From Jeffrey.Gosper@brunel.ac.uk Fri Feb 10 05:38:35 1995 Received: from monge.brunel.ac.uk for Jeffrey.Gosper@brunel.ac.uk by www.ccl.net (8.6.9/930601.1506) id FAA11128; Fri, 10 Feb 1995 05:23:10 -0500 Received: from chem-pc-18.brunel.ac.uk by monge.brunel.ac.uk with SMTP (PP) id <12276-0@monge.brunel.ac.uk>; Fri, 10 Feb 1995 10:21:50 +0000 Date: Fri, 10 Feb 1995 10:21:42 GMT From: Jeffrey J Gosper Reply-To: Jeffrey.Gosper@brunel.ac.uk Subject: Re: CCL:POVRAY file ? To: Michael R Rothwell cc: Bonvoisin Jacques , CCL Computational Chemistry Message-ID: Priority: Normal MIME-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII > I would also be interested in a PDB (or other format) - to - POVRAY converter. > POVRAY is a cheap (free) fast raytracer available on almost any platform. It > uses ASCII scripts as source files. It seems like a tool just waiting to be > used for scientific visualization. > My program Re_view can do this, the ray-trace option produces (and optionally runs POVray input files). A demo version is available see below and this program is also cheap. Subject: RE_VIEW molecular viewer/animator/analyzer, mopac converter RE_VIEW is essentially a molecular viewer, animator, analyzer, and MOPAC reaction path converter. The major functions of RE_VIEW include the ability to: 1) Display and manipulate molecules in 3D; 2) Animate reaction pathways; 3) Align the steps/frames within an animation, along a vectors or onto a plane; 4) Animate normal modes of vibration; 5) Monitor geometries (lengths, angles and dihedrals); 6) Provide tabulated geometrical data (which can be readily incorporated into spreadsheets); and 7) Automatically produce high quality 'ray-traced' images and animation sequences. It's ShareWare, online as file micros/ibmpc/win/e/e026/rev_demo.zip From msraf@csv.warwick.ac.uk Fri Feb 10 06:38:26 1995 Received: from crocus.csv.warwick.ac.uk for msraf@csv.warwick.ac.uk by www.ccl.net (8.6.9/930601.1506) id FAA11300; Fri, 10 Feb 1995 05:59:39 -0500 From: David Hirst Message-Id: <9713.199502101059@crocus.csv.warwick.ac.uk> Received: by crocus.csv.warwick.ac.uk id KAA09713; Fri, 10 Feb 1995 10:59:27 GMT Subject: Handbook for Computaional Chemistry To: CHEMISTRY@ccl.net Date: Fri, 10 Feb 1995 10:59:26 +0000 (GMT) X-Mailer: ELM [version 2.4 PL21] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 446 E. Lewars referred to a new book `Computational Chemistry' published 1995 by Oxford University Press. I haven't seen this yet but it is in a series of short texts for undergraduates. May I mention my own book, `A Computational Approach to Chemistry', Blackwell Scientific Publications, 1990. It was written before DFT became fashionable and doesn't cover this topic. David M. Hirst Dept of Chemistry, University of Warwick, Coventry CV4 7AL, UK From maitre@cth.u-psud.fr Fri Feb 10 07:27:01 1995 Received: from cth.cth.u-psud.fr for maitre@cth.u-psud.fr by www.ccl.net (8.6.9/930601.1506) id FAA11121; Fri, 10 Feb 1995 05:22:13 -0500 Received: (from maitre@localhost) by cth.cth.u-psud.fr (8.6.9/8.6.6) id LAA32529; Fri, 10 Feb 1995 11:22:39 +0100 Date: Fri, 10 Feb 1995 11:22:39 +0100 From: Maitre Ph Message-Id: <199502101022.LAA32529@cth.cth.u-psud.fr> To: chemistry@ccl.net Subject: benchmarks (gaussian92 and gamess on SUN versus IBM) Cc: d3e102@ames.pnl.gov, help@gaussian.com Dear netters, Does anyone know where we can get informations on Gaussian92 and Gamess running on the following machines : Computer Type Processor type Nproc SUN MP670 SuperSPARC (66Mhz) 2 SUN MP670 HyperSPARC (72Mhz) 2 SUN SparcServer 1000 SuperSPARC (66Mhz) 2 SUN SparcServer 1000 Ultra Sparc coming soon IBM RS6000/58H IBM RS6000/390 Thanks in advance, Philippe Maitre Laboratoire de Chimie Theorique Batiment 490 Universite de Paris XI 91405 Orsay Cedex e-mail address : maitre@cth.u-psud.fr PS : We (unsuccessfully) tried to locate the updated informations proposed by D. Feller in the e-mail attached at the end of this message. Occassionally people post inquiries on the Comp. Chem. List about benchmarks of various ab initio packages. Since version 2.0 of the EMSL Ab Initio Benchmarks Report is currently being cleared for publication, this seemed like a good time to announce its impending availability. In July of 1993 we released version 1.0 in both hardcopy and anonymous ftp forms suitable for downloading. The new version will probably be available near the end of December (in electronic form) or sometime in January (for printed copies). Since we rapidly ran out of the 300 copies of version 1.0 that we had printed and this year's edition is considerable larger, we intend to make this new release available through Mosaic (under the EMSL home page at URL http://www.emsl.pnl.gov:2080/) as well as have a limited number of hardcopies. This year's edition will include an initial sample of parallel benchmarks run by Dr. Rick Kendall and Matt Brightman of PNL and Dr. Martin Feyereisen of Cray Research. The report contains information on the following methods, packages and machines. Method Method ---------------------------------------------- 1. Conventional RHF 12. MP4(SDTQ) 2. Direct RHF 13. SDCI 3. Analytical RHF Gradient 14. CCSD 4. Analytical RHF Hessian 15. CCSD(T) 5. Conventional UHF 16. QCISD 6. Conventional MP2 17. QCISD(T) 7. Direct MP2 18. CASSCF 8. Analytical MP2 Gradient 19. CAS-CI 9. Analytical MP2 Hessian 10. DFT/SVWN (LSD) 11. DFT/BLYP (NLSD) Codes ---------------------------------- 1. Gaussian 90 2. Gaussian 92 and G92/DFT 3. MOLPRO 92.3 and 94.3 4. DISCO 1.82 5. GAMESS(US) 6/17/92 and 7/17/93 6. HONDO 8.3 and 8.4 7. GAMESS(UK) 8. ACES II 9. SPARTAN 3.0 10.SUPERMOLECULE 1.08 Machine Machine ------------------------------------------------------------------------ 1. Intel 486 DX2 (50 MHz) 16. DEC AXP model 300 (150 MHz) 2. Intel 486 DX2 (66 MHz) 17. DEC AXP model 600 (175 MHz) 3. Sun SPARCstation 2 (40 MHz) 18. DEC AXP model 800 (200 MHz) 4. Sun SPARCstation 10/41 (40 MHz) 19. DEC AXP model 900 (300 MHz) 5. IBM PowerPC 250 (66 MHz) 20. SGI Indigo (50/100 MHz R4000) 6. IBM RS/6000 340 (33 MHz) 21. SGI Onyx (50/100 MHz R4400) 7. IBM RS/6000 370 (63 MHz) 22. SGI Indigo (75/150 MHz R4400) 8. IBM RS/6000 550 (42 MHz) 23. SGI PowerChallenge (75 MHz R8000) 9. IBM RS/6000 580 (63 MHz) 24. Fujitsu VPX240/10 (300 MHz) 10.IBM RS/6000 590 (66 MHz) 25. HP 9000 model 730 (66 MHz) 11.KSR2 (80 processors) 26. HP 9000 model 735 (99 MHz) 12.Cray YMP 27. HP 9000 model 735/125 (125 MHz) 13.Cray YMP EL 28. Intel Paragon (512 processors) 14.Cray C90 15.Cray T3D (1000 processors) We are always looking for external contributions if people wish to see other machines or platforms than the ones listed. Input files for a variety of applications are available to hopefully make the benchmarking easier. Constructive criticism is always welcomed. David Feller David Feller Molecular Science Research Center Battelle Pacific Northwest Labs Mail Stop K1-96 Battelle Blvd Richland, WA 99352 From M.J.C.Crabbe@reading.ac.uk Fri Feb 10 07:34:53 1995 Received: from mail3.rdg.ac.uk for M.J.C.Crabbe@reading.ac.uk by www.ccl.net (8.6.9/930601.1506) id FAA11278; Fri, 10 Feb 1995 05:50:51 -0500 Received: from sksscsc1 (actually host sksscsc1.rdg.ac.uk) by suma2.rdg.ac.uk with SMTP - Local (PP); Fri, 10 Feb 1995 10:48:31 +0000 Date: Fri, 10 Feb 1995 10:47:48 +0000 (GMT) From: James Crabbe X-Sender: skscrabb@sksscsc1 To: m.j.c.crabbe@reading.ac.uk Cc: CHEMISTRY@ccl.net