39 -0500 (EST) Received: by inetnif.niftyserve.or.jp (8.6.9+2.4W/3.3W8-950117-Mail-Gateway) id SAA03254; Fri, 5 Jan 1996 18:25:07 +0900 Message-Id: <199601050925.SAA03254@inetnif.niftyserve.or.jp> Date: Fri, 05 Jan 1996 18:21:00 +0900 From: "JDA03546@niftyse" Subject: UHF v.s. ROHF To: chemistry@ccl.net Dear all, I asked about the UHF/ROHF calculation last year. The answers are not really consistent. Any further comments are welcome. The original post is followed by the answers. Many thanks to those who responded. --- original post 1 --- I'm calculating some open shell systems with gaussian 94. I've been using UHF but since my systems are suffering from the terrible spin contaminations, I'm considering to use ROHF. Anyway, I just tested with the simplest case, dissociated H2. I set the atomic distance 5A and calculated with both UHF and ROHF. The total energy and MO coeff. were equal. UHF: SCF Done: E(UHF) = -.933163683734 A.U. after 1 cycles Alpha Molecular Orbital Coefficients 1 2 (SGG)--O (SGU)--O EIGENVALUES -- -.46668 -.46648 1 1 H 1S .70707 .70714 2 2 H 1S .70707 -.70714 Beta Molecular Orbital Coefficients. 1 2 (SGG)--V (SGU)--V EIGENVALUES -- .30788 .30817 1 1 H 1S .70707 .70714 2 2 H 1S .70707 -.70714 ROHF: SCF Done: E(ROHF) = -.933163683734 A.U. after 1 cycles Molecular Orbital Coefficients 1 2 (SGG)--O (SGU)--O EIGENVALUES -- -.05293 -.05277 1 1 H 1S .70707 .70714 2 2 H 1S .70707 -.70714 Since this is dissociated, the electrons should be delocalized. To obtain this picture, I did natural orbital analysis. And here UHF and ROHF contradicts. UHF: Natural Orbital Coefficients 1 2 EIGENVALUES -- 1.00000 1.00000 1 1 H 1S .96171 -.27406 2 2 H 1S .27395 .96174 ROHF: Natural Orbital Coefficients 1 2 EIGENVALUES -- 1.00000 1.00000 1 1 H 1S .78213 -.62311 2 2 H 1S .62303 .78220 Now a question rises. What I understand is in ROHF alpha and beta electrons are restricted to occupy the same spacial orbitals. Then, shouldn't all the properties calculated from ROHF and from UHF be the same if alpha and beta orbitals are equal (and equal to the ROHF orbitals) as this case? What am I missing? --- original post 2 --- I posted this yesterday and have already received some replies. I really appreciate those who responded! I'm sorry that I forgot to say an important thing. Since my purpose is to compare UHF and ROHF, the system has to be open shell. So the calculation was done in triplet state and both UHF and ROHF gave the S**2 value exactly 2. --- answer 1 --- Date: Tue, 12 Dec 1995 22:59:30 -0500 From: David Heisterberg To: JDA03546@niftyserve.or.jp >Then, shouldn't all the properties calculated from ROHF and from UHF >be the same if alpha and beta orbitals are equal (and equal to the ROHF >orbitals) as this case? What am I missing? I'll bet if you check you'll find all the properties are the same. Natural orbitals, however, are not a property! The NOs are the eigenvectors of the density matrix. Since you have two eigenvectors with the same eigenvalue, any linear combination of the two is also an eigenvector. In general, NOs are only determined up to a unitary transformation of all NOs with the same occupation number. So ROHF and UHF are free to disagree about the composition of the NOs, but must agree about the occupation numbers, in this case. Dave Heisterberg --- answer 2 --- Date: Wed, 13 Dec 1995 00:24:55 -0500 (EST) From: qiang@euch4e.chem.emory.edu To: "JDA03546@niftyse" Hi! I'm not perfectly sure, but I think it's cause RHF solution is also a stationary point in the parameter space. (not a minimum though) Thus, even u claim a UHF calculation, u may still get a RHF solution,especially when u have a closed-shell system. Actually I've observed similar situation for C2H-H dissociation. Another point maybe is that even u are dissociating, alpha and beta may not be quite different at small nuclear distances. If u can access to Szabo's famous text book "advanced electrnic structure theory", there is a table at the back of the book listing M.O. energies for H2 at various nuclear distances. It might be helpful... If I've missed anything, please tell me. I'd also appreciate any reply u will get for this question... Have a nice day... --- answer 3 --- Date: Wed, 13 Dec 1995 12:54:24 +0100 (NFT) From: ccl@cric.chemres.hu To: "JDA03546@niftyse" You have misunderstood the concept of ROHF: it means doubly filled orbitals EXCEPT the open shell for which a spin eigenfunction is formed. In H2 the closed-shell part is absent, so you have ONLY the open shell, which is a mixture of singlet and triplet in UHF and a pure singlet in ROHF. However, the singlet and triplet energies are (practically) equal at the large distance you have used. Try shorter distances, too, in order to see the difference. Regards, Prof. I. Mayer --- answer 