From JAS@CHEM.UNI.WROC.PL Thu Apr 13 08:59:27 1995 Received: from indigo2 for JAS@CHEM.UNI.WROC.PL by www.ccl.net (8.6.10/930601.1506) id IAA21646; Thu, 13 Apr 1995 08:44:57 -0400 Received: from [156.17.86.161] by indigo2 via SMTP (931110.SGI/930416.SGI) for chemistry@ccl.net id AA05041; Thu, 13 Apr 95 14:44:29 +0200 Received: from ICHUWR/SMTPQueue by chem.uni.wroc.pl (Mercury 1.11); Thu, 13 Apr 95 14:46:06 +0100 Received: from Mailqueue by ICHUWR (Mercury 1.11); Thu, 13 Apr 95 14:45:37 +0100 From: "Janusz Dzielendziak" To: chemistry@ccl.net Date: Thu, 13 Apr 1995 14:45:29 GMT+1 Subject: GROMOS parameters: Ag+, K+, Rb+, Cs+ X-Pmrqc: 1 Priority: normal X-Mailer: Pegasus Mail v3.1 (R1) Message-Id: <6777C7151BD@chem.uni.wroc.pl> Hi netters, I'm looking for parametrs for GROMOS : Ag+, K+, Cs+, Rb+. Can somebody help me? Thanks for advance, ********************************************************************** Janusz Dzielendziak University of Wroclaw phone: +48 71 204345 Institute of Chemistry fax: +48 71 222348 14 F.Joliot Curie st. e-mail: jas@chem.uni.wroc.pl 50-383 Wroclaw POLAND ********************************************************************** From polowin@hyper.hyper.com Thu Apr 13 10:59:30 1995 Received: from www.hyper.com for polowin@hyper.hyper.com by www.ccl.net (8.6.10/930601.1506) id KAA23770; Thu, 13 Apr 1995 10:48:12 -0400 Received: from hyper.hyper.com (hyper.hyper.com [204.50.3.217]) by www.hyper.com (8.6.9/8.6.9) with SMTP id KAA26200 for <@www.hyper.com:CHEMISTRY@ccl.net>; Thu, 13 Apr 1995 10:41:13 -0400 Received: by hyper.hyper.com (920330.SGI/920502.SGI) for @www.hyper.com:CHEMISTRY@ccl.net id AA21528; Thu, 13 Apr 95 11:00:19 -0400 Date: Thu, 13 Apr 95 11:00:19 -0400 From: polowin@hyper.hyper.com (Joel Polowin) Message-Id: <9504131500.AA21528@hyper.hyper.com> To: CHEMISTRY@ccl.net Subject: Hypercube Home Page Officially Open We'd like to announce that our WWW home page is now (at last!) officially open. The address: http://www.hyper.com/ . Some parts are still under construction, but we've got descriptions of our products, access to demo versions of our HyperChem, ChemPlus, and HyperNMR modeling software, an FAQ list, and links to other sites of interest... and so on. Come take a look! Regards, Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com Hypercube Inc, 7-419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" to hyperchem-request@hyper.com WWW: http://www.hyper.com/ From ross@cgl.ucsf.EDU Thu Apr 13 14:14:31 1995 Received: from socrates.ucsf.EDU for ross@cgl.ucsf.EDU by www.ccl.net (8.6.10/930601.1506) id OAA27793; Thu, 13 Apr 1995 14:08:07 -0400 From: Received: (from ross@localhost) by socrates.ucsf.EDU (8.6.11/GSC4.24) id LAA00965; Thu, 13 Apr 1995 11:07:52 -0700 Date: Thu, 13 Apr 1995 11:07:52 -0700 Message-Id: <199504131807.LAA00965@socrates.ucsf.EDU> To: JAS@CHEM.UNI.WROC.PL Subject: Re: CCL:GROMOS parameters: Ag+, K+, Rb+, Cs+ Cc: chemistry@ccl.net Assuming you are using the R*, epsilon vdw form and want to model with TIP3 or SPC waters (i.e. 'fat' oxygen enclosing no-vdw H's), the Aqvist parameters here should do the job. I am throwing in anions too, the provenance of which I haven't personally inspected, for the complete ion parameters from the AMBER force field. These parameters would need to be adapted if you are using any other combining rules or calculating interactions with any 'normal'-sized atoms - see the discussion on deriving new parameters on http://www.amber.ucsf.edu/amber/amber.html and/or Ross, W.S. and Hardin, C.C., JACS 116, 6070-6080 (1994). Bill Ross Li 1.1370 0.0183 Li+ Aqvist JPC 1990,94,8021. (adapted) Na 1.8680 0.00277 Na+ Aqvist JPC 1990,94,8021. (adapted) K 2.6580 0.000328 K+ Aqvist JPC 1990,94,8021. (adapted) Rb 2.9560 0.00017 Rb+ Aqvist JPC 1990,94,8021. (adapted) Cs 3.3950 0.0000806 Cs+ Aqvist JPC 1990,94,8021. (adapted) F 1.75 0.061 Gough et al. JCC 13,(1992),963. I 2.35 0.40 JCC,7,(1986),230; Cl 2.47 0.1 Cl- Smith & Dang, JCP 1994,100:5,3757 -- From adrian@silver.chem.nwu.edu Thu Apr 13 14:29:32 1995 Received: from silver.chem.nwu.edu for adrian@silver.chem.nwu.edu by www.ccl.net (8.6.10/930601.1506) id OAA27967; Thu, 13 Apr 1995 14:18:14 -0400 Received: by silver.chem.nwu.edu (950221.405.SGI.8.6.10/921111.SGI.jml) for chemistry@ccl.net id NAA23215; Thu, 13 Apr 1995 13:18:15 -0500 From: adrian@silver.chem.nwu.edu (Adrian Roitberg) Message-Id: <199504131818.NAA23215@silver.chem.nwu.edu> Subject: ab-initio on Power Mac To: chemistry@ccl.net Date: Thu, 13 Apr 95 13:18:15 CDT X-Mailer: ELM [version 2.3 PL9] Dear