Subject: Re: email addresses In-Reply-To: <"Thu Feb 9 14:42:42 199501*/I=F/G=Karl/S=Moschner/OU=4267EDUR/O=TMUS.URL/PRMD=LANGATE/ADMD=TELEMAIL/C=GB/"@MHS> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I would be most grateful for the email addresses of the following : Professor Peter A. Kollman, Dept. of Pharmaceutical chemistry, UC San Francisco. Professor Isiah Shavitt, Dept. of Chemistry, Ohio state University, Columbus, USA. Dr. Arthur Olsen, Scripps Institute, La Jolla, California. Professor Charles L. Wilkins, Dept. of Chemistry, UC Riverside, California. Professor Iwao Ohmine, Institute for Molecular Science, Myodaiji-Machi, Okazaki-shi 444, Japan. Many thanks, James Crabbe. From herbert.homeier@rchs1.chemie.uni-regensburg.de Fri Feb 10 07:38:46 1995 Received: from comsun.rz.uni-regensburg.de for herbert.homeier@rchs1.chemie.uni-regensburg.de by www.ccl.net (8.6.9/930601.1506) id GAA11366; Fri, 10 Feb 1995 06:08:11 -0500 Received: from rchs1.chemie.uni-regensburg.de by comsun.rz.uni-regensburg.de with SMTP id AA11644 (5.65c/IDA-1.4.4 for ); Fri, 10 Feb 1995 12:07:07 +0100 Received: by rchs1.chemie.uni-regensburg.de (4.1/URRZ-sub (1.5)) id AA16612; Fri, 10 Feb 95 12:08:43 +0100 Date: Fri, 10 Feb 95 12:08:43 +0100 From: Herbert Homeier (t4720) Message-Id: <9502101108.AA16612@rchs1.chemie.uni-regensburg.de> To: CHEMISTRY@ccl.net Subject: Re: CCL:D20h-symmetry Cc: beck@work2.ch-cip.uni-koeln.de Reply-To: nedwed@ptc.tu-graz.ac.at Michael Beck tel. 4816 (beck@work2.ch-cip.Uni-Koeln.DE) Thu, 9 Feb 1995 08:49:22 +0100 (MET) writes: >Dear netters! > >Does anybody know the character-table of the point-group D_20h>? >Is there a public domain program available, which calculates >the character-tables for arbitrary point-groups? >Any reply will be helpful! There is the program SYMAPPS 2.0 for MS-Windows that can compute the character table of D20h. The author is Karl NEDWED Institute for Physical and Theoretical Chemistry Graz Institute of Technology Rechbauerstr. 12 A-8010 Graz Austria E-mail address: nedwed@ptc.tu-graz.ac.at Best regards Herbert Homeier -------------------------------------------------------------- Dr. Herbert H. H. Homeier Institut fuer Physikalische und Theoretische Chemie Universitaet Regensburg D-93040 Regensburg, Germany Phone: +49-941-943 4720 FAX : +49-941-943 2305 email: na.hhomeier@na-net.ornl.gov HOMEPAGE --------------------------------------------------------------- From gl@coil.mdy.univie.ac.at Fri Feb 10 07:43:53 1995 Received: from coil.mdy.univie.ac.at for gl@coil.mdy.univie.ac.at by www.ccl.net (8.6.9/930601.1506) id EAA10716; Fri, 10 Feb 1995 04:40:18 -0500 Received: by coil.mdy.univie.ac.at (931110.SGI/930416.SGI.AUTO) for CHEMISTRY@ccl.net id AA06062; Fri, 10 Feb 95 10:38:47 +0100 From: "Gerald Loeffler" Message-Id: <9502101038.ZM6060@coil.mdy.univie.ac.at> Date: Fri, 10 Feb 1995 10:38:45 +0100 X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: CHEMISTRY@ccl.net Subject: SUMMARY: Literature on Mix of DFT and MD Mime-Version: 1.0 Encoding: 2 TEXT BOUNDARY, 46 MESSAGE, 2 TEXT BOUNDARY, 127 MESSAGE, 3 TEXT BOUNDARY Content-Type: multipart/mixed; boundary="PART-BOUNDARY=.19502101038.ZM6060.mdy.univie.ac.at" -- --PART-BOUNDARY=.19502101038.ZM6060.mdy.univie.ac.at Encoding: 43 TEXT Content-Type: text/plain; charset=us-ascii Dear Computational Chemists, I asked you about books dealing with the mixture of classical MD with Density Functional Calculations. Finally I got many answers, but unfortunately there doesn't seem to exist any book on this subject. Nevertheless, the answers contained a wealth of hints and pointers to groups working in this area. I think this information will considerably ease the process of getting familiar and catching up with this subject for everyone interested - including me. I would like to thank everyone who responded, namely Christopher Cramer, David Case, E. R. Bittner, Isaac B. Bersuker, Robert Murphy, Ton Rullmann, Veronique Deguelle, Karl F. Moschner The list of responses is attached to this mail. Cheers, gerald -- Gerald Loeffler PhD student in Theoretical Biochemistry Email: gl@mdy.univie.ac.at Phone: +43 1 40480 612 Fax: +43 1 4028525 Mail: University of Vienna Institute for Theoretical Chemistry Theoretical Biochemistry Group Waehringerstrasse 17/Parterre A-1090 Wien, Austria #include "fancy_ASCII_picture" #include "funny_statement" #include "standard_disclaimer" --PART-BOUNDARY=.19502101038.ZM6060.mdy.univie.ac.at Encoding: 122 text X-Zm-Content-Name: summary Content-Description: plain text Content-Type: text/plain ; charset=us-ascii -------------------------------------------------------------------------------- Christopher Cramer ------------------ Re below. The trouble is, you are asking for something very hard, because it sounds as though you plan to have your QM/MM boundary passing through one or more covalent bonds. When the boundary can be placed in such a way that no bonds are crossed, there are many examples of people using this technology, e.g., Warshel; Bash, Field, and Karplus; Gao; Merz and Stanton; Thompson; and, I believe, some people at Biosym whose names escape me. Nevertheless, all of this technology remains very non-black-box. In terms of theory for systems where covalent bonds are broken, you might look at Thery et al. in J. Comp. Chem. 15 (1994) 269. This paper deals with an MM/QM link using semiempirical NDDO theory for the QM side, but uses some nice tricks to decouple the levels within broken bonds. -------------------------------------------------------------------------------- David Case ---------- I think you got a complete reply already of all books and thorough reviews on this subject :-) You might check out recent papers by the Biosym people (Arnie Hagler and co-workers). -------------------------------------------------------------------------------- E. R. Bittner ------------- As far as I know there exist no books on mixed DFT/MD methods. However, you may be interested in some of the recent work by Emily Carter at UCLA and Martin Head-Gordon (UC-Berkeley) in which the electronic schrodinger eqn is solved at each MD time step. There's John Tully's work which introduces non-adiabatic transitions into MD simulations via a "hopping" algorithm. You may also want to check out the work by Peter Rossky regarding electron solvation in water. Most of the important papers by the above names have appeared in J. Chem. Phys. with in the past few years. -------------------------------------------------------------------------------- Isaac B. Bersuker ----------------- See R. Carr and M. Parrinello, Phys. Rev. Lett. 55, 2471 (1985) -------------------------------------------------------------------------------- Robert Murphy ------------- Hi, I read your reques in the cc-mail. I know of one reference which tries to combine QM regions with force fields; M. Karplus et. al. J. COmp. Chem. vol. 11 pg. 700 (1990) hope thats helpful. -------------------------------------------------------------------------------- Ton Rullmann ------------ You might want to have a look at this: http://rugch5.chem.rug.nl/~alexxx/DRF/HOME.html and a corresponding paper: http://rugch5.chem.rug.nl/~alexxx/ECCC/ECCC.html It is not DFT, but it is a combination of quantummechanical and (semi)classical treatments. -------------------------------------------------------------------------------- Veronique Deguelle ------------------ here are some references : -("Quantum Molecular Dynamics with Gaussian Basis Set"), B. Feuston, C. Lee and E. Clementi, in Modern Techniques in Computational Chemistry: MOTECC-91 (1991) -("Strucure and Dynamics of Molecular Systems with Density Functional Theory"), D.A.Estrin, G.Corongiu and E.Clementi, in Methods and Techniques in Computational Chemistry: METECC-94, edited by E.Clementi (1993) -E.Clementi and al., Chem. Rev., 91, 679 (1991) -D.K.Remler,P.A.Madden,Molecular physics,70, 921 (1990) -R.Car, M.Parrinello, Phys. Rev. Letters,55,2471 (1985) -G. Galli and A. Pasquarello, in Computer Simulation in Chemical Physics, edited by M.P. Allen and D.J. Tildesley, Kluwer (1993) I hope it can help you -------------------------------------------------------------------------------- Karl F. Moschner ---------------- I keep these two within reach: W. J. Hehre, L. Radom, P. v.R. Schleyer and J. A. Pople, "ab Initio Molecular Orbital Theory", John Wiley & Sons, New York, NY. 1986. ISBN 0-471-81241-2. J. B. Foresman and Ae. Frisch, "Exploring Chemistry with Electronic Structure Methods: A Guide to Using Gaussin", Gaussian Inc., Pittsburgh, PA. 1993. ISBN 0-9636769-0-3 Phone: (412) 279-6700 e-mail: info@gaussian.com and, if you're looking for a laboratory workbook, you might be interested in: W. J. Hehre, L. D. Burke, A. J. Shusterman, and W. J. Pietro, "Experiments in Computational Organic Chemistry", Wavefunction Inc., Irvine, CA. 1993. Phone: (714) 955-2120 e-mail: support@wavefun.com But I haven't found a good "experimental" DFT book yet. It may be too soon. -------------------------------------------------------------------------------- --PART-BOUNDARY=.19502101038.ZM6060.mdy.univie.ac.at-- From tennant%hau410.uk.sb.com@sb.com Fri Feb 10 09:38:34 1995 Received: from hau410.uk.sb.com for tennant%hau410.uk.sb.com@sb.com by www.ccl.net (8.6.9/930601.1506) id JAA13865; Fri, 10 Feb 1995 09:14:05 -0500 Received: by hau410.uk.sb.com (931110.SGI/921111.SGI.ANONFTP) for CHEMISTRY@ccl.net id AA08272; Fri, 10 Feb 95 14:13:29 GMT Date: Fri, 10 Feb 1995 14:13:28 +0000 From: Mike Tennant To: CHEMISTRY@ccl.net Subject: Re: CCL:conformer generator for MOPAC In-Reply-To: <"Thu Feb 9 14:42:42 199501*/I=F/G=Karl/S=Moschner/OU=4267EDUR/O=TMUS.URL/PRMD=LANGATE/ADMD=TELEMAIL/C=GB/"@MHS> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII > please suggest me a program which takes up the given geometry (cartesian > or internal) and generates a lot of conformers from that for the MOPAC > input. It would be nice if the program works in UNIX. (FORTRAN source > would be excellent). > > Thank you! > Dr. Ivar Martin Ivar, you can use macromodel to generate a set of unique conformations and then extract these confs to individual mopac input files using babel. Both progs run under unix. Mike From nick@BCH.UMontreal.CA Fri Feb 10 10:38:42 1995 Received: from condor.CC.UMontreal.CA for nick@BCH.UMontreal.CA by www.ccl.net (8.6.9/930601.1506) id KAA16036; Fri, 10 Feb 1995 10:08:06 -0500 Received: from merck.BCH.UMontreal.CA by condor.CC.UMontreal.CA with SMTP id AA16585 (5.65c/IDA-1.4.4 for CHEMISTRY@ccl.net); Fri, 10 Feb 1995 10:06:13 -0500 Received: from crysbio1.BCH.UMontreal.CA by merck.BCH.UMontreal.CA (940816.SGI.8.6.9/5.17) id PAA18235; Fri, 10 Feb 1995 15:08:08 GMT Received: by crysbio1.BCH.UMontreal.CA (931110.SGI/5.17) id AA00265; Fri, 10 Feb 95 10:07:53 -0500 Date: Fri, 10 Feb 95 10:07:53 -0500 From: nick@BCH.UMontreal.CA (Nick Blom) Message-Id: <9502101007.ZM263@crysbio1.BCH.UMontreal.CA> X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: CHEMISTRY@ccl.net Subject: rotational sampling Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 same message posted on protein-crystallography@net.bio.net Dear , I am looking for an algorithm which gives me a uniform, non-redundant, sampling of the rotation function based on a equal stepsize in all three directions. I know that a lot of people have already designed such an algorithm, thus in order to prevent me from re-doing other (wo)mans work, I am posting this question on the net. Results can be either Euler-, Lattman-, spherical angles, quaternions or the rotation matrices themselves. Can anyone be of help? Thanks for the effort, Nick Blom -- ================================================================== Dr. Nick Blom Tel : +1-514-3436111 ext 5352 Departement de Biochimie Fax : +1-514-3432210 Universite de Montreal Email: nick@bch.umontreal.ca C.P. 6128, Station Centre-Ville Montreal, PQ, H3C 3J7 Canada ================================================================== From Jeffrey.Gosper@brunel.ac.uk Fri Feb 10 10:47:29 1995 Received: from monge.brunel.ac.uk for Jeffrey.Gosper@brunel.ac.uk by www.ccl.net (8.6.9/930601.1506) id JAA14371; Fri, 10 Feb 1995 09:42:53 -0500 Received: from chem-pc-18.brunel.ac.uk by monge.brunel.ac.uk with SMTP (PP) id <09133-0@monge.brunel.ac.uk>; Fri, 10 Feb 1995 14:39:22 +0000 Date: Fri, 10 Feb 1995 14:39:18 GMT From: Jeffrey J Gosper Reply-To: Jeffrey.Gosper@brunel.ac.uk Subject: Re_view's location To: chemistry@ccl.net Message-ID: Priority: Normal MIME-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Sorry but the address I gave to my program re_view was incomplete. Here is the full location (one in the UK, the other in the States). The location of re_view is micros.hensa.ac.uk in micros/ibmpc/win/e/e026/rev_demo.zip its also on Oak.Oakland.edu in SimTel/win3/chem/rev_demo.zip More info. on re_view RE_VIEW is essentially a molecular viewer, animator, analyzer, and MOPAC reaction path converter. The major functions of RE_VIEW include the ability to: 1) Display and manipulate molecules in 3D; 2) Animate reaction pathways; 3) Align the steps/frames within an animation, along a vectors or onto a plane; 4) Animate normal modes of vibration; 5) Monitor geometries (lengths, angles and dihedrals); 6) Provide tabulated geometrical data (which can be readily incorporated into spreadsheets); and 7) Automatically produce high quality 'ray-traced' images and animation sequences. Jeff Gosper From smb@smb.chem.niu.edu Fri Feb 10 12:38:29 1995 Received: from mp.cs.niu.edu for smb@smb.chem.niu.edu by www.ccl.net (8.6.9/930601.1506) id MAA19081; Fri, 10 Feb 1995 12:17:23 -0500 Received: from cz2.chem.niu.edu by mp.cs.niu.edu with SMTP id AA16741 (5.67b/IDA-1.5 for <@mp.cs.niu.edu.chem.niu.edu:chemistry@ccl.net>); Fri, 10 Feb 1995 11:16:42 -0600 Received: from smb.chem.niu.edu by cz2.chem.niu.edu via SMTP (920330.SGI/890607.SGI) (for @mp.cs.niu.edu.chem.niu.edu:chemistry@ccl.net) id AA21400; Fri, 10 Feb 95 10:10:06 -0600 Received: by smb.chem.niu.edu (920330.SGI/890607.SGI) (for @cz2.chem.niu.edu:chemistry@ccl.net) id AA05109; Fri, 10 Feb 95 10:10:05 -0600 Date: Fri, 10 Feb 95 10:10:05 -0600 From: smb@smb.chem.niu.edu (Steven Bachrach) Message-Id: <9502101610.AA05109@smb.chem.niu.edu> To: chemistry@ccl.net Subject: 1995 Summer Gordon Research Conference Info Online I am pleased to announce that the final schedules for the 1995 Summer Gordon Research Conferences are available online through the Northern Illinois University Chemistry WWW/Gopher Site. These files can be obtained in any of the follwoing three ways: 1) via WWW The URL is http://hackberry.chem.niu.edu:70/0/webpage.html 2) via gopher to hackberry.chem.niu.edu 3) via anonymous ftp to hackberry.chem.niu.edu The files are in the directory /pub/GRC I hope that this information will be of use to many. Steve Steven Bachrach Department