4 --- Date: Wed, 13 Dec 1995 09:42:40 -0600 From: badnhoop@thchem.siu.edu To: jda03546@niftyserve.or.jp I am one of the authors of the NBO program. I believe the difference comes in the fact that the first decomposition you cite is that of the MOs, while the Natural Orbital Coeffs are those of the NAOs. It is possible that a different set of NAOs was used for the UHF vs ROHF even though the same set of MOs is used. However, I cannot be sure just from the information in your message. Would you be willing to Email me the entire log files. Then I could be certain. Thank you. --- answer 5 --- Date: Thu, 14 Dec 1995 08:42:47 -0500 From: Renee Peloquin Mattie To: "'JDA03546@niftyse'" The nice thing about a two-unpaired-electron triplet state is that it is a single reference state -- it requires only ONE determinant to describe it. You could do this state with RHF. You could do it with UHF, and get the same thing. You could do it with ROHF. But you never know exactly how ROHF orbitals are going to be defined, unless you have some control over that issue. There might be some kind of canonicalization procedure. There might be some other kind of procedure for making the orbitals fit for some particular correlated calculation. You should check into that. In the meantime, you might as well stick to RHF for this particular state. It is the two-unpaired-electron singlet that is supposed to give you fits! --- answer 6 --- Date: Thu, 14 Dec 1995 08:53:31 -0500 (EST) From: Wang Youliang To: "JDA03546@niftyse" On Thu, 14 Dec 1995, JDA03546@niftyse wrote: > (Large output part was snipped.) > I posted this yesterday and have already received some replies. > I really appreciate those who responded! > I'm sorry that I forgot to say an important thing. Since my purpose > is to compare UHF and ROHF, the system has to be open shell. So the > calculation was done in triplet state and both UHF and ROHF gave the > S**2 value exactly 2. I'll summarize the answers. > Thank you. > ** JDA03546@niftyserve.or.jp/Kazuo Teraishi <12/14 09:38> ** > Your problem is due to single-determinant wavefunction. You can simply test the stability of wavefunction for UHF calculations by using STABLE=OPT (or other options, see Gaussian Manual for details). Good lucky Y. Wang --- answer 7 --- Date: Thu, 14 Dec 1995 10:52:54 -0500 (EST) From: Mike Peterson (System Admin) To: JDA03546@niftyserve.or.jp >I posted this yesterday and have already received some replies. >I really appreciate those who responded! >I'm sorry that I forgot to say an important thing. Since my purpose >is to compare UHF and ROHF, the system has to be open shell. So the >calculation was done in triplet state and both UHF and ROHF gave the >S**2 value exactly 2. I'll summarize the answers. In any case where all the orbitals are occupied by only alpha spin electrons (i.e. there are no doubly occupied and no beta spin orbitals), and there are no degenerate levels that are not exactly half full, you will always get exact agreement between UHF and ROHF since the UHF will be an exact spin eigenfunction. Try a case like Li atom (1s,1s, 2s) to see a different result. Also be aware that you can not do open shell singlet excited states that have the same symmetry as the ground state with ROHF, even though it may appear to give you a result that looks believable. In fact you have a lot of triplet character mixed in if I remember my ROHF theory correctly. You need some sort of MC-SCF or CI (e.g. at least CI Singles) that produces multiple roots simultaneously to get higher excited states of the same symmetry as a lower state. Mike. From ldw@csb0.IPC.PKU.EDU.CN Fri Jan 5 06:45:48 1996 Received: from csb0.IPC.PKU.EDU.CN for ldw@csb0.IPC.PKU.EDU.CN by www.ccl.net (8.6.10/950822.1) id GAA09407; Fri, 5 Jan 1996 06:38:25 -0500 Received: by csb0.IPC.PKU.EDU.CN (920330.SGI/940406.SGI.AUTO) for CHEMISTRY@www.ccl.net id AA19166; Fri, 5 Jan 96 19:35:10 -0800 Date: Fri, 5 Jan 1996 19:35:04 -0800 (PST) From: ldw To: proteins@net.bio.net Cc: CHEMISTRY@www.ccl.net, biophysics@net.bio.net Subject: I want to experimental data of folding intermediates Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters, At presents I predict some folding nuleated site by searching the PDB. Now I need some experimental data to test them. All kinds of experimental data which have the detail information about where is the folding nuleaated site or folding initiation site are welcome. (the information like the paper on Nature Vol.269 Page 192-197, which states that N and C terminal helix fold ealier. This kind of information is most favorate). I will summarize what is intereting I receive to this list. Thanks in advance, Dawei ----------< *** Dawei LIN *** >---------------- Ph.D student of Molecular Design Lab Institute of