From jkshin@radon.sait.samsung.co.kr Thu Jan 13 00:49:34 1994 Received: from han.hana.nm.kr for jkshin@radon.sait.samsung.co.kr by www.ccl.net (8.6.4/930601.1506) id AAA14147; Thu, 13 Jan 1994 00:46:19 -0500 Received: from (saitgw.sait.samsung.co.kr) by han.hana.nm.kr (4.1/KUM-0.1) id AA12230; Thu, 13 Jan 94 14:47:37 KST Received: from radon.sait.samsung.co.kr by (4.1/SMI-4.1) id AA25467; Thu, 13 Jan 94 14:47:06 KST Received: by radon.sait.samsung.co.kr (920330.SGI/920502.SGI.AUTO) for @saitgw.sait.samsung.co.kr:chemistry@ccl.net id AA04142; Fri, 14 Jan 94 14:50:09 +0900 Date: Fri, 14 Jan 94 14:50:09 +0900 From: jkshin@radon.sait.samsung.co.kr (Jaikwang Shin) Message-Id: <9401140550.AA04142@radon.sait.samsung.co.kr> To: chemistry@ccl.net Subject: Green Function MC Dear Netters: Does anyone know about the "Diffusion Monte Carlo method" or "Green Function Monte Carlo method"? Any information related to them or other kind of Quantum Monte Carlo method will be appreciated. Thanks a lot in advance Jai K. Shin jkshin@radon.sait.samsung.co.kr From pettsj@visigoth.demon.co.uk Thu Jan 13 02:49:35 1994 Received: from post.demon.co.uk for pettsj@visigoth.demon.co.uk by www.ccl.net (8.6.4/930601.1506) id CAA14635; Thu, 13 Jan 1994 02:40:45 -0500 Received: from visigoth.demon.co.uk by post.demon.co.uk id aa09238; 13 Jan 94 7:30 GMT Date: Thu, 13 Jan 94 07:32:32 GMT From: James Petts Subject: Cysteine-Bridged Small Peptides To: chemistry@www.ccl.net X-Mailer: LeeMail 2.0.3 Message-Id: Can anybody point me to experimental and/or theoretical studies on conformations of small (n=3-7 residues) disulphide-bridged peptides? -- == James Petts == P.S. Please excuse my rottn' english you see moomins go to school only as long as it amuses them. From JEREMYW@num-alg-grp.co.uk Thu Jan 13 06:49:45 1994 Received: from ben.britain.eu.net for JEREMYW@num-alg-grp.co.uk by www.ccl.net (8.6.4/930601.1506) id GAA15400; Thu, 13 Jan 1994 06:39:50 -0500 Received: from num-alg-grp.co.uk by ben.britain.eu.net via JANET with NIFTP (PP) id ; Thu, 13 Jan 1994 11:27:26 +0000 Message-Id: <7374.9401131125@nags2.nag.co.uk> Received: from vax.nag.co.uk (nagvax) by nags2.nag.co.uk (4.1/UK-2.1) id AA07374; Thu, 13 Jan 94 11:25:07 GMT Date: 13 Jan 94 11:23:00 WET From: JEREMY WALTON Subject: Re: Molecular Simulation To: CHEMISTRY >> >Who is the editor in chief and >> >What is the mailing address to send manuscript? >> > >> Editor in Chief is N. Quirke. manuscripts can be sent to him or to one of >> the appropriate regional editors (Gubbins, Cornell or van Gunsteren, ETH). >> I suppose you should submit to Quirke. His address is: BP Research Centre, >>> Chertsey Road, Sunbury-on-Thames, MiddlesexTW16 7LN, England, UK. Nick Quirke is no longer at BP Research. He's now working for Biosym at their Paris office - I'm sorry, I don't have the address, but Biosym should be able to tell you. Hope this helps. Cheers, Jeremy -------------------------------------------------------------------------------- | Jeremy Walton nagjpw@vax.oxford.ac.uk | | The Numerical Algorithms Group Ltd, Oxford, UK jeremyw@nag.co.uk | | Tel: +44 865 511245 | | Fax: +44 865 310139 | -------------------------------------------------------------------------------- From czernek@chemi.muni.cz Thu Jan 13 09:49:44 1994 Received: from aragorn.ics.muni.cz for czernek@chemi.muni.cz by www.ccl.net (8.6.4/930601.1506) id JAA16850; Thu, 13 Jan 1994 09:38:37 -0500 Received: from bilbo.chemi.muni.cz by aragorn.ics.muni.cz with SMTP id AA21619 (5.67a8/IDA-1.4.4 for ); Thu, 13 Jan 1994 15:38:20 +0100 Received: by bilbo.chemi.muni.cz id AA13301 (5.67a/IDA-1.4.4 for chemistry@ccl.net); Thu, 13 Jan 1994 15:38:57 +0100 Date: Thu, 13 Jan 1994 15:38:57 +0100 From: Jiri Czernek Message-Id: <199401131438.AA13301@bilbo.chemi.muni.cz> To: chemistry@ccl.net Subject: ab initio on I486/BSD Unix Dear Netters , I'd like to run ab initio (GAMESS and/or COLUMBUS) calculations on I486 under BSD Unix. Has anyone been ever succesful in porting these programs on that platform? Thank you in advance for any suggestions/comments. czernek@bilbo.chemi.muni.cz From burkhart@goodyear.com Thu Jan 13 09:56:43 1994 Received: from goodyear.com for burkhart@goodyear.com by www.ccl.net (8.6.4/930601.1506) id JAA16673; Thu, 13 Jan 1994 09:10:21 -0500 Received: from rdsrv2 (rdsrv2.goodyear.com) by goodyear.com (4.1/SMI-4.1) id AA17051; Thu, 13 Jan 94 09:10:19 EST Received: from rds325 by rdsrv2 (4.1/SMI-4.1) id AA01360; Thu, 13 Jan 94 09:10:19 EST Received: by rds325 (920330.SGI/920502.SGI.AUTO) for @rdsrv2:chemistry@ccl.net id AA26776; Thu, 13 Jan 94 09:09:52 -0500 Date: Thu, 13 Jan 94 09:09:52 -0500 From: burkhart@goodyear.com (Craig W. Burkhart) Message-Id: <9401131409.AA26776@rds325> To: chemistry@ccl.net Subject: Green's Function Monte Carlo There was a nice article by Mike Lee and Kevin Schmidt awhile ago on this very subject. The reference is Michael A. Lee & Kevin E. Schmidt, "Green's Function Monte Carlo", Computers in Physics, Vol. 6(2), 192-97(1992). You will find this article as part of the regular "Computer Simulations" articles done by the journal. Hope this helps... -------------------------------------------------------------------------- Craig W. Burkhart, Ph.D. Senior Research Chemist E-mail: cburkhart@goodyear.com The Goodyear Tire & Rubber Co. Fone: 216.796.3163 Research Center Fax: 216.796.3304 142 Goodyear Boulevard Akron, OH 44305 -------------------------------------------------------------------------- For a successful technology, reality must take precedence over public relations, for Nature cannot be fooled - Feynman -------------------------------------------------------------------------- From