of Chemistry Northern Illinois University DeKalb, Il 60115 Phone: (815)753-6863 smb@smb.chem.niu.edu Fax: (815)753-4802 From abc@future.polytech.yaroslavl.su Fri Feb 10 12:58:08 1995 Received: from uucp-gw.innet.yaroslavl.su for abc@future.polytech.yaroslavl.su by www.ccl.net (8.6.9/930601.1506) id MAA18896; Fri, 10 Feb 1995 12:06:53 -0500 Received: from polytec.UUCP by uucp-gw.innet.yaroslavl.su with UUCP id AA16534 (5.65.kiae-1 for CHEMISTRY@ccl.net); Fri, 10 Feb 1995 19:59:38 +0300 Received: from future.polytech.yaroslavl.su by polytech.polytech.yaroslavl.su with SMTP id AA04734 (5.65.kiae-1 for ); Fri, 10 Feb 1995 19:36:08 +0300 Received: from FUTURE/SpoolDir by future.polytech.yaroslavl.su (Mercury 1.13); Fri, 10 Feb 95 19:38:21 +300 Received: from SpoolDir by FUTURE (Mercury 1.13); Fri, 10 Feb 95 19:37:53 +300 To: CHEMISTRY@ccl.net From: abc@polytech.yaroslavl.su (A.V.Sokolov) Message-Id: Organization: Yaroslavl State Technical University Date: Fri, 10 Feb 1995 19:37:24 +0300 (MSK) X-Mailer: dMail [Demos Mail for DOS v1.23] Return-Receipt-To: abc@polytech.yaroslavl.su Subject: TS compared with PMO; Re: Prediction of reactive sites. Lines: 55 Hullo, chemists! Michael D. Bartberger wrote: >Dear Netters: >I would very much appreciate references concerning any methods used to >correlate a given molecule's regioselectivity in a given reaction with a >property calculable with ab initio methods. >For example, using a simple FMO approach, we are taught that ...... ............ skipped >I had asked a question similar to this some time ago; asking whether it is >possible to obtain a "total" coefficient of a given AO at a certain MO, or >whether one of the coefficients generated in this way should be "plucked >out" and used as "the" coefficient. I have some comments on the topic. To study validity of PMO calculations (pi-aproximation) I compared its results with directly calculated activation energies, NOT WITH EXPERIMENTAL DATA. Using MNDO I got the following radical reactions TS (and so activation energies): CH2=CXY + HOO, CH3, CH3O, CCl3, CF3 and some substituted peroxy and alkyl radicals, where X is H, CH3, Cl, -COOCH3, -O-COCH3 or C6H5. Having compared these act. energies with "charge transfer" energies of PMO methods I dare state now that Frontier MO approximation is good for nothing (in my case it fails completely). So, FIRST: using PMO use full summing over set of MOs (or subset, in pi-approximation). Then, if you don't want to deal with a great deal of MOs, either: 1. project occupied shell on AOs of your reactive center and brood upon the coefficients and H{_i_i} of localized MO (when center is non-conjugated projection will give MO nearly 99% localized on it) or 2. I can propose an additive scheme of PMO sums evaluation. (you need to calculate some sums beforehand to parametrizate your compounds. Each reagent gets 2 parameters, you can use them instead of FMO coefficients). I've tested it on my set of reactions. BUT: all said doesn't mean that you will correctly predict results of direct calculations (in my case there were also strong influence of steric effect). ________________________________ Bye for now. Respectfully yours, A. Sokolov, Dept. of Phys.Chem., Yaroslavl Polytech. Inst., Russia """"""""""""""""""""""""""""""""""""""""""""""""""""""" abc@polytech.yaroslavl.su From tudor@t10.Lanl.GOV Fri Feb 10 13:03:16 1995 Received: from transposon.lanl.gov for tudor@t10.Lanl.GOV by www.ccl.net (8.6.9/930601.1506) id LAA18508; Fri, 10 Feb 1995 11:47:33 -0500 Received: from zygote.lanl.gov by transposon.lanl.gov (4.1/SMI-4.1) id AA02187; Fri, 10 Feb 95 09:47:31 MST From: tudor@t10.Lanl.GOV (Tudor Oprea) Received: by zygote.lanl.gov; (5.65/1.1.8.2/05Dec94-0117PM) id AA18888; Fri, 10 Feb 1995 09:47:06 -0700 Date: Fri, 10 Feb 1995 09:47:06 -0700 Message-Id: <9502101647.AA18888@zygote.lanl.gov> To: TOMKINSON_NP@fisonspharm.co.uk, chemistry@ccl.net Subject: Re: charges schemes with CoMFA I will not discuss the impact of choosing partial charges in conformational analysis (CA), for two reasons: their magnitude (and "correctness") will influence the choice of your local minima [to the extent that empirical charges may give a different energy map than quantum-mechanical ones], and the choice of the dielectric D will definitely contribute to that [smaller D will result in higher probability of intra-molecular H-bonds]. MNDO ESP calculations may be slow in MOPAC, but they correlate well with 631G* ESP charges - 0.94-0.96 R^2 for charge to charge correlation - better than STO-3G ESP for the same molecules [these with G92]. PM3 has been previously reported to go wrong with Nitrogens - it was previously posted on CCL - so browse in the 93-94 archive and look for messages from Drs JJP Stewart, A Holder, E Zoebisch [and others...]. In CoMFA, the choice of charges does not matter as long as you are consistent throughout the series: "If you can't be right, be consistent" (David Patterson). In my experience, MNDO vs MNDO ESP charges have no significant impact on the sets I studied. Of course, there might be some tricky ones out there 8=) but for systems where no fancy electronic distribution occurs, MNDO or AM1 can do the works. Chris Waller has noted that PM3 gives better correlations than Gasteiger-Huckel, but I would point out that both models were correlating well in CoMFA. A paper I reviewed (I believe it is out in JMC) reported on the side that comparing AM1 vs Gasteiger-Marsili, they found no difference. In sum, as long as your CA results are ok, your CoMFA model is unlikely to yield significant differences by using different partial charges. As for the dielectric in CoMFA - I recently started using constant D instead of distance dependent one - again, it is unlikely to have a tremendous impact on the robustness/predictive/explanatory qualities of your model. --Tudor **************************************************************************** * Tudor I. Oprea, MD PhD Tel: (505) 667 2682 * * Postdoctoral Research Associate Fax: (505) 665 3493 * * Theoretical Biology and Biophysics (T-10) Email: * * Los Alamos National Laboratory tudor@t10.lanl.gov * * Mail Stop K710, Los Alamos NM 87545 * **************************************************************************** From mmccar@postman.essex.ac.uk Fri Feb 10 13:38:29 1995 Received: from postman.essex.ac.uk for mmccar@postman.essex.ac.uk by www.ccl.net (8.6.9/930601.1506) id NAA20032; Fri, 10 Feb 1995 13:03:30 -0500 Received: from postman.essex.ac.uk by postman.essex.ac.uk with SMTP (PP) id <13891-0@postman.essex.ac.uk>; Fri, 10 Feb 1995 18:02:31 +0000 From: Mccarron M Date: Fri, 10 Feb 95 18:02:28 GMT Message-Id: <5200.9502101802@solb1.essex.ac.uk> To: chemistry Subject: Tidor or Karplus e-mail address Does anybody know the e-mail address of either Bruce Tidor or Martin Karplus Department of Chemistry Harvard University Cambridge Massachusetts 02138 or alternatively has anybody carried out amino acid mutations using CHARMM using the slow growth method during MD simulation Thanks in advance Matthew McCarron e-mail: mmccar@essex.ac.uk From KUS%SUEARN2.BITNET@mps.ohio-state.edu Fri Feb 10 13:43:55 1995 Received: from ohstpw.mps.ohio-state.edu for KUS%SUEARN2.BITNET@mps.ohio-state.edu by www.ccl.net (8.6.9/930601.1506) id MAA19538; Fri, 10 Feb 1995 12:40:57 -0500 Received: from SUEARN2.BITNET (MAILER@SUEARN2) by MPS.OHIO-STATE.EDU (PMDF V4.3-10 #9122) id <01HMVUZM851C8WWGOR@MPS.OHIO-STATE.EDU>; Fri, 10 Feb 1995 12:40:55 -0500 (EST) Date: Fri, 10 Feb 95 20:08 MSK From: Mikhail Kuzminsky -135-6388 (095) Subject: Re: benchmarks (gaussian92 and gamess on SUN versus IBM) To: CHEMISTRY@ccl.net Message-id: <01HMVUZM9H9E8WWGOR@MPS.OHIO-STATE.EDU> Content-transfer-encoding: 7BIT One small comment for this discussion: > Since we rapidly ran out of the 300 copies of version 1.0 that we had printed > and this year's edition is considerable larger, we intend to make this new > release available through Mosaic (under the EMSL home page at URL > http://www.emsl.pnl.gov:2080/) as well as have a limited number of hardcopies > > David Feller > Molecular Science Research Center It look very attractive if WWW-browsers working in line mode will be also usable for access to this files. If it's possible just now, please inform which starting html- document may be used. Mikhail Kuzminsky N.D. Zelinsky Institute of Organic Chemistry, Moscow From moviemol@madonna.Kemi.UU.SE Fri Feb 10 13:50:17 1995 Received: from madonna.Kemi.UU.SE for moviemol@madonna.Kemi.UU.SE by www.ccl.net (8.6.9/930601.1506) id MAA19751; Fri, 10 Feb 1995 12:52:20 -0500 Received: by madonna.Kemi.UU.SE id AA25312 (5.65c+/IDA-1.4.4 for CHEMISTRY@ccl.net); Fri, 10 Feb 1995 19:04:53 +0100 Date: Fri, 10 Feb 1995 19:04:53 +0100 From: Hermansson Ojam{e Message-Id: <199502101804.AA25312@madonna.Kemi.UU.SE> To: CHEMISTRY@ccl.net Subject: CCL:Molecular animation; Moviemol ============================================================================ MOVIEMOL version 1.1 - an easy-to-use molecular display and animation program ============================================================================ Moviemol displays o molecular structures o movies (e.g. MD trajectories, normal vibrations) o crystal structures Moviemol features: o Easy-to-use, simple input (flexible when desired) o Ball-and-stick molecules o Fast animation & rotations o Interfacable to an MD simulation run (for workstations) o Nice postscript output Moviemol runs on o PC (under DOS) o Silicon graphics Indigo and IBM RS/6000 workstations Moviemol can be obtained by anonymous ftp from 'chem-ftp.mps.ohio-state.edu'. In the '/moviemol' directory you will find executable Moviemol modules, six test examples and manual. See also: http://chem-www.mps.ohio-state.edu/~lars/moviemol.html Free-of-charge for academic usage, modest fee for teaching and non-academic usage. More information can be obtained from: ================================================================================ Kersti Hermansson & Lars Ojamae Dept. of Inorganic Chemistry, | Dept. of Chemistry, Ohio State University Uppsala University | 120 West 18th Avenue, Box 531, S-75121 Uppsala /Sweden | Columbus, OH 43210-1173 Fax: +46 18 508542 e-mail: moviemol@kemi.uu.se WWW URL: http://chem-www.mps.ohio-state.edu/~lars/moviemol.html ================================================================================ From mmh1203@ggr.co.uk Fri Feb 10 13:55:11 1995 Received: from gate.ggr.co.uk for mmh1203@ggr.co.uk by www.ccl.net (8.6.9/930601.1506) id NAA20424; Fri, 10 Feb 1995 13:18:25 -0500 Received: from mailhub.ggr.co.uk (uk0x07.ggr.co.uk) by gate.ggr.co.uk; Fri, 10 Feb 1995 18:15:57 GMT Received: from uk6x06.ggr.co.uk by mailhub.ggr.co.uk; Fri, 10 Feb 1995 18:08:03 GMT Received: by uk6x06.ggr.co.uk (8.6.8.1/imd110593) id SAA01193; Fri, 10 Feb 1995 18:16:51 GMT Date: Fri, 10 Feb 1995 18:16:49 +0000 (GMT) From: Mike Hann X-Sender: mmh1203@uk6x06 To: chemistry@ccl.net Subject: COMPUTATIONAL ASPECTS OF CHEMICAL LIBRARIES - MGMS meeting Message-ID: MIME-Version: 1.0 Content-Type: MULTIPART/MIXED; BOUNDARY="-1048570092-156928419-792440209=:1168" This message is in MIME format. The first part should be readable text, while the remaining parts are likely unreadable without MIME-aware tools. Send mail to mime@docserver.cac.washington.edu for more info. ---1048570092-156928419-792440209=:1168 Content-Type: TEXT/PLAIN; charset=US-ASCII ---------------------------------------------------------------- Mike Hann Head of Computational Chemistry Glaxo Research and Development Greenford Rd Greenford Middlesex UB6 0HE England mmh1203@ggr.co.uk tel: 081-966-2413 fac: 081-966-2156 ---1048570092-156928419-792440209=:1168 Content-Type: TEXT/PLAIN; charset=US-ASCII; name="junk.lis" Content-Transfer-Encoding: BASE64 Content-ID: Content-Description: CQ0KCU1PTEVDVUxBUiBHUkFQSElDUyBBTkQgTU9ERUxMSU5HIFNPQ0lFVFkg KE1HTVMpDQoNCk1HTVMgTWVldGluZyAtIENPTVBVVEFUSU9OQUwgQVNQRUNU UyBPRiBDSEVNSUNBTCBMSUJSQVJJRVMNCiANCiANClRoZSB2ZW51ZSBmb3Ig dGhlIGFib3ZlIGNvbmZlcmVuY2UgaXMgRGV2b25zaGlyZSBIYWxsLCBVbml2 ZXJzaXR5IG9mIExlZWRzLCANCkxlZWRzLEVuZ2xhbmQgb24gdGhlIDEwLTEy IEFwcmlsIDE5OTUuDQogDQpUaGUgcHJvdmlzaW9uYWwgcHJvZ3JhbW1lIGlu Y2x1ZGVzIHRvcGljcyBvbiB0aGUgZm9sbG93aW5nOg0KIA0KMQlDYWxjdWxh 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-0500 Date: Fri, 10 Feb 1995 14:01:07 -0500 (EST) From: Neil McKelvie Subject: Optimised programs for Power Macintosh computers? To: chemistry@ccl.net Message-id: <01HMVY6CV8XE984XO6@phem3.acs.ohio-state.edu> Content-transfer-encoding: 7BIT Does anyone know if there are any useful chemistry computational programs that have been OPTIMISED for the Power Macintosh computers? We can, of course, use the CUNY mainframes for any large computations, and have available Gaussian etc., but many of my colleagues, as well as myself at home, have Power Macs and would like the option of using them directly. I have several older programs that have been adapted for earlier Mac's, but these, as well as MS-DOS and Windows programs, run relatively slowly in emulation. Please E-mail replies to NEMCC@CUNYVM.CUNY.EDU or NEMCC@CUNYVM.BITNET Thank you - (Prof) Neil McKelvie; Dept of Chemistry; The City College; New York, NY 10031 212-650-6062 Fax 212-650-6107 From shubin@email.unc.edu Fri Feb 10 14:49:40 1995 Received: from email.unc.edu for shubin@email.unc.edu by www.ccl.net (8.6.9/930601.1506) id NAA21201; Fri, 10 Feb 1995 13:51:54 -0500 Received: by email.unc.edu (AIX 3.2/UCB 5.64/4.03) id AA36300; Fri, 10 Feb 1995 13:52:00 -0500 Date: Fri, 10 Feb 1995 13:52:00 -0500 (EST) From: Shubin Liu X-Sender: shubin@isisa.oit.unc.edu To: chemistry@osu.edu Cc: chemistry@ccl.net Subject: CCL: Protein Structure Prediction In-Reply-To: <01HMT8OL23DU000081@CHEMNA.DICHI.UNINA.IT> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear netters: I am not sure if it is appropriate to post this message here in this newsgroup. Anyway, I will be glad to hear your oppinions. Recently, I am interested in the theoretical prediction of the secondary structure, that is, folding, of proteins. It seems to me that there should exist some tools, which may be either theoretical or empirical, to predict the folding process of each protein based on its sequence. The fundamental blocks of this process is believed to be the alapha-helix and beta-sheet, which are also believed not to be formed arbitrarily. I found that there seems exist some regularities in the folding of these helixes and sheets, which govern the shape of the secondary structure of the protein. These regularities or rules seem not to be well-recogized or mentioned in references, as of my knowledge whose major is not biology. My questions are, then, is it possible to predict it? if not impossible, what progress has been made in this topic? Has someone mentioned the regularities or rules during the folding process