Physical chemistry Peking University Beijing 100871 P.R.China Phone: 86-10-2751490 Fax: 86-10-2751725 Email: ldw@pschnetware.pku.edu.cn ldw@ipc.pku.edu.cn URL: http://www.ipc.pku.edu.cn/ldw/ldw.htm ------------------------------------------------ From owner-chemistry@ccl.net Fri Jan 5 09:15:48 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id JAA12042; Fri, 5 Jan 1996 09:09:48 -0500 Received: from gig.usda.gov for srheller@origin.gig.usda.gov by bedrock.ccl.net (8.7.1/950822.1) id JAA17612; Fri, 5 Jan 1996 09:09:45 -0500 (EST) Received: by gig.usda.gov (5.x/SMI-SVR4) id AA22950; Fri, 5 Jan 1996 08:55:25 -0500 Date: Fri, 5 Jan 1996 08:55:25 -0500 (EST) From: "Stephen R. Heller" To: jcicshelp , chemistry@ccl.net, chminf-l@iubvm.ucs.indiana.edu, orgchem@extreme.chem.rpi.edu, analysis-l@fs4.in.umist.ac.uk Subject: Chemical Concepts - Job Opening Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Chemicals Concepts of Weinheim, Germany is seeking to recruit a Sales Manager for marketing its spectroscopy software and related databases. The successful applicant should have a degree in science, preferably in chemistry or physics, and have hands-on NMR, IR, and spectrometry experience. In addition the applicant should have experience with both PC's and UNIX workstations. Consulting is an important aspect of the Chemical Concepts sales strategy, thus knowledge of the operating procedures of analytical labs in the USA will be quite helpful. Well developed interpersonal skills and sales experience are very important. Knowledge of German is desirable. The chosen applicant will be required to go to Germany for about one month to learn the various Chemical Concepts systems. The position is expected to be located in either northern New Jersey or St. Louis, Missouri. Chemical Concepts is an equal opportunity employer. Please direct all responses and salary requirements to: Dr. Reinhard Neudert Managing Director Chemical Concepts GmbH Boschstrasse 12 PO Box 10 02 02 D-69469 Weinheim GERMANY E-mail: Neudert@cc.vchgroup.de FAX: 011-49-6201-606-430 Phone: 011-49-6201-606-438 From ppaneth1@zsku.p.lodz.pl Fri Jan 5 09:30:48 1996 Received: from zsku.p.lodz.pl for ppaneth1@zsku.p.lodz.pl by www.ccl.net (8.6.10/950822.1) id JAA12221; Fri, 5 Jan 1996 09:29:32 -0500 Received: by zsku.p.lodz.pl (5.65/25-eef) id AA06671; Fri, 5 Jan 96 15:18:43 +0100 Date: Fri, 5 Jan 1996 15:18:39 +0100 (MET) From: Piotr Paneth To: chemistry@www.ccl.net Subject: CCL:M:COSMO In-Reply-To: <9511162146.AA18077@hamby.tx.ncsu.edu> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi All: need help on the following problem; I'm trying to use the COSMO solvation model on a claster of two molecules. My MOPAC93 is compiled for 200 heavy and 200 light atoms. Optimization quits however with the following message: NPS GREATER THAN MAXNPS, USE SMALLER NSPA this problem remains till NSPA is set al low as 5, then the error reads: VALUE OF NPPA NOT ALLOWED: IT MUST BE 10*3**K*4**L+2 The system has charge of +1, when instead of setting charge a counterion is added the message changes to: PARAMETER LENABC MUST BE INCREASED FOR THIS SYSTEM Evidently parameters specific to cosmo subroutine have to be changed, which do not appear in SIZES. I'd appreciate help on how to change these reasonably or how to calculate what they should be. Please, respond to ppaneth1@axp.p.lodz.pl (note that ppaneth1=ppaneth"one" and not ppaneth"el" Thanks in advance, Piotr Paneth From netsci@awod.com Fri Jan 5 10:15:49 1996 Received: from sumter.awod.com for netsci@awod.com by www.ccl.net (8.6.10/950822.1) id KAA12573; Fri, 5 Jan 1996 10:09:41 -0500 Received: from [198.81.225.152] (ppp143.awod.com [198.81.225.152]) by sumter.awod.com (8.6.11/8.6.9) with SMTP id KAA24582; Fri, 5 Jan 1996 10:07:31 -0500 X-Sender: arichon@awod.com Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Fri, 5 Jan 1996 11:27:07 +0000 To: chemistry@www.ccl.net From: netsci@awod.com (Network Science) Subject: January Issue of NetSci Cc: netsci@awod.com The January issue of Network Science highlighting QSAR is on-line at: http://www.awod.com/netsci/ QSAR Challenges and Opportunities: A Commentary, Eugene Coats, Amylin Pharmaceuticals QSAR and Drug Design, David Bevan, Virginia Polytechnic Institute and State University A New QSAR Algorithm Combining Principal Component Analysis with a Neural Network: Application to Calcium Channel Antagonists, Vellarkad N. Viswanadhan (Gensia, Inc.), Geoffrey A. Mueller (National Cancer Institute), Subhash C. Basak (University of Minnesota) and John N. Weinstein (National Cancer Institute) Using Theoretical Descriptors in Quantitative Structure Activity Relationships and Linear Free Energy Relationships, George R. Famini (U.S. Army Edgewood R&D) and Leland Y. Wilson (La Sierra