chiremv!andromeda!jeffb@uunet.UU.NET Thu Jan 13 02:00:08 1994 Received: from relay2.UU.NET for chiremv!andromeda!jeffb@uunet.UU.NET by www.ccl.net (8.6.4/930601.1506) id CAA14450; Thu, 13 Jan 1994 02:00:07 -0500 Received: from spool.uu.net (via LOCALHOST) by relay2.UU.NET with SMTP (5.61/UUNET-internet-primary) id AA13047; Thu, 13 Jan 94 02:00:05 -0500 Received: from chiremv.UUCP by uucp3.uu.net with UUCP/RMAIL (queueing-rmail) id 015817.10099; Thu, 13 Jan 1994 01:58:17 EST Received: from andromeda by chiron.com (4.1/SMI-4.1) id AA21347; Wed, 12 Jan 94 21:36:41 PST Received: by andromeda (920330.SGI/911001.SGI) for chiremv!uunet!ccl.net!chemistry-request id AA14919; Wed, 12 Jan 94 21:20:55 -0800 Date: Wed, 12 Jan 94 21:20:55 -0800 From: chiremv!andromeda!jeffb@uunet.UU.NET (Jeff Blaney) Message-Id: <9401130520.AA14919@andromeda> To: uunet!ccl.net!chemistry@uunet.UU.NET Subject: Re: SB Drug Design from a Model Binding Site Ring, C. S., Sun, E., Mckerrow, J. H., Lee, G. K., Rosenthal, P. J., Kuntz, I. D., Cohen, F. E. "Structure-Based Inhibitor Design by Using Protein Models for the Development of Antiparasitic Agents", Proc. Natl. Acad. Sci. USA 1993, 90, 3583-3587 is a good example of how to use a homology model for structure based design. Jeff Blaney Chiron From Sundar_Sundararajan.XRCC@xerox.com Thu Jan 13 11:49:46 1994 Received: from omega.xerox.com for Sundar_Sundararajan.XRCC@xerox.com by www.ccl.net (8.6.4/930601.1506) id LAA18457; Thu, 13 Jan 1994 11:17:31 -0500 Received: from XRCC_MAIL.XRCC.XEROX.xns by omega.xerox.com via XNS id <29574(3)>; Thu, 13 Jan 1994 08:16:51 PST X-NS-Transport-ID: 080037006B5DF71330CA Date: Thu, 13 Jan 1994 08:16:47 PST From: Sundar_Sundararajan.XRCC@xerox.com Subject: Re: Green Function MC In-Reply-to: <9401140550.AA04142@radon.sait.samsung.co.kr> To: jkshin@radon.sait.samsung.co.kr cc: chemistry@ccl.net Message-ID: <"13-Jan-94 11:16:31".*.Sundar_Sundararajan.XRCC@Xerox.com> I am not sure if the following would be of any help, but look at the following reference : R. C. Shukla and H. Hubschle, Phys. Rev., B, v40, 1555 (1989). : Sundar (sundar.xrcc@xerox.com) From atina!criba!rvgloss@uunet.UU.NET Thu Jan 13 12:49:44 1994 Received: from relay1.UU.NET for atina!criba!rvgloss@uunet.UU.NET by www.ccl.net (8.6.4/930601.1506) id MAA19198; Thu, 13 Jan 1994 12:18:11 -0500 Received: from spool.uu.net (via LOCALHOST) by relay1.UU.NET with SMTP (5.61/UUNET-internet-primary) id AB15221; Thu, 13 Jan 94 12:18:07 -0500 Received: from atina.UUCP by uucp5.uu.net with UUCP/RMAIL (queueing-rmail) id 121629.15066; Thu, 13 Jan 1994 12:16:29 EST Received: from criba.edu.ar by atina.ar with UUCP (5.59/Vxxiii) id AA26162; Thu, 13 Jan 94 14:09:41 ARG Received: by arcriba.edu.ar (5.59/25-eef) id AA07170; Thu, 13 Jan 94 14:07:20 ARG Received: by arcriba.edu.ar (5.59/25-eef) id AA07162; Thu, 13 Jan 94 14:07:18 ARG Message-Id: <9401131807.AA07162@arcriba.edu.ar> From: atina!criba!rvgloss@uunet.UU.NET (Daniel Glossman) X-Mailer: SCO System V Mail (version 3.2) To: atina!ccl.net!chemistry@uunet.UU.NET Subject: semiempirical methods for hypervalent sulfur Date: Thu, 13 Jan 94 14:07:17 ARG Dear netters: Perhaps these are two FAQs but: 1) Is there any semiempirical method that can deal successfully with the optimization of geometries of organic molecules containing hypervalent sulfur atoms? 2) A bit more theoretical question: If a semiempirical method, i.e., MNDO is not reliable in the calculation of heats of formation of organic molecules containing hypervalent sulfur atoms, this means that the optimized geometries with the same method are also not reliable? Is there any relationship or general rule to be used as a guide in these situations? I do not want to start a discussion (perhaps it has been already discussed in the list), so please answer directly to me: rvgloss@arcriba.edu.ar or rvgloss@arcriba.bitnet. I will summarize the answers for the list if there exists enough interest. Thanks in advance Daniel Glossman *************************************************************************** Dr. Daniel Glossman Phone: (54) 1 - 553 3797 Programa QUINOR - CONICET (54) 21 - 259485 Facultad de Ciencias Exactas FAX: (54) 1 - 856 5963 Universidad Nacional de La Plata (54) 1 - 259485 Casilla de Correo 962 E-mail: rvgloss@arcriba.edu.ar 1900 La Plata rvgloss@arcriba.bitnet Republica Argentina ***************************************************************************** From DSMITH@uoft02.utoledo.edu Thu Jan 13 13:50:57 1994 Received: from uoft02.utoledo.edu for DSMITH@uoft02.utoledo.edu by www.ccl.net (8.6.4/930601.1506) id NAA19997; Thu, 13 Jan 1994 13:23:56 -0500 Received: from UOFT02.UTOLEDO.EDU by UOFT02.UTOLEDO.EDU (PMDF V4.2-10 #3438) id <01H7MVE4BRSW00111E@UOFT02.UTOLEDO.EDU>; Thu, 13 Jan 1994 13:20:45 EST Date: Thu, 13 Jan 1994 13:20:45 -0500 (EST) From: "DR. DOUGLAS A. SMITH, UNIVERSITY OF TOLEDO" Subject: Re: semiempirical methods for hypervalent sulfur To: atina!criba!rvgloss@uunet.UU.NET Cc: chemistry@ccl.net Message-id: <01H7MVE4DNBM00111E@UOFT02.UTOLEDO.EDU> X-Envelope-to: chemistry@ccl.net X-VMS-To: IN%"atina!criba!rvgloss@uunet.UU.NET" X-VMS-Cc: CHEMISTRY MIME-version: 1.0 Content-transfer-encoding: 7BIT Dan: Please excuse me for answering to the list, but I think that I have seen too many questions and not enough discussions recently. I have been looking for a good thread to expand and discuss (I am not qualified to get into the MM of TM discussion) and you offer a good opportunity. A while back I published a paper inthe Journal of Fluorine Chemistry on "Semiempirical studies on the structure and bonding of fluorosulfuranes