for alapha-helix and beta-sheet as I believed above? Looking forward to hearing from you! Thanks for your attention! Shubin ............................................................................. Shubin Liu Department of Chemistry Email: shubin@email.unc.edu University of North Carolina sliu@mulliken.chem.unc.edu Chapel Hill, NC 27599-3290 Tel : (919) 962-0150(O) ............................................................................. From hk0x+@andrew.cmu.edu Fri Feb 10 15:38:34 1995 Received: from po2.andrew.cmu.edu for hk0x+@andrew.cmu.edu by www.ccl.net (8.6.9/930601.1506) id PAA23556; Fri, 10 Feb 1995 15:31:26 -0500 Received: (from postman@localhost) by po2.andrew.cmu.edu (8.6.9/8.6.9) id PAA25709 for chemistry@ccl.net; Fri, 10 Feb 1995 15:31:08 -0500 Received: via switchmail; Fri, 10 Feb 1995 15:30:54 -0500 (EST) Received: from peeper.se.cs.cmu.edu via qmail ID ; Fri, 10 Feb 1995 15:28:20 -0500 (EST) Received: from peeper.se.cs.cmu.edu via qmail ID ; Fri, 10 Feb 1995 15:28:19 -0500 (EST) Received: from Messages.8.5.N.CUILIB.3.45.SNAP.NOT.LINKED.peeper.se.cs.cmu.edu.HP9000.712 via MS.5.6.peeper.se.cs.cmu.edu.hp700_ux90; Fri, 10 Feb 1995 15:28:19 -0500 (EST) Message-ID: <0jCwlX200jeN0lA8Q0@andrew.cmu.edu> Date: Fri, 10 Feb 1995 15:28:19 -0500 (EST) From: Harry Karatassos To: chemistry@ccl.net Subject: CCL:Nucleic Acid and Protein Sequence Analysis workshop at the PSC NUCLEIC ACID AND PROTEIN SEQUENCE ANALYSIS WORKSHOP FOR BIOMEDICAL RESEARCHERS Pittsburgh, Pennsylvania June 4-9, 1995 Pittsburgh Supercomputing Center (PSC) is again offering a five-day workshop on "Nucleic Acid and Protein Sequence Analysis," June 4-9, 1995. It is funded by a grant from the National Center for Human Genome Research of the National Institutes of Health. The workshop will familiarize biomedical researchers with computational methods and provide practice in applying supercomputing resources to problems of concern in macromolecular sequence analysis. Emphasis will be on alignment of and pattern extraction from multiple sequences. Participants will gain practical experience on PSC's Cray C-90 and T3D in (1) comparing and aligning sequences, (2) identifying informative patterns in a set of sequences; and (3) using extracted informative patterns to identify related sequences. Researchers will also learn several approaches to database searching and multiple sequence alignment, how to use profile analysis effectively, and how to identify patterns in their sequences. Participants are encouraged to bring sequence analysis problems from their current research. Extensive documentation will be given at the outset on the PSC computing environment as well as on the specific programs to be employed in the workshop. No prior supercomputing experience is required. Workshop leaders are Dr. Gary Churchill, Cornell University, Dr. Michael Gribskov, San Diego Supercomputing Center, and Dr. Hugh Nicholas, PSC. A limited number of grants to cover travel and hotel accommodations are available for U.S. academic participants. ALL PARTICIPANTS ARE REQUIRED TO PAY A $135 REGISTRATION FEE, IN ADVANCE, UPON ACCEPTANCE INTO THE WORKSHOP. The deadline for submitting applications is April 17, 1995. Enrollment is limited to 20 participants. Additional information about this workshop can be found in http://pscinfo.psc.edu/biomed/workshops95.html * * * * * PITTSBURGH SUPERCOMPUTING CENTER NUCLEIC ACID AND PROTEIN SEQUENCE ANALYSIS WORKSHOP FOR BIOMEDICAL RESEARCHERS June 4-9, 1995 APPLICATION Name: ________________________________________________________________ Affiliation: ________________________________________________________________ Address: ________________________________________________________________ (Business) ________________________________________________________________ ________________________________________________________________ (Home) ________________________________________________________________ Telephone: ____________________________ ______________________________ (Business) (Home) *Social Security Number: _______-_____-_______ Citizenship:___________________ Electronic Mail Address:_______________________________________________________ Status: ___Graduate ___Post-doctoral Fellow ___Faculty ___Other (specify) In order to attend the workshop, will you need funds for travel?___ lodging?___ Please indicate specifically any special housing, transportation or dietary arrangements you will need: __________________________________________ How did you learn about this workshop:_________________________________________ REQUIREMENTS: Applicants must submit a completed application form and a cover letter. The letter should describe, in one or two paragraphs, the sequence analysis problems encountered in your research, and how participating in the workshop will enhance this research. Please include a brief statement describing your level of experience with computers. Faculty members, staff and post-docs should provide a curriculum vita. Graduate students must have a letter of recommendation from a faculty member. If you have requested travel funds, please include the cost of roundtrip air fare from your home to Pittsburgh and indicate the amount of travel funds you will need. ALL PARTICIPANTS WILL BE REQUIRED TO PAY A $135 ADVANCE REGISTRATION FEE UPON ACCEPTANCE INTO THE WORKSHOP. Please return all application materials by APRIL 17, 1995 to: Biomedical Workshop Applications Committee Pittsburgh Supercomputing Center 4400 Fifth Avenue, Suite 230C Pittsburgh, PA 15213 Direct inquiries to: Nancy Blankenstein, blankens@psc.edu or 412/268-4960. *Disclosure of Social Security Number is voluntary. PSC does not discriminate on the basis of race, color, religion, sex, age, creed, national or ethnic origin, or handicap. From jkl@ccl.net Fri Feb 10 15:42:15 1995 Received: for jkl@ccl.net by www.ccl.net (8.6.9/930601.1506) id PAA23112; Fri, 10 Feb 1995 15:10:32 -0500 Date: Fri, 10 Feb 1995 15:10:32 -0500 From: Jan Labanowski Message-Id: <199502102010.PAA23112@www.ccl.net> To: chemistry@ccl.net Subject: WARNING to list participants Cc: jkl@ccl.net Dear Netters, This is your coordinator speaking. I want to remind you that everyone who posts address inquires (or other messages which do not agree with the rules of Comp.Chem.List) goes to "reject" file. The reject file prevents people >from posting to the list directly, and if your address is there, your message will be posted only after I reviewed it and found appropriate. The review process may take a long time. Needless to say, I am not enjoying the job of the censor since it takes my time. So please adhere to the rules. The rules are available by sending a message: HELP CHEMISTRY to MAILSERV@ccl.net On another theme: --- CCL Support plea --- Thank you for people who already send me the letters of support for the CCL. However, I need many more letters to claim general support for the list. For those who did not send a letter yet, please understand that I really need them. For more details send a message: select chemistry cd ccl-proposal ls get message.txt quit to MAILSERV@ccl.net Thank you for your attention. Jan jkl@ccl.net -- Dr. Jan K. Labanowski, Senior Research/Supercomputer Scientist/Specialist, etc. Ohio Supercomputer Center, 1224 Kinnear Rd, Columbus, OH 43212-1163 ph:(614)-292-9279, FAX:(614)-292-7168, E-mail: jkl@ccl.net JKL@OHSTPY.BITNET From EWING@jcvaxa.jcu.edu Fri Feb 10 16:38:45 1995 