University) APEX-3D Expert System for Drug Design, Valery Golender (DCL Systems), Boris Vesterman (DCL Systems), and Erich Vorpagel (Biosym/MSI) Adding Chemical Information to CoMFA Models with Alternative 3D QSAR Fields, Chris L. Waller (US-EPA) and Glen E. Kellogg (Virginia Commonwealth) CoMFA: A Field of Dreams?, Simon Semus, Astra Arcus USA QSAR in Three Dimensions: Exploiting Receptor Structural Information, Konrad Koehler, IRBM Special Notice for software authors and distributors - The software section of NetSci is being significantly enhanced with the addition of a table which categorizes software by functionality and platform. A prototype is available for viewing. Please contact the editors of NetSci (netsci@awod.com) with specific information/changes/additions about your programs. From sash@milkyway.tripos.com Fri Jan 5 11:00:49 1996 Received: from gatekeeper.tripos.com for sash@milkyway.tripos.com by www.ccl.net (8.6.10/950822.1) id KAA13039; Fri, 5 Jan 1996 10:47:10 -0500 Received: (from news@localhost) by gatekeeper.tripos.com (8.6.12/8.6.12) id JAA02756; Fri, 5 Jan 1996 09:41:23 -0600 Received: from tripos.tripos.com(192.160.145.1) by gatekeeper.tripos.com via smap (V1.3) id sma002749; Fri Jan 5 09:41:19 1996 Received: from milkyway (milkyway.tripos.com [192.160.145.210]) by tripos.tripos.com (8.6.12/8.6.12) with ESMTP id JAA15549; Fri, 5 Jan 1996 09:41:36 -0600 Received: from 192.160.145.25 by milkyway via SMTP (940816.SGI.8.6.9/940406.SGI) id JAA03570; Fri, 5 Jan 1996 09:41:50 -0600 From: "Sheila Ash" Message-Id: <9601050941.ZM20815@192.160.145.25> Date: Fri, 5 Jan 1996 09:41:26 -0600 X-Mailer: ZM-Win (3.2.1 09Sep94) To: acsmedi@cms.cc.wayne.edu, chemind-l@derwent.co.uk, chemistry@www.ccl.net, chemistry@ccl.net, chminf-l@iubvm.ucs.indiana.edu Subject: Tripos To Provide Aldrich Catalog Database In UNITY/UNISON Format Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii This press release is cross posted. FOR IMMEDIATE RELEASE Contact:Michael Sullivan Marketing Communications Manager 800-323-2960 314-647-1099 mike@tripos.com Tripos Reaches Agreement with Aldrich Chemical To Provide Catalog Database in UNITY/UNISON Format St. Louis, MO January 2, 1996 Today Tripos, Inc. (NASDAQ: TRPS) and Aldrich Chemcial Co. (Milawaukee, Wisconsin) announced an agreement to provide the Aldrich chemical database in UNITY/UNISON format. UNITY/UNISON is Tripos' client-server chemical information management system used by pharmaceutical and chemical companies worldwide. The new database will include information from the Aldrich, Sigma, Fluka, Supeloc, and Rare Chemicals catalogs. The Aldrich collection is the most extensive dataset of available chemicals with over a hundred thousand compounds. Tripos will use its Concord technology to convert the 2D chemical structural data into 3D structures. The 3D structures may be searched using the UNITY system to find commercially available compounds matching user defined pharmacophores or a set of structural characteristics. These searches will play a key role in the discovery of new chemical and pharmaceutical products. "The Aldrich chemical database is a recognized standard in the industry. Access to this dataset through UNITY/UNISON will allow chemists to combine chemical availability with structural and biological parameters in their route to new chemical discovery and applications," said Sheila Ash, Marketing Manager for Chemical Information at Tripos. "The availability of the Aldrich collection of chemicals in UNITY/UNISON format will be important to the implementation of new combinatorial chemistry strategies by helping to target commercially available chemical building blocks. These components are critical to the development of potentially new products," stated Dr. Mark Schwartz, Vice President of Accelerated Discovery Services (ADS) at Tripos. Tripos plans to make the Aldrich chemical database available in the new format during the Spring of 1996. Aldrich Chemical Co., based in Milwaukee, Wisconsin, is one of the world's largest sources of chemical and biochemical products for research use. Tripos, Inc., founded in 1979, is the recognized leading supplier of scientific software and services to facilitate the discovery of new therapeutic and bioactive compounds in pharmaceutical, biotechnology, chemical and agrochemical industries. From owner-chemistry@ccl.net Fri Jan 5 11:03:45 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id KAA13044; Fri, 5 Jan 1996 10:47:16 -0500 Received: from gatekeeper.tripos.com for sash@milkyway.tripos.com by bedrock.ccl.net (8.7.1/950822.1) id KAA18727; Fri, 5 Jan 1996 10:47:14 -0500 (EST) Received: (from news@localhost) by gatekeeper.tripos.com (8.6.12/8.6.12) id JAA02756; Fri, 5 Jan 1996 09:41:23 -0600 Received: from