and aminofluorosulfuranes" (1990, 50, 427-432). At that time, we knew that the MNDO parameters for sulfur were not particularly great and the AM1 sulfur parameters had not yet been published. We therefore used PM3. The bottom line is that the optimized structures of SF4 and (Me)2NSF3, did not agree well with the experimental geometries, particularly because there was no real difference between the axial and equitorial positions on sulfur. This was in agreement with ab initio calculations by Hay (JACS 1977, 99, 1003) and Reed and Schleyer (JACS 1990, 112, 1434) whose results indicated the need for 3d orbitals in the calculations. Ionization potentials at the PM3 level were inconsistent with experiment. The calculated structure of [(Me)2N]2SF2 was in much better agreement with experiment, and the trend upon adding amino groups was for bond angles to become more accurate than bond lengths. This may be a simple steric result rather than an electronic one. I have not seen a test of SAM1 on these types of compounds. If the parameters for CHNFS are all available, it might be worth my going back and doing a small follow up project (Andy Holder, are you listening?). If anyone wants reprints of the J. Fluorine Chem. paper, send me your mailing address. I know that journal is not always readily available. Doug Douglas A. Smith Assistant Professor Department of Chemistry and member, Center for Drug Design and Development The University of Toledo Toledo, OH 43606-3390 voice 419-537-2116 fax 419-537-4033 email dsmith@uoft02.utoledo.edu From kallick@nemesis.medc.umn.edu Thu Jan 13 15:49:49 1994 Received: from nemesis.medc.umn.edu for kallick@nemesis.medc.umn.edu by www.ccl.net (8.6.4/930601.1506) id OAA21993; Thu, 13 Jan 1994 14:54:52 -0500 From: Received: by nemesis.medc.umn.edu (920330.SGI/890607.SGI) (for chemistry@ccl.net) id AA26253; Wed, 13 Jan 71 13:46:16 -0600 Date: Wed, 13 Jan 71 13:46:16 -0600 Message-Id: <7101131946.AA26253@nemesis.medc.umn.edu> To: chemistry@ccl.net Subject: DIANA 2 PDB Thanks to everyone who responded to my request for help in determining the correct syntax for using COFIMA, a program written by Guentert in Zurich to convert distance geometry files to PDB files. Cheers Deborah Kallick Department of Medicinal Chemistry University of Minnesota Minneapolis, MN 55455 kallick@nemesis.medc.umn.edu phone 612 626 1962 fax 612 626 4429 From tripos!jupiter!kathy@uunet.UU.NET Thu Jan 13 15:56:03 1994 Received: from relay1.UU.NET for tripos!jupiter!kathy@uunet.UU.NET by www.ccl.net (8.6.4/930601.1506) id OAA21943; Thu, 13 Jan 1994 14:54:18 -0500 Received: from spool.uu.net (via LOCALHOST) by relay1.UU.NET with SMTP (5.61/UUNET-internet-primary) id AA15455; Thu, 13 Jan 94 14:54:05 -0500 Received: from tripos.UUCP by uucp5.uu.net with UUCP/RMAIL (queueing-rmail) id 145256.24566; Thu, 13 Jan 1994 14:52:56 EST Received: from jupiter.tripos by tripos (4.1/SMI-4.0) id AA18594; Thu, 13 Jan 94 13:34:53 CST Received: by jupiter.tripos (920330.SGI/5.6) id AA09640; Thu, 13 Jan 94 13:34:52 -0600 Date: Thu, 13 Jan 94 13:34:52 -0600 From: tripos!jupiter!kathy@uunet.UU.NET (Kathy Clark Jupiter1) Message-Id: <9401131934.AA09640@jupiter.tripos> To: uunet!extreme.chem.rpi.edu!sybyl@uunet.UU.NET, uunet!ccl.net!CHEMISTRY@uunet.UU.NET Subject: Recent Advances in Biopharmaceutical Compound Design Seminar Tripos is sponsoring two seminars entitled "Recent Advances in Biopharmaceutical Compound Design." They will be held on February 10th in LaJolla, CA and February 11th in San Francisco. Dr. Richard Cramer of Tripos Associates will moderate the following presentations: Dr. Jeffrey Skolnick The Scripps Research Institute "MatchMaker: A Topology Approach to Inverse Protein Folding" Dr. Garland Marshall Washington University "Modeling, De Novo Design, and Prediction of Activity" Dr. Scott DePriest Tripos Associates "Designing Inhibitors of Thermolysin: A DISCO Validation Study" The seminar is free and Tripos will provide lunch and other refreshments. If you are interested in attending, please send me e-mail or call 1-800-323-2960 and I will mail you more information and directions. Please include your address in your e-mail correspondance. Kathy G. Clark Manager of Customer Support kathy@tripos.com From EDGECOMK@QUCDN.QUEENSU.CA Thu Jan 13 16:00:36 1994 Received: from QUCDN.QueensU.CA for EDGECOMK@QUCDN.QUEENSU.CA by www.ccl.net (8.6.4/930601.1506) id PAA23108; Thu, 13 Jan 1994 15:41:05 -0500 Message-Id: <199401132041.PAA23108@www.ccl.net> Received: from QUCDN.QUEENSU.CA by QUCDN.QueensU.CA (IBM VM SMTP V2R2) with BSMTP id 2700; Thu, 13 Jan 94 15:39:45 EST Received: from QUCDN.QUEENSU.CA (NJE origin EDGECOMK@QUCDN) by QUCDN.QUEENSU.CA (LMail V1.1d/1.7f) with RFC822 id 2386; Thu, 13 Jan 1994 15:39:44 -0500 Date: Thu, 13 Jan 1994 15:36 EST From: EDGECOMK@QUCDN.QueensU.CA To: chemistry@ccl.net Subject: 2nd CCCC revised announcement Please find attached the revised 2nd announcement for the Canadian Computational Chemistry Conference. This will hopefully answer some questions that have been asked. Take care! Ken Edgecombe Second Announcement and Call for Papers (Jan. 12/94 rev.) 2nd Canadian Computational Chemistry Conference Deuxieme Conference Canadienne en Chimie Computationelle Queen's University, Kingston, Ontario, Canada May 21-25, 1994 This is the second announcement of the 2nd CCCC and the second call for contributed papers and posters. Bringing together Computational Chemists from academia, government, and industry from around the world, the CCCC consists of invited talks, contributed talks, and poster sessions. The program is divided into four general subject areas: Applications of Computational Chemistry: Biological, Pharmaceutical, Material Science, and Chemical Electronic Structure Computations: Density Functional Theory and Ab Initio Methods Collision and Dynamics Computations Current and Future Trends Confirmed invited speakers (to date) A. Bandrauk (Sherbrooke) P. Mezey (Saskatchewan) R. Bartlett (Florida) G. Patey (U.B.C.) P. Brumer (Toronto) R. Poirier (M.U.N.) C. Bunge (U.N.A.M., Mexico) D. Salahub (Montreal) E. Carter (U.C.L.A.) J. Tirado-Rives (Yale) G. Diercksen (Max Planck Inst.) R. Wyatt (Texas) D.A. Dixon (Dupont) W. Yang (Duke) M. Dupuis (IBM) M. Zerner (Florida) S. Fraga (Alberta) T. Ziegler (Calgary) P. Kollman (U.C.S.F.) As well, there will be hardware and software vendor exhibits. Confirmed corporate participants (to date) Cray Research Silicon Graphics High Performance Computing Sun Microsystems IBM Travel: Kingston is accessible directly by bus and train from Montreal, Ottawa, and Toronto and by airplane directly from Montreal and Toronto. Registration: To encourage participation in the conference by undergraduate and graduate students, the conference registration fees for these students have been set slightly lower: Regular Student Plan A: $360.00 (CDN) $310.00 (CDN) Includes accommodation (4 nights), breakfasts, lunches, coffee breaks, and wine and cheese socials. The accommodation consists of a single room in the university residence. Regular Student Plan B: $200.00 (CDN) $170.00 (CDN) Includes lunches, coffee breaks, and wine and cheese socials. Alternate accommodation and restaurants are within walking distance of the conference site. Due to numerous inquiries, spousal and group accomodation/rates have been arranged. Contact Ken Edgecombe (see below) for details. NOTE: Registration deadline: Feb. 15, 1994 Registrations postmarked after Feb. 15, 1994, will be required to pay registration fees of $380.00 and $220.00 for Plans A and B, respectively. The corresponding student fees become $330.00 and $190.00. To register, send cheque or money order made payable to 2nd Canadian Computational Chemistry Conference along with registration information to: Dr. Ken Edgecombe Dept. of Chemistry cccc94@qucdn.queensu.ca Queen's University Kingston, Ontario FAX (613) 545-6669 Canada K7L 3N6 Organizing Committee for the 2nd CCCC: A. D. Becke, K. E. Edgecombe, V. H. Smith, Jr., D. M. Wardlaw, D. F. Weaver, Dept. of Chem., Queen's University Registration Form: -------------------------------------- Name: .............................................................. Address: ........................................................... ........................................................... ........................................................... e-mail: ............................................................ Phone: ........................ FAX: .............................. Status: __ regular __ student __ contributed poster __ attend only Registration Selection: Plan A:__ Plan B:__ Subject area: ...................................................... Title: ............................................................. ............................................................. ............................................................. ABSTRACT DEADLINE: April 1, 1994 Abstracts should be submitted in camera ready form and limited to one page. If submitted by e-mail use standard ASCII characters only. From sienny@water.lbl.gov Thu Jan 13 16:05:05 1994 Received: from water.lbl.gov for sienny@water.lbl.gov by www.ccl.net (8.6.4/930601.1506) id OAA22366; Thu, 13 Jan 1994 14:59:24 -0500 From: Received: by water.lbl.gov (AIX 3.2/UCB 5.64/4.03) id AA16235; Thu, 13 Jan 1994 11:54:03 -0800 Date: Thu, 13 Jan 1994 11:54:03 -0800 Message-Id: <9401131954.AA16235@water.lbl.gov> To: chemistry@ccl.net Subject: graphics program Hello, Several days agao, I was looking for graphics programs. I got several replies and would like to thank every person who gave me any suggestions. Here are the responses that I received: ------------------------------------------------------------------------------- Date: 10 Jan 1994 07:44:28 +0100 From: bayard@pixies.univ-lyon1.fr (BAYARD Francois) Subject: Re: looking for graphics To: sienny@water.lbl.gov Message-Id: <9401100644.AA28533@pixies.univ-lyon1.fr> X-Envelope-To: sienny@water.lbl.gov Content-Transfer-Encoding: 7BIT Status: RO try SYBYL sold by Tripos Ltd from St Louis Francois BAYARD | e-mail bayard@pixies.univ-lyon1.fr | COMS - CNRS | tel (+33) 72 44 53 21 CPE - ESCIL - Bat 308 | 43 Bd du 11 Novembre 1918 | fax (+33) 72 44 28 52 F-69616 VILLEURBANNE - FRANCE | -------------------------------------------------------------------------- Date: Sat, 8 Jan 1994 08:32:18 -0800 From: "(Antonio M. Marquez 455-7177)" Message-Id: <9401081732.AA16548@quantix.us.es> To: sienny@water.lbl.gov (Non Receipt Notification Requested) In-Reply-To: "from \"sienny@water.lbl.gov\"<9401072157.AA15716@water.lbl.gov>": Subject: Re: looking for graphics X-Mailer: ELM [version 2.4 PL21] Content-Type: text Content-Transfer-Encoding: 7BIT Content-Length: 821 Status: RO Powerful graphics programs available for RS6000 are: gnuplot: distributed freely by the GNU software group allows for two- and three-dimension plots of functions and data sets. t: Re: looking for graphics X-Mailer: ELM [version 2.4 PL21] Content-Type: text Content-Transfer-Encoding: 7BIT Content-Length: 821 Status: RO Powerful graphics programs available for RS6000 are: gnuplot: distributed freely by the GNU software group allows for two- and three-dimension plots of functions and data sets. data explorer: distributed by IBM Corp. Yorktown