Received: from jcvaxa for EWING@jcvaxa.jcu.edu by www.ccl.net (8.6.9/930601.1506) id QAA25220; Fri, 10 Feb 1995 16:22:37 -0500 Received: from jcvaxa.jcu.edu by jcvaxa.jcu.edu (PMDF V4.3-7 #9465) id <01HMW2R3QIZW8Y6KA9@jcvaxa.jcu.edu>; Fri, 10 Feb 1995 16:24:14 EST Date: Fri, 10 Feb 1995 16:24:14 -0500 (EST) From: "David W. Ewing (216) 397-4241" Subject: MNDO90 To: chemistry@ccl.net Message-id: <01HMW2R3QSN28Y6KA9@jcvaxa.jcu.edu> X-VMS-To: IN%"chemistry@ccl.net" X-VMS-Cc: EWING MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Who does one contact to buy MNDO90? Thanks! Dave Ewing John Carroll University ewing@jcvaxa.jcu.edu From hk0x+@andrew.cmu.edu Fri Feb 10 17:39:15 1995 Received: from po6.andrew.cmu.edu for hk0x+@andrew.cmu.edu by www.ccl.net (8.6.9/930601.1506) id QAA26313; Fri, 10 Feb 1995 16:59:55 -0500 Received: (from postman@localhost) by po6.andrew.cmu.edu (8.6.9/8.6.9) id QAA17564 for chemistry@ccl.net; Fri, 10 Feb 1995 16:59:35 -0500 Received: via switchmail; Fri, 10 Feb 1995 16:59:33 -0500 (EST) Received: from peeper.se.cs.cmu.edu via qmail ID ; Fri, 10 Feb 1995 16:59:30 -0500 (EST) Received: from peeper.se.cs.cmu.edu via qmail ID ; Fri, 10 Feb 1995 16:59:27 -0500 (EST) Received: from Messages.8.5.N.CUILIB.3.45.SNAP.NOT.LINKED.peeper.se.cs.cmu.edu.HP9000.712 via MS.5.6.peeper.se.cs.cmu.edu.hp700_ux90; Fri, 10 Feb 1995 16:59:27 -0500 (EST) Message-ID: <0jCy6z200jeN0lAAo0@andrew.cmu.edu> Date: Fri, 10 Feb 1995 16:59:27 -0500 (EST) From: Harry Karatassos To: chemistry@ccl.net Subject: CCL: NMR workshop offered at the PSC STRUCTURE DETERMINATION FROM NMR Pittsburgh Supercomputing Center June 25-28, 1995 Pittsburgh Supercomputing Center (PSC) is offering biomedical researchers a "Structure Determination From NMR" Workshop. The objective is to introduce participants to the different techniques for the elucidation of solution structures of biological macromolecules from nuclear magnetic resonance data. The workshop is free to academic participants. The worskhop will consist of lectures and extensive hands-on sessions. The programs AMBER, Mardigras and MidasPlus will be discussed. Hands-on sessions will be emphasized. Participants will be able to work on the examples provided or on their own experimental data. No prior supercomputing experience is necessary. Workshop leaders are: Dr. David Case, The Scripps Research Institute; and Drs Thomas James, Julie Newdoll and Uli Schmitz, University of California, San Francisco. This workshop is funded by a grant from the Biomedical Research Technology Program, National Center for Research Resources, National Institutes of Health. Travel, meals and hotel accommodations for researchers affilated with U.S. academic institutions are supported by this grant. Enrollment is limited to 20. An application form is included. Deadline for applications is: April 28, 1995. Additional information about this workshop can be found in http://pscinfo.psc.edu/biomed/workshops95.html * * * * * * * * * * PITTSBURGH SUPERCOMPUTING CENTER BIOMEDICAL INITIATIVE STRUCTURE DETERMINATION USING NMR June 25-28, 1995 APPLICATION Name:________________________________________________________________________ Affiliation:_________________________________________________________________ Address:_____________________________________________________________________ (Business) _____________________________________________________________________________ ____________________________________________________________________________ (Home) ____________________________________________________________________________ Telephone: ____________________ ______________________ (Business) (Home) *Social Security Number: _______-_____-_______ Citizenship: ____________ Electronic Mail Address:____________________________________________________ Status: ___Graduate ___Post-doctoral Fellow ___Faculty ___Other (specify) Please indicate specifically any special housing, transportation or dietary arrangements you will need: _______________________________________________ How did you learn about this workshop? _____________________________________ REQUIREMENTS: Applicants must submit a completed application form and a cover letter. The letter should describe, in one or two paragraphs, your current research and how participating in the workshop will enhance this research. Please include a brief statement describing your level of experience with computers. Faculty members, staff and post-docs should provide a curriculum vita. Graduate students must have a letter of recommendation from a faculty member. Please return all application materials by APRIL 28, 1995 to: Biomedical Workshop Applications Committee Pittsburgh Supercomputing Center 4400 Fifth Avenue, Suite 230C Pittsburgh, PA 15213 Direct inquiries to: Nancy Blankenstein, blankens@psc.edu or 412/268-4960. *Disclosure of Social Security Number is voluntary. PSC does not discriminate on the basis of race, color, religion, sex, age, creed, national or ethnic origin, or handicap. From hk0x+@andrew.cmu.edu Fri Feb 10 17:44:18 1995 Received: from andrew.cmu.edu for hk0x+@andrew.cmu.edu by www.ccl.net (8.6.9/930601.1506) id RAA26452; Fri, 10 Feb 1995 17:06:21 -0500 Received: (from postman@localhost) by andrew.cmu.edu (8.6.9/8.6.9) id RAA20193 for chemistry@ccl.net; Fri, 10 Feb 1995 17:06:18 -0500 Received: via switchmail; Fri, 10 Feb 1995 17:06:16 -0500 (EST) Received: from peeper.se.cs.cmu.edu via qmail ID ; Fri, 10 Feb 1995 17:06:00 -0500 (EST) Received: from peeper.se.cs.cmu.edu via qmail ID ; Fri, 10 Feb 1995 17:05:53 -0500 (EST) Received: from Messages.8.5.N.CUILIB.3.45.SNAP.NOT.LINKED.peeper.se.cs.cmu.edu.HP9000.712 via MS.5.6.peeper.se.cs.cmu.edu.hp700_ux90; Fri, 10 Feb 1995 17:05:51 -0500 (EST) Message-ID: <0jCyAz200jeN0lA1g0@andrew.cmu.edu> Date: Fri, 10 Feb 1995 17:05:51 -0500 (EST) From: Harry Karatassos To: chemistry@ccl.net Subject: CCL: MM and MD of Biopolymers workshop at the PSC "METHODS OF MOLECULAR MECHANICS AND DYNAMICS OF BIOPOLYMERS" WORKSHOP Pittsburgh Supercomputing Center August 16-19, 1995 The Pittsburgh Supercomputing Center (PSC) is hosting a workshop on "Methods of Molecular Mechanics and Dynamics of Biopolymers," August 16-19, 1995. The workshop will familiarize biomedical researchers with computational methods and provide practice in applying supercomputing resources to problems of concern in molecular mechanics. Practical experience on our supercomputers will be gained in the application to: (1) the theory and practice of molecular mechanics and dynamics; (2) the development and refinement of molecular mechanics force fields; (3) the problem of conformation mapping and analysis of polypeptide structures, including the refinement of structure from measured NMR data; and (4) computation of interaction energies and free energies for protein-drug interactions and conformational thermodynamics. Workshop leaders are Dr. Charles L. Brooks III, The Scripps Research Institute and Dr. Alexander D. MacKerell Jr., University of Maryland at Baltimore. The worskhop will consist of lectures and extensive hands-on sessions. General aspects of molecular mechanics software will be discussed and a number of packages are available for use at the PSC. However, the programs CHARMM and QUANTA will be utilized most extensively in demonstrations. Hands-on sessions will be emphasized. Participants will be able to work on the examples provided or on their own