tripos.tripos.com(192.160.145.1) by gatekeeper.tripos.com via smap (V1.3) id sma002749; Fri Jan 5 09:41:19 1996 Received: from milkyway (milkyway.tripos.com [192.160.145.210]) by tripos.tripos.com (8.6.12/8.6.12) with ESMTP id JAA15549; Fri, 5 Jan 1996 09:41:36 -0600 Received: from 192.160.145.25 by milkyway via SMTP (940816.SGI.8.6.9/940406.SGI) id JAA03570; Fri, 5 Jan 1996 09:41:50 -0600 From: "Sheila Ash" Message-Id: <9601050941.ZM20815@192.160.145.25> Date: Fri, 5 Jan 1996 09:41:26 -0600 X-Mailer: ZM-Win (3.2.1 09Sep94) To: acsmedi@cms.cc.wayne.edu, chemind-l@derwent.co.uk, chemistry@www.ccl.net, chemistry@ccl.net, chminf-l@iubvm.ucs.indiana.edu Subject: Tripos To Provide Aldrich Catalog Database In UNITY/UNISON Format Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii This press release is cross posted. FOR IMMEDIATE RELEASE Contact:Michael Sullivan Marketing Communications Manager 800-323-2960 314-647-1099 mike@tripos.com Tripos Reaches Agreement with Aldrich Chemical To Provide Catalog Database in UNITY/UNISON Format St. Louis, MO January 2, 1996 Today Tripos, Inc. (NASDAQ: TRPS) and Aldrich Chemcial Co. (Milawaukee, Wisconsin) announced an agreement to provide the Aldrich chemical database in UNITY/UNISON format. UNITY/UNISON is Tripos' client-server chemical information management system used by pharmaceutical and chemical companies worldwide. The new database will include information from the Aldrich, Sigma, Fluka, Supeloc, and Rare Chemicals catalogs. The Aldrich collection is the most extensive dataset of available chemicals with over a hundred thousand compounds. Tripos will use its Concord technology to convert the 2D chemical structural data into 3D structures. The 3D structures may be searched using the UNITY system to find commercially available compounds matching user defined pharmacophores or a set of structural characteristics. These searches will play a key role in the discovery of new chemical and pharmaceutical products. "The Aldrich chemical database is a recognized standard in the industry. Access to this dataset through UNITY/UNISON will allow chemists to combine chemical availability with structural and biological parameters in their route to new chemical discovery and applications," said Sheila Ash, Marketing Manager for Chemical Information at Tripos. "The availability of the Aldrich collection of chemicals in UNITY/UNISON format will be important to the implementation of new combinatorial chemistry strategies by helping to target commercially available chemical building blocks. These components are critical to the development of potentially new products," stated Dr. Mark Schwartz, Vice President of Accelerated Discovery Services (ADS) at Tripos. Tripos plans to make the Aldrich chemical database available in the new format during the Spring of 1996. Aldrich Chemical Co., based in Milwaukee, Wisconsin, is one of the world's largest sources of chemical and biochemical products for research use. Tripos, Inc., founded in 1979, is the recognized leading supplier of scientific software and services to facilitate the discovery of new therapeutic and bioactive compounds in pharmaceutical, biotechnology, chemical and agrochemical industries. From owner-chemistry@ccl.net Fri Jan 5 11:30:49 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id LAA13762; Fri, 5 Jan 1996 11:22:37 -0500 Received: from robin.mcnc.org.mcnc.org for gotwals@mcnc.org by bedrock.ccl.net (8.7.1/950822.1) id LAA19171; Fri, 5 Jan 1996 11:22:34 -0500 (EST) Received: from [128.109.178.113] by robin.mcnc.org.mcnc.org (8.6.9/MCNC/8-10-92) id LAA21776; Fri, 5 Jan 1996 11:22:09 -0500 for Date: Fri, 5 Jan 1996 11:22:09 -0500 Message-Id: <199601051622.LAA21776@robin.mcnc.org.mcnc.org> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemclub@umslvma.umsl.edu, chemconf%umdd.bitnet@listserv.net, chemed-l@uwf.cc.uwf.edu, chemistry@ccl.net, dohs@psyber.com, kturner@mrcemis.ms.nwu.edu, nordstrb@pr.erau.edu, s-canagaratna@onu.edu From: gotwals@mcnc.org (Bob Gotwals) Subject: ONLINE COURSE! Computational Chemistry for Chemistry Educators The North Carolina Supercomputing Center (NCSC) in Research Triangle Park, NC, is pleased to offer an on-line course entitled "Computational Chemistry for Chemistry Educators". This course is intended for secondary, community college and undergraduate educators of chemistry, as well as graduate students who are interested in chemistry education. The course syllabus and registration information can be viewed by setting your World Wide Web browser to this URL: http://www.mcnc.org/HTML/ITD/NCSC/ccsyllabus.html Description of the workshop: The goal of this course is to introduce chemistry educators to computational techniques in quantum chemistry. The course is intended as an enrichment activity, designed to