Heights, NY (contact you IBM representative). Designed for the analysis and graphics representation of complex sets of data. Chem-station: distributed by IBM Corp. Kingston, NY. Designed for the analysis and representation of molecular geometries, IR and RAMAN spectra and vibrational modes, electrostatic potentials, MO densities as well as total electronic densities and much more options. These are the three most important graphics packages that I use currently or have used on a RS6k. Antonio M. Marquez Dpt. of Physical Chemistry University of Seville 41012 Sevilla (SPAIN) ---------------------------------------------------------------------- Date: Fri, 7 Jan 1994 19:24:28 -0500 From: jle@world.std.com (Joe M Leonard) Content-Identifier: Re: looking f... Content-Identifier: Re: looking f... e three most important graphics packages that I use currently or have used on a RS6k. Antonio M. Marquez Dpt. of Physical Chemistry University of Seville 41012 Sevilla (SPAIN) ---------------------------------------------------------------------- Date: Fri, 7 Jan 1994 19:24:28 -0500 From: jle@world.std.com (Joe M Leonard) Content-Identifier: Re: looking f... Content-Identifier: Re: looking f... Message-Id: <199401080024.AA01586@world.std.com> To: sienny@water.lbl.gov Subject: Re: looking for graphics Status: RO Are you looking for numerical or chemical graphics software? If it's the former, I can't think of much other than AVS, Explorer, DataExplorer and the like. If it's chemical, perhaps Spartan or one of the many other packages can help... Joe ------------------------------------------------------------------------- Date: 10 Jan 94 10:26:00 WET From: JEREMY WALTON Subject: RE: looking for graphics To: sienny Status: RO Hi Sienny, Regarding your request for graphics software, you may be interested to know that we're currently porting IRIS Explorer to the RS/6000. This is a powerful visualisation package which has been used by many workers for the display of chemistry and molecular data. Two papers on its use in the latter area are alg-grp.co.uk> Subject: RE: looking for graphics To: sienny Status: RO Hi Sienny, Regarding your request for graphics software, you may be interested to know that we're currently porting IRIS Explorer to the RS/6000. This is a powerful visualisation package which has been used by many workers for the display of chemistry and molecular data. Two papers on its use in the latter area are currently in press at J. Mol. Graphics. The following gives some general information about IRIS Explorer, but if you would like more specific information, I'd be happy to provide it. Cheers, Jeremy ------------------------------------------------------------------------------- - | Jeremy Walton nagjpw@vax.oxford.ac.uk | | The Numerical Algorithms Group Ltd, Oxford, UK jeremyw@nag.co.uk | | Tel: +44 865 511245 | | Fax: +44 865 310139 | ------------------------------------------------------------------------------- - Introduction to IRIS Explorer ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | Tel: +44 865 511245 | | Fax: +44 865 310139 | ------------------------------------------------------------------------------- - Introduction to IRIS Explorer ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Jeremy Walton The Numerical Algorithms Group Ltd, Oxford, UK What is IRIS Explorer? ~~~~~~~~~~~~~~~~~~~~~ IRIS Explorer was originally developed by Silicon Graphics for their workstations. It is a modular visualisation environment - you create your application interactively by connecting modules together using a point-and -click interface. IRIS Explorer comes with about 150 modules (more are available) which perform tasks such as reading in data, filtering it, transforming it; creating graphical objects like line graphs, histograms, contours, surfaces, isosurfaces, volumes, vector plots, etc; and displaying them together in a window with full 3D interaction. A number of modules are built using Silicon Graphics' ImageVision library, and provide a large amount of image processing functionality. You can create your own modules to read or translate data using a point-and-click tool called the DataScribe, or use the Module Builder - another tool bundled with the system - to transforom your existing routines (in the form of C, C++ or FORTRAN source, or even as pure executables) into modules for use from within IRIS Explorer. Finally, IRIS Explorer provides the application developer with the ability to customise the look and feel of raphical objects like line graphs, histograms, contours, surfaces, isosurfaces, volumes, vector plots, etc; and displaying them together in a window with full 3D interaction. A number of modules are built using Silicon Graphics' ImageVision library, and provide a large amount of image processing functionality. You can create your own modules to read or translate data using a point-and-click tool called the DataScribe, or use the Module Builder - another tool bundled with the system - to transforom your existing routines (in the form of C, C++ or FORTRAN source, or even as pure executables) into modules for use from within IRIS Explorer. Finally, IRIS Explorer provides the application developer with the ability to customise the look and feel of your existing routines (in the form of C, C++ or FORTRAN source, or even as pure executables) into modules for use from within IRIS Explorer. Finally, IRIS Explorer provides the application developer with the ability to customise the look and feel of the application before handing it over to the end-user. Last year, Silicon Graphics licenced IRIS Explorer to NAG, who are currently porting it to Sun, HP, IBM