experimental data. No prior supercomputing experience is necessary. This workshop is funded by a grant from the Biomedical Research Technology Program, National Center for Research Resources, National Institutes of Health. Travel, meals and hotel accommodations for researchers affilated with U.S. academic institutions are supported by this grant. Enrollment is limited to 20. An application form is included. Deadline for applications is: June 22, 1995. Please direct inquires or send the following application form to blankens@psc.edu. Additional information about this workshop can be found in http://pscinfo.psc.edu/biomed/workshops95.html PITTSBURGH SUPERCOMPUTING CENTER BIOMEDICAL INITIATIVE ************************************** August 16-19, 1995 APPLICATION Name:________________________________________________________________________ Affiliation:_________________________________________________________________ Address:_____________________________________________________________________ (Business) _____________________________________________________________________________ ____________________________________________________________________________ (Home) ____________________________________________________________________________ Telephone: ____________________ ______________________ (Business) (Home) *Social Security Number: _______-_____-_______ Citizenship: ____________ Electronic Mail Address:____________________________________________________ Status: ___Graduate ___Post-doctoral Fellow ___Faculty ___Other (specify) Please indicate specifically any special housing, transportation or dietary arrangements you will need: _______________________________________________ How did you learn about this workshop? _____________________________________ REQUIREMENTS: Applicants must submit a completed application form and a cover letter. The letter should describe, in one or two paragraphs, your current research and how participating in the workshop will enhance this research. Please include a brief statement describing your level of experience with computers. Faculty members, staff and post-docs should provide a curriculum vita. Graduate students must have a letter of recommendation from a faculty member. Please return all application materials by June 22, 1995 to: Biomedical Workshop Applications Committee Pittsburgh Supercomputing Center 4400 Fifth Avenue, Suite 230C Pittsburgh, PA 15213 Direct inquiries to: Nancy Blankenstein, blankens@psc.edu or 412/268-4960. *Disclosure of Social Security Number is voluntary. PSC does not discriminate on the basis of race, color, religion, sex, age, creed, national or ethnic origin, or handicap. From d3e102@ames.pnl.gov Fri Feb 10 18:38:50 1995 Received: from pnlg.pnl.gov for d3e102@ames.pnl.gov by www.ccl.net (8.6.9/930601.1506) id SAA27975; Fri, 10 Feb 1995 18:24:41 -0500 Received: from ames.pnl.gov by pnlg.pnl.gov (PMDF V4.2-15 #6012) id <01HMW0PXSWRK8WW29N@pnlg.pnl.gov>; Fri, 10 Feb 1995 15:24:56 PST Received: by ames.pnl.gov (931110.SGI/890607.SGI) id AA10358; Fri, 10 Feb 95 15:24:22 -0800 Date: Fri, 10 Feb 1995 15:24:22 -0800 From: d3e102@ames.pnl.gov (Dave Feller) Subject: Ab Initio Benchmarks To: CHEMISTRY@ccl.net Message-id: <9502102324.AA10358@ames.pnl.gov> Content-transfer-encoding: 7BIT Some months ago I posted an announcement about the impending (I assumed) availability of version 2.0 of the EMSL Ab Initio Benchmark Report. The report is still working it's way through the Battelle clearance process. Simultaneously, someone is working on the Mosaic form. Our present approach is to make the PostScript version available via a PostScript previewer. Since I drastically underestimated the amount of time needed to get this document cleared, I would hesitate to make a new guess. During this lull I've had the opportunity to add data for some newer machines (e.g. IBM's RS/6000 390). When the report is finally available electronically I will post an announcement. Printed version will take another 1 - 2 months. David Feller Environmental Molecular Sciences Laboratory Battelle Pacific Northwest Labs Mail Stop K1-96 Battelle Blvd Richland, WA 99352 From landman@hal.physics.wayne.edu Fri Feb 10 18:42:35 1995 Received: from CMS.CC.WAYNE.EDU for landman@hal.physics.wayne.edu by www.ccl.net (8.6.9/930601.1506) id SAA27874; Fri, 10 Feb 1995 18:11:25 -0500 Received: from hal.physics.wayne.edu by CMS.CC.WAYNE.EDU (IBM VM SMTP V2R2) with TCP; Fri, 10 Feb 95 18:11:10 EST Received: from hal (hal.physics.wayne.edu) by hal.physics.wayne.edu (4.1/SMI-4.1) id AA01434; Fri, 10 Feb 95 18:11:12 EST Date: Fri, 10 Feb 1995 18:11:11 -0500 (EST) From: Joe Landman Subject: Re: CCL:PC/Windows used in computational chemistry To: Leif Laaksonen Cc: chemistry@ccl.net In-Reply-To: Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Leif: You wrote: > > Hi, > > I want to thank everybody who have sent me a mail as a reply to my > question about the status of the PC/Windows market for computational > chemistry. As I can see it now the PC/Windows and specially (Windows > NT) market is still to premature. There is excellent work going on by some > software houses but not too much in other places. OS/2 Warp is also > mixing up the situation in Europe. Specially in Germany shops seem > to bundle OS/2 Warp with their hardware in favour of MS Windows. > I don't know if this is done because they think Warp is better than > Windows or if they just feel uncomfortable with Microsoft. I do a significant amount of my program development and testing work under Warp with the watcom fortran compiler. I can and do run 45 meg memory footprint ab-initio molecular dynamics simulations on my home box, an 8 meg ram 486 DX 33, something that windows versions of the same code couldnt do. I then ftp the working code from the home box to the production workstation or Cray, only changing the makefiles. I generally find Warp to be a superior product to windows, and an excellent platform on which to run windows applications. The multitasking is smoother, and I can use the machine while large calculations are in progress. HyperChem runs nicely under Warp, as does RASMol and other useful tools. There are a few useful tools for scientists under Warp, such as Octave, Mathematica, full compliment of GNU tools, ksh, etc. On some masochistic occasions, I run X at home over the 14.4k modem to use the Cray ATExpert or Xmol apps. I just wanted to add this note to let you know that Warp is a productive environment for serious work, and worthy of consideration for PC platform frontends to heavy computational metal. Joe Landman Physics Dept Wayne State University landman@hal.physics.wayne.edu From garciae@ucsub.colorado.edu Fri Feb 10 20:38:46 1995 Received: from ucsub.colorado.edu for garciae@ucsub.colorado.edu by www.ccl.net (8.6.9/930601.1506) id UAA29221; Fri, 10 Feb 1995 20:09:22 -0500 Received: (from garciae@localhost) by ucsub.colorado.edu (8.6.9/8.6.9/CNS-3.5) id SAA21360; Fri, 10 Feb 1995 18:09:22 -0700 Date: Fri, 10 Feb 1995 18:09:21 -0700 (MST) From: Garcia Edgardo To: chemistry@ccl.net Subject: CCL: Internal -> x,y,z coordinates Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Two questions: 1. Does somebody know where I can get a code (C,C++,FORTRAN) that transforms internal mol. coordinates in x,y,z ? 2. A program (code) that gets a molecular file with charges and calculates the dipole. Thanks !! Edgardo Univ. of Colorado BOULDER CO