help educators understand the use of high-performance computing tools and their role in chemical research. Educators are not expected to integrate these technologies into their teaching activities, but the course will offer discussions on how this might be accomplished for those educators interested in doing so. Using commercial third-party software (Gaussian94 and MOPAC) resident on the North Carolina Supercomputing Center's Cray T90 supercomputer, educators will investigate, using computational tools,techniques, and technologies, a number of chemical properties, such as single-point energies, geometry optimizations, frequency calculations, potential energy surfaces, and thermochemical properties. Participants will also have the opportunity to complete a number of case studies for potential use in the classroom. Prerequisites: Participants must have access to the Internet via the World Wide Web (WWW), preferably using Netscape 1.1. Text-based access (i.e., via lynx) is inadequate. Access assumes electronic mail capabilities. Participants who have Internet connections through America Online or other non-Internet service are advised to ensure good Web connectivity prior to registering. Educators should also have a basic background in quantum chemistry and atomic structure. Completion of a basic course in physical chemistry at the undergraduate level is the appropriate level. A solid mathematics background, particularly in calculus, is helpful but not mandatory. Participants should also have basic computer literacy skills: use of a word processor, basic understanding of the concepts of an operating system, keyboarding skills, etc. A UNIX background is helpful but not required. No programming skills are required. Prospective participants who wish to discuss their qualifications PRIOR to registering are encouraged to do so with the instructor. Workshop Logistics: The course is designed as a self-paced "seminar" series, consisting of 15 sessions. Each week, a new topic and assignment will be posted to the World Wide Web. Students need to complete the reading and assignment, ask questions via electronic mail, and submit their work via email to the course instructor. Students will be able to interact via an email discussion list (listserv). All reading materials and resources are available electronically, although the use of a basic physical chemistry textbook (Atkins is recommended) is strongly advised. Access to the lessons and the supercomputer will begin on February 12, 1996, and will close on June 14, 1996. The course instructor will be available for electronic support during that period. The fee for this activity is $150. Tuition includes access to all Web materials, addition to the class discussion group maililing list, and computing time on the supercomputer. As there is limited enrollment, participants are asked to give considerable consideration to their commitment PRIOR to registering for this activity. The course will require time (roughly four to five hours per week), effort, and intellectual energy. At this point, no grades or continuing education credit is available; however, certificates of completion with an accompanying descriptive letter are provided to all course "graduates". To register for this course, use the form-clickable registration off the syllabus page OR complete the form below and email it to Robert R. Gotwals (gotwals@mcnc.org). There is limited enrollment in this course. Registration is on a first-come, first-serve basis. Please feel free to send questions about this course to gotwals@mcnc.org Tentative Schedule: Session 1: Overview of Computational Chemistry; Overview of the Cray T90 and the UNIX operating system Session 2: Logging On; Using Gaussian94 on the Cray supercomputer; creating and submitting G94 input files Session 3: Basis sets and approximations; Input file options; Calculating Single Point Energies Session 4: Single Point Energies. Analyzing output files Session 5: Case Study: Energies of Isomers Session 6: Geometry Optimizations I Session 7: Geometry Optimizations II Session 8: Preparing Geometry Inputs Session 9: Frequency Calculations I Session 10: Frequency Calculations II Session 11: Potential Energy Scans Session 12: Case Study/Teaching Module: Problem Development and Investigation Session 13: Case Study/Teaching Module: Lab Writeup and Instructor Guide Session 14: Overview of other tools for computational chemistry; Classroom integration Session 15: "Final Exam"; Course Wrap-up / Evaluation ****************************************************************** "Computational Chemistry for Chemistry Educators" Registration Form Last Name: First Name: Position: Phone: Curriculum Area: Primary Courses Taught (intro, AP Chem., etc.) School: District( if appropriate): School Address: FAX: E-mail Address: Degree(s): BS [ ] MS [ ] Doctorate [ ] Other [ ] Subject area(s) of degree(s): Years of Teaching Experience: 1-5 [ ] 6-10 [ ] 11-15 [ ] >16 [ ] Years of Technology Experience: 1-5 [ ] 6-10 [ ] 11-15 [ ] Do you own your own computer system? Yes [ ] No [ ] If yes, indicate the hardware platform: Describe the hardware you will use to access the Web lessons: Describe your Web connection (Dialup SLIP or PPP, America Online, etc.) Describe your chemistry, mathematics, and computing background (coursework, workshops, experiences, etc.) Return this registration form to Robert R. Gotwals, Jr.