and DEC platforms. The Sun port is available now; the others will follow soon. Please contact the IRIS Explorer Centers (see below) for details of availability and pricing. The IRIS Explorer Centers ~~~~~~~~~~~~~~~~~~~~~~~~ NAG has also set up and is managing two IRIS Explorer Centers: IRIS Explorer Center (Europe) IRIS Explorer Center (North America) PO Box 50 1400 Opus Place, Suite 200 Oxford OX2 8JU Downers Grove IL 60551-5702 UK USA Tel: +44 (0)865 516377 Tel: +1 708 971 2367 Fax: +44 (0)865 516388 Fax: +1 708 971 2706 email: helpdesk@iec.co.uk email: infodesk@nag.com These act as sources of information for users, developers and porters of IRIS Explorer, and also sell IRIS Explorer on behalf of the various suppliers. Explorer Center (North America) PO Box 50 1400 Opus Place, Suite 200 Oxford OX2 8JU Downers Grove IL 60551-5702 UK USA Tel: +44 (0)865 516377 Tel: +1 708 971 2367 Fax: +44 (0)865 516388 Fax: +1 708 971 2706 email: helpdesk@iec.co.uk email: infodesk@nag.com These act as sources of information for users, developers and porters of IRIS Explorer, and also sell IRIS Explorer on behalf of the various suppliers. sell IRIS Explorer on behalf of the various suppliers. There is a user group (meetings in 1993 were held at SIGGRAPH in Anaheim, and at Eurographics '93 in Barcelona), an Internet newsgroup (comp.graphics.explorer) and ftp sites where modules have been contributed for everyone's use. IRIS Explorer Center gopher access ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ More information on all aspects of IRIS Explorer is available from the IRIS Explorer Center gopher server: Gopher Name=IRIS Explorer Center Bulletin Board Type=1 Path=1/visual/IE/iecbb Host=nags2.nag.co.uk [at 192.156.217.7] Port=70 For sites not able to connect to NAG over the Internet a dial-in capability is provided. Set your modem to 1200 baud, 7 bit, even parity and call on +44 (0)865 56169. The login name is GOPHER and there is no password. This will connect to the NAG Gopher from which it is possible to connect to the IRIS Explorer Center gopher server (under Visualisation Software, IRIS Explorer). At present, only one line is provided for this form of access. ost=nags2.nag.co.uk [at 192.156.217.7] Port=70 For sites not able to connect to NAG over the Internet a dial-in capability is provided. Set your modem to 1200 baud, 7 bit, even parity and call on +44 (0)865 56169. The login name is GOPHER and there is no password. This will connect to the NAG Gopher from which it is possible to connect to the IRIS Explorer Center gopher server (under Visualisation Software, IRIS Explorer). At present, only one line is provided for this form of access. -------------------------------------------------------------------------- Message-Id: <199401101141.MAA01875@hydra.appli.mimuw.edu.pl> Subject: looking for graphics To: sienny@water.lbl.gov Date: Mon, 10 Jan 1994 12:41:12 +0100 (MET) X-Mailer: ELM [version 2.4 PL23] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 368 Status: RO Consider AVS (Application Visualization System) form AVS (Advanced Visual Systems) (e-mail info@avs.com or service@avs.com, extensive info at avs@ncsc.org) or IBM Data Explorer as universal packages. Best regards -- Krzysztof (Chris) S. Nowinski Inst. of Applied Math. Warsaw University Banacha 2 Warsaw, Poland vs.com or service@avs.com, extensive info at avs@ncsc.org) or IBM Data Explorer as universal packages. Best regards -- Krzysztof (Chris) S. Nowinski Inst. of Applied Math. Warsaw University Banacha 2 Warsaw, Poland ph (48)(2)6583236 know@helium.appli.mimuw.edu.pl ----------------------------------------------------------------------------- Date: Mon, 10 Jan 1994 09:50:54 -0500 (EST) From: "DR. DOUGLAS A. SMITH, UNIVERSITY OF TOLEDO" Subject: Re: looking for graphics To: sienny@water.lbl.gov Message-Id: <01H7IHMIQ6LK000BLP@UOFT02.UTOLEDO.EDU> X-Envelope-To: sienny@water.lbl.gov X-Vms-To: IN%"sienny@water.lbl.gov" Mime-Version: 1.0 Content-Transfer-Encoding: 7BIT Status: RO The AVS Chemistry Viewer Version 1.5 Price list current as of 12/1/93 The AVS Chemistry Viewer is now marketed and supported by DASGroup of Toledo, OH. Until Q2/1994, tapes will still be distributed through Molecular Simulations, Inc. (MSI). Prices for all platforms, includes technical support (some restrictions apply, see platform specific notes), maintenence releases, and upgrades for one year. Current prices and availability for a single license on a single workstation are: The AVS Chemistry Viewer Version 1.5 Price list current as of 12/1/93 The AVS Chemistry Viewer is now marketed and supported by DASGroup of Toledo, OH. Until Q2/1994, tapes will still be distributed through Molecular Simulations, Inc. (MSI). Prices for all platforms, includes technical support (some restrictions apply, see platform specific notes), maintenence releases, and upgrades for one year. Current prices and availability for a single license on a single workstation are: nd upgrades for one year. Current prices and availability for a single license on a single workstation are: Commercial license, single machine $5000 U.S. Government agency $2500 Academic $500 Additional 1 year maintenance, commercial $1000 Additional 1 year maintenance, gov. and academic $500 HP 9000/700 series: HP-UX 8.07 or greater; HP-UX 9.01 strongly preferred due to many bugs in HP-UX 8.07. Distributed on 4 mm tapes. SGI (all platforms): IRIX 4.0.5 or greater. Distributed on QIC tapes. IBM RS/6000 (all current platforms; not tested on newer platforms, especially PowerPC models): AIX 3.2 or greater. Distributed on QIC tapes. DECStation 5000/PGX Turbo: Ultrix 4.2A. Distributed on TK50 tapes.1* Titan 3000 (P3/G3): Titan OS 4.2. Distributed on QIC tapes.2* Sun SPARCStation 2: SunOS 4.1.3. Distributed on QIC tapes.3 all platforms): IRIX 4.0.5 or greater. Distributed on QIC tapes. IBM RS/6000 (all current platforms; not tested on newer platforms, especially PowerPC models): AIX 3.2 or greater. Distributed on QIC tapes. DECStation 5000/PGX Turbo: Ultrix 4.2A. Distributed on TK50 tapes.1* Titan 3000 (P3/G3): Titan OS 4.2. Distributed on QIC tapes.2* Sun SPARCStation 2: SunOS 4.1.3. Distributed on QIC tapes.3 User training courses are available. Custom development of tools is also available. For more information, contact: Douglas A. Smith DASGroup 3807 Elmhurst Road Toledo, OH 43613-4209 voice (419)537-2116 fax (419)537-4033 email dsmith@uoft02.utoledo.edu _______________________________ 1 The Chem Viewer is not compatible with ULTRIX version 4.3 or higher. Technical support is limited to non-hardware and non-operating system specific problems. 2 The Chem Viewer has not been tested with operating systems higher than version 4.2. Technical support is limited to non-hardware and non- operating system specific problems. 3 The Chem Viewer has not yet been tested with the Solaris operating system. * Support for this platform is not anticipated past Q2/1994. Migration 1 The Chem Viewer is not compatible with ULTRIX version 4.3 or higher. Technical support is limited to non-hardware and non-operating system specific problems. 2 The Chem Viewer has not been tested with operating systems higher than version 4.2. Technical support is limited to non-hardware and non- operating system specific problems. 3 The Chem Viewer has not yet been tested with the Solaris operating system. * Support for this platform is not anticipated past Q2/1994. Migration pathways will be provided to purchasers of the Chem Viewer for this platform. ===================================================================== FOR IMMEDIATE RELEASE DASGROUP AND MOLECULAR SIMULATIONS SIGN AVS CHEMISTRY VIEWER DEVELOPMENT AND MARKETING AGREEMENT Burlington, MA, December 20, 1993 -- DASGroup of Toledo, OH and Molecular Simulations Inc. (MSI) announced that they have finalized an agreement under which DASGroup will undertake scientific development, technical support, marketing and sales of the AVS Chemistry Viewer, a program for the visualization of the results of computational chemistry calculations. Under the terms of the agreement, DASGroup will immediately begin marketing and sales efforts of the product throughout most of the world. Teijin Molecular Simulations Inc. (TMSI), a joint venture of MSI and Teijin Limited, will continue as the exclusive distributor of AVS Chemistry Viewer in the Far East. In addition, DASGroup will immediately take over scientific and technical development and worldwide support of the Chemistry Viewer. "The Chemistry Viewer is an excellent, extensible tool for visualization of computational chemistry input and output, technical support, marketing and sales of the AVS Chemistry Viewer, a program for the visualization of the results of computational chemistry calculations. Under the terms of the agreement, DASGroup will immediately begin marketing and sales efforts of the product throughout most of the world. Teijin Molecular Simulations Inc. (TMSI), a joint venture of MSI and Teijin Limited, will continue as the exclusive distributor of AVS Chemistry Viewer in the Far East. In addition, DASGroup will immediately take over scientific and technical development and worldwide support of the Chemistry Viewer. "The Chemistry Viewer is an excellent, extensible tool for visualization of computational chemistry input and output, mmediately take over scientific and technical development and worldwide support of the Chemistry Viewer. "The Chemistry Viewer is an excellent, extensible tool for visualization of computational chemistry input and output, analysis of results, and transfer of information between various programs," said Dr. Douglas A Smith, President of DASGroup. "We plan to enhance and extend the Chemistry Viewer to be a user friendly graphical interface to as many computational chemistry programs as possible over the next year, including programs for quantum mechanics, molecular mechanics and dynamics, Monte Carlo and FEP, crystallography and more. Protein display and analysis tools are high on our list of priorities as well." "MSI is delighted that it has found an excellent home for the continued development and distribution of the AVS Chemistry Viewer product," said Michael J. Savage, President and CEO of MSI. "This arrangement will allow MSI to focus additional resources on the continued development of computational chemistry applications within MSI's own development environment". Founded in 1984, Molecular Simulations Inc. is a privately-held company with yearly revenues in excess of $20 million. MSI's products enable scientists to predict the behavior and properties of organic and inorganic materials through molecular modeling, a technique that simulates and visualizes materials at an atomistic level. Companies and academicians around the world have found that simulation technology can help increase the efficiency and productivity of research, development, and manufacturing processes in industries as diverse as biotechnology, well." "MSI is delighted that it has found an excellent home for the continued development and distribution of the AVS Chemistry Viewer product," said Michael J. Savage, President and CEO of MSI. "This arrangement will allow MSI to focus additional resources on the continued development of computational chemistry applications within