(gotwals@mcnc.org) or by FAX (919) 248-1101. We are unable to process credit card payments. Send tuition check or PO (payable to MCNC) to the address below. Please do NOT make checks payable to Rober Gotwals or Faye Ellis: Robert R. Gotwals, Jr. Course Instructor -OR- Faye McLean Ellis Course Registrar North Carolina Supercomputing Center 3021 Cornwallis Road Research Triangle Park, NC 27709 From nash@chem.wisc.edu Fri Jan 5 13:45:52 1996 Received: from audumla.students.wisc.edu for nash@chem.wisc.edu by www.ccl.net (8.6.10/950822.1) id NAA16943; Fri, 5 Jan 1996 13:38:28 -0500 Received: from caseyir by audumla.students.wisc.edu; id MAA43691; 8.6.9W/42; Fri, 5 Jan 1996 12:38:27 -0600 Date: Fri, 5 Jan 1996 12:38:27 -0600 Message-Id: <199601051838.MAA43691@audumla.students.wisc.edu> X-Sender: jrnash@students.wisc.edu X-Mailer: Windows Eudora Light Version 1.5.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: CHEMISTRY@www.ccl.net From: "John R. Nash" Subject: PowerMac as computational workstation On the subject of FORTRAN on PCs for computational chemistry, wally@CompChem.com wrote: >I've spent an inordinate amount of time over the past year and a half or so >fiddling around with PC FORTRAN compilers, and the bottom line, IHMO, is >that you'd better not count on them being like what you're accustomed to >under UNIX. In general, PCs seem like a false economy to me. ...and... >You don't mention which OS you're using, but MS FPS only runs under NT or >Win95. If you're running Win95, or DOS/Win, that's the first thing to get >rid of. Windows NT is a reasonable OS; many say OS/2 is also. There are >also UNIXes available for Intel CPUs. Just don't waste your time with a 16 >bit OS like DOS or a hybrid 16/32 system like 95. > Many 'big program' problems are related to trying to run in 16 bits or >tricking a 16 bit OS into looking like a 32 bit one. It sounds like what is needed is a FORTRAN that runs on a personal computer with a 32-bit OS and sufficient computational power to run serious calculations. It would be foolish, I think, to ignore the Power Macintosh as such a system based on long-held OS biases as to what a "real PC" is. Until recently, there was a need for a good FORTRAN compiler on this platform; the arrival of Language Systems FORTRAN makes the PowerMac a quite viable system for quant. mech. development. GAMESS for PowerMac is a full port of that computational package, and it runs at about 1/3 the speed of an RS/6000 model 350 on a PM 7100/66. See http://www.msg.ameslab.gov/GAMESS/dist.mac.html for details. I hope that developers will not ignore this platform with its obvious strengths and cost-to-performance advantages. I personally cannot comment on Language Systems FORTRAN for Power Mac -- I am an end user, not a developer. However, MacGAMESS seems to me a good proof-of-concept that this kind of development is feasible. -==-John R. Nash-==-nash@chem.wisc.edu-==-Dept of Chemistry, UW-Madison-==- From haney@netcom.com Fri Jan 5 15:15:52 1996 Received: from netcom22.netcom.com for haney@netcom.com by www.ccl.net (8.6.10/950822.1) id PAA17989; Fri, 5 Jan 1996 15:12:00 -0500 Received: by netcom22.netcom.com (8.6.12/Netcom) id MAA11637; Fri, 5 Jan 1996 12:08:29 -0800 From: haney@netcom.com (Dr. David N. Haney) Message-Id: <199601052008.MAA11637@netcom22.netcom.com> Subject: Re: CCL:xmol for MS-Windows? To: tony@schroeder.newcastle.edu.au (Tony Dyson) Date: Fri, 5 Jan 1996 12:08:29 -0800 (PST) Cc: CHEMISTRY@www.ccl.net In-Reply-To: from "Tony Dyson" at Jan 5, 96 11:43:07 am X-Mailer: ELM [version 2.4 PL23] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 912 Mr. Anthony J. Dyson writes: > I'm looking for a MS-Windows program that has the functionality of xmol - > specifically, the ability to animate multi-step cartesian trajectories. > Has anybody come across such a thing? It need not be free. XMOL for windows sounds like a nice idea. You might consider setting up an Xwindow interface with one of the software packages like InsightII, Sybyl or maybe even XMOL. The limit there will be the network speed of the X, but animating on a PC may have some limits too. -- ************** David