MSI's own development environment". Founded in 1984, Molecular Simulations Inc. is a privately-held company with yearly revenues in excess of $20 million. MSI's products enable scientists to predict the behavior and properties of organic and inorganic materials through molecular modeling, a technique that simulates and visualizes materials at an atomistic level. Companies and academicians around the world have found that simulation technology can help increase the efficiency and productivity of research, development, and manufacturing processes in industries as diverse as biotechnology, $20 million. MSI's products enable scientists to predict the behavior and properties of organic and inorganic materials through molecular modeling, a technique that simulates and visualizes materials at an atomistic level. Companies and academicians around the world have found that simulation technology can help increase the efficiency and productivity of research, development, and manufacturing processes in industries as diverse as biotechnology, pharmaceuticals, agriculture/food processing, and materials sciences. The company has the world's largest installed base of licensed applications and the industry's broadest line of modeling and visualization software. MSI develops products for many major workstations and scientific computing platforms. Headquartered in Burlington, MA, the company has 130 employees worldwide. DASGroup, founded in 1992, is a privately-held company which specializes in molecular modeling and computational chemistry, both products and applications. The company performs contract research and development in a variety of areas and sells products including software for visualization. DASGROUP CONTACT: Douglas A. Smith, Ph.D. President DASGroup voice: 419-537-2116 or 419-472-9160 fax: 419-537-4033 eling and computational chemistry, both products and applications. The company performs contract research and development in a variety of areas and sells products including software for visualization. DASGROUP CONTACT: Douglas A. Smith, Ph.D. President DASGroup voice: 419-537-2116 or 419-472-9160 fax: 419-537-4033 email: dsmith@uoft02.utoledo.edu mailing address: 3807 Elmhurst Road Toledo, OH 43613-4209 MSI CONTACT: Steve Herbert, VP Marketing (617) 229-9800 ------------------------------------------------------------------ Date: Mon, 10 Jan 1994 09:52:12 -0500 (EST) From: "DR. DOUGLAS A. SMITH, UNIVERSITY OF TOLEDO" Subject: Re: looking for graphics To: sienny@water.lbl.gov Message-Id: <01H7IHNYL1E6000BLP@UOFT02.UTOLEDO.EDU> X-Envelope-To: sienny@water.lbl.gov X-Vms-To: IN%"sienny@water.lbl.gov" Mime-Version: 1.0 Content-Transfer-Encoding: 7BIT Status: RO If you will send me your US mail address, I will send you more information on the AVS Chemistry Viewer, including details of its abilities. r.lbl.gov Message-Id: <01H7IHNYL1E6000BLP@UOFT02.UTOLEDO.EDU> X-Envelope-To: sienny@water.lbl.gov X-Vms-To: IN%"sienny@water.lbl.gov" Mime-Version: 1.0 Content-Transfer-Encoding: 7BIT Status: RO If you will send me your US mail address, I will send you more information on the AVS Chemistry Viewer, including details of its abilities. Doug Douglas A. Smith, Ph.D. President DASGroup voice: 419-537-2116 or 419-472-9160 fax: 419-537-4033 email: dsmith@uoft02.utoledo.edu mailing address: 3807 Elmhurst Road Toledo, OH 43613-4209 --------------------------------------------------------------------------- From pbays@saintmarys.edu Thu Jan 13 16:49:49 1994 Received: from jade.saintmarys.edu for pbays@saintmarys.edu by www.ccl.net (8.6.4/930601.1506) id QAA24200; Thu, 13 Jan 1994 16:34:16 -0500 Received: by jade.saintmarys.edu (1.37.109.8/16.2) id AA10644; Thu, 13 Jan 1994 16:37:51 -0500 Date: Thu, 13 Jan 1994 16:33:08 -0500 (EST) From: Phil Bays Subject: Rasmol To: Chemistry Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I am contemplating downloading RasMol and have a couple of questions. 1. How much disk space does it require (I am beginning to run short)? 2. I understand that it will need to be compiled. I am running on an R3000 Indigo and am not a UNIX guru. What will compiling require (steps)? Phil Bays Saint Mary's College Notre Dame IN 46556 pbays@saintmarys.edu From eslone@mason1.gmu.edu Thu Jan 13 17:49:48 1994 Received: from mason1.gmu.edu for eslone@mason1.gmu.edu by www.ccl.net (8.6.4/930601.1506) id RAA25168; Thu, 13 Jan 1994 17:28:43 -0500 Received: by mason1.gmu.edu (5.65/DEC-Ultrix/4.3/GMUv3) id AA04563; Thu, 13 Jan 1994 17:28:36 -0500 Message-Id: <9401132228.AA04563@mason1.gmu.edu> Subject: Request for Comments: CAOS Software To: chemistry@ccl.net Date: Thu, 13 Jan 1994 17:28:36 -0500 (EST) From: "J. Eric Slone" X-Mailer: ELM [version 2.4 PL23] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 1034 I would appreciate any comments from anyone who is currently using, or has used and Computer Aided Organic Synthesis (CAOS) programs. I am currently evaluating LHASA, SYNGEN, and CAMEO and am particularly interested in experiences with those products. I would also be interested in hearing of any other programs being used and impressions from a "user/chemist" standpoint. Please forward all messages to eslone@mason1.gmu.edu Thank you in advance, Eric ________________________________________________________________________________ J. Eric Slone Scientific Consulting Services Serving Government & Industry Since 1982 Internet: eslone@mason1.gmu.edu Compuserve: 73757,2776 "True science teaches, above all, to Fax: (703) 751-6639 doubt, and to be ignorant." Voice: (703) 461-7078 Miguel do Unamuno ________________________________________________________________________________