N. Haney, Ph.D. **************** * Haney Associates Phone - 619-566-1127 * * 12010 Medoc Ln. * * San Diego, CA 92131 Fax - 619-586-1481 * * http://www.i2020.net/edusoft/haney/haney.html * ************** Email - haney@netcom.com *************** From eofstead@goodyear.com Fri Jan 5 15:45:53 1996 Received: from goodyear.com for eofstead@goodyear.com by www.ccl.net (8.6.10/950822.1) id PAA18321; Fri, 5 Jan 1996 15:37:28 -0500 Received: from rdsrv2 (rdsrv2.goodyear.com) by goodyear.com (4.1/SMI-4.1) id AA15794; Fri, 5 Jan 96 15:37:25 EST Received: from [163.243.12.103] (rds991) by rdsrv2 (4.1/SMI-4.1) id AA16628; Fri, 5 Jan 96 15:37:22 EST Message-Id: <9601052037.AA16628@rdsrv2> X-Sender: t410b16@rdsrv2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Fri, 5 Jan 1996 15:37:09 -0500 To: CHEMISTRY@www.ccl.net From: eofstead@goodyear.com (Eilert Ofstead) Subject: POWERMAC clones for compchem To follow-up on the recent comments of John Nash (1-5-96): >It would be foolish, I think, to ignore the Power Macintosh >as such a system based on long-held OS biases as to what a "real PC" is. >Until recently, there was a need for a good FORTRAN compiler on this >platform; the arrival of Language Systems FORTRAN makes the PowerMac a quite >viable system for quant. mech. development. GAMESS for PowerMac is a full >port of that computational package, >and it runs at about 1/3 the speed of an RS/6000 model 350 on a PM 7100/66. >See http://www.msg.ameslab.gov/GAMESS/dist.mac.html for details. I hope >that developers will not ignore this platform with its obvious strengths and >cost-to-performance advantages. I wonder if this suggestion might be extended to include the DayStar Genesis MP machine, which is a 4-cpu 604-chip parallizable machine for under 20,000$, I believe. This could potentially be a pretty interesting alternative in this market, it would seem. Any thoughts? Eilert Ofstead - --------------------------------------------------------------------------- Eilert Ofstead, Sr R&D Assoc /\ Research Division eofstead@goodyear.com hands / \ CPUs Goodyear Tire & Rubber Co voice: 216-796-3983 /pick\ 142 Goodyear Blvd fax: 216-796-3304 / two \ Akron, OH 44305 USA -------- neurons --------------------------------------------------------------------------- From nash@chem.wisc.edu Fri Jan 5 16:15:53 1996 Received: from audumla.students.wisc.edu for nash@chem.wisc.edu by www.ccl.net (8.6.10/950822.1) id QAA18936; Fri, 5 Jan 1996 16:02:40 -0500 Received: from caseyir by audumla.students.wisc.edu; id PAA33187; 8.6.9W/42; Fri, 5 Jan 1996 15:02:36 -0600 Date: Fri, 5 Jan 1996 15:02:36 -0600 Message-Id: <199601052102.PAA33187@audumla.students.wisc.edu> X-Sender: jrnash@students.wisc.edu X-Mailer: Windows Eudora Light Version 1.5.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: CHEMISTRY@www.ccl.net From: "John R. Nash" Subject: more on RISC-y PC computations... In response to my thoughts on PowerPC computations, eofstead@goodyear.com said: >I wonder if this suggestion might be extended to include the DayStar >Genesis MP machine, which is a 4-cpu 604-chip parallizable machine for >under 20,000$, I believe. This could potentially be a pretty interesting >alternative in this market, it would seem. Which reminds me of one other thing to consider: the BeBox. This new PC is still very much in its infancy (i.e. not intended for end-users at all until more software gets written and things are ironed out), but it uses two PPC chips and an OS that would be likely be mroe suited to hard-core computations than the current MacOS. Definitely not a solution for the time being, but IMHO it may be a system to watch as a hot little desktop computational box if it survives its teething pains... Just food for thought.... -==-John R. Nash-==-nash@chem.wisc.edu-==-Dept of Chemistry, UW-Madison-==- From toni@athe.wustl.edu Fri Jan 5 17:15:54 1996 Received: from wugate.wustl.edu for toni@athe.wustl.edu by www.ccl.net (8.6.10/950822.1) id RAA20675; Fri, 5 Jan 1996 17:03:22 -0500 Received: from athe.wustl.edu by wugate.wustl.edu (8.6.12/8.6.11) with SMTP id QAA21833; Fri, 5 Jan 1996 16:03:20 -0600 Received: by athe.wustl.edu (5.x/SMI-SVR4) id AA06089; Fri, 5 Jan 1996 16:03:18 -0600 Date: Fri, 5 Jan 1996 16:03:18 -0600 From: toni@athe.wustl.edu (Toni Kazic) Message-Id: <9601052203.AA06089@athe.wustl.edu> To: nash@chem.wisc.edu Cc: CHEMISTRY@www.ccl.net In-Reply-To: <199601051838.MAA43691@audumla.students.wisc.edu> (nash@chem.wisc.edu) Subject: Re: CCL:PowerMac as computational workstation Dear Netters, Perhaps I missed this in the current thread, but do the Unix FORTRAN compilers run on PCs running Linux, and does this combination provide the performance expected from the raw numbers? Toni Kazic Institute for Biomedical Computing Washington University