CCLers; We have recently purchased a PowerMac. What ab initio programs (both DFT and "regular") packages are available for this machine? Thank you, Adrian E. Roitberg ============================================================================= Dept. of Chemistry | Phone: (708) 491-3423 Northwestern University | Fax : (708) 491-7713 2145 Sheridan Road. Evanston, IL |E-mail:adrian@chem.nwu.edu 60208-3113 | ============================================================================= From ashutosh@sol.acs.unt.edu Thu Apr 13 15:14:33 1995 Received: from mercury.unt.edu for ashutosh@sol.acs.unt.edu by www.ccl.net (8.6.10/930601.1506) id PAA29090; Thu, 13 Apr 1995 15:09:16 -0400 Received: from sol.acs.unt.edu by mercury.unt.edu with SMTP id AA01782 (5.65c/IDA-1.4.4 for ); Thu, 13 Apr 1995 14:09:12 -0500 Received: (ashutosh@localhost) by sol.acs.unt.edu (8.6.9/8.6.4) id OAA00354 for chemistry@ccl.net; Thu, 13 Apr 1995 14:09:12 -0500 From: Misra Ashutosh Message-Id: <199504131909.OAA00354@sol.acs.unt.edu> Subject: Question on Iodine Basis Sets To: chemistry@ccl.net Date: Thu, 13 Apr 1995 14:09:11 -0500 (CDT) X-Mailer: ELM [version 2.4 PL22] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 533 Hello all CCL Users: I am currently looking for 6-31g* and 6-311G (including supplementary d,f and diffuse functions) quality basis sets for iodine for use in ab initio calculations. I am aware that basis sets of such quality are available for bromine, but I havent found any for iodine. I would really appreciate if any of you could direct me to the proper resources where I could find such basis sets if they are available. Many thanks in advance Ashutosh Misra Dept. of Chemistry University of North Texas Denton, TX 76203 From youkha@iris75.biosym.com Thu Apr 13 15:25:48 1995 Received: from bioc1.biosym.com for youkha@iris75.biosym.com by www.ccl.net (8.6.10/930601.1506) id PAA29048; Thu, 13 Apr 1995 15:06:45 -0400 Received: from iris75.biosym.com by bioc1.biosym.com (5.64/0.0) id AA18209; Thu, 13 Apr 95 12:06:06 -0700 Received: by iris75.biosym.com (940816.SGI.8.6.9/930416.SGI) id MAA12142; Thu, 13 Apr 1995 12:06:04 -0700 Date: Thu, 13 Apr 1995 12:06:04 -0700 From: youkha@biosym.com (Philippe Youkharibache) Message-Id: <199504131906.MAA12142@iris75.biosym.com> To: chemistry@ccl.net Subject: Re: CCL:Searching for sequences Cc: youkha@iris75.biosym.com For those searching for sequences in relation to known 3D structures: I would suggest to give a look at ENTREZ. Certainly in its last version it has PDB sequences searchable through BLAST, in the same way than for GenBank for example, and it also access references through Medline, thanks to Steve Bryant at NCBI. I don't think they have a viewer yet, but once you have located the PDB name, you can use your graphics program. Rather than advertising for a modeling program, I think it is of interest to modelers to give a look at ENTREZ, to say, broaden our perspective. They have an information e-mail address : info@ncbi.nlm.nih.gov and a Web home page: http://www.ncbi.nlm.nih.gov/ Original posting: > I want to search the PDB for structures that have the tripeptide > sequence Asn-X-Glu where X is any amino acid. The purpose of the > search is to identify possible structural motifs for the sequence > within proteins. Thus far, I have not found how to do this using the > Brookhaven search engines on the WWW. Does any one have a way to > perform this search? > > Alternatively, I could search sequence databases such as SWISS-Prot > and then cross-reference the hits with the PDB. However, I have yet > to find a way to perform the search using wildcards. > > Any suggestions? > > Thanks in advance... > Jeff Nauss ************************************************************************** Dr. Philippe Youkharibache e-mail: youkha@biosym.com Biosym Technologies Inc. 9685 Scranton Road tel: (619) 546 5562 San Diego, CA 92121 fax: (619) 458 0136 ************************************************************************** From OSMAN@mdli.com Thu Apr 13 15:59:38 1995 Received: from iat.holonet.net for OSMAN@mdli.com by www.ccl.net (8.6.10/930601.1506) id PAA00140; Thu, 13 Apr 1995 15:58:47 -0400 Received: from jubal.mdli.com by iat.holonet.net (OSMAN@mdli.com) id MAA10975; Thu, 13 Apr 1995 12:58:44 -0700 Received: from gimli.mdli.com by jubal.mdli.com (AIX 3.2/UCB 5.64/9393.1) id AA47785; Thu, 13 Apr 1995 12:56:40 -0700 Received: from mdli.com by mdli.com (PMDF V4.3-10 #6626) id <01HPAHNHWD808ZE9CJ@mdli.com>; Thu, 13 Apr 1995 12:58:55 -0800 (PST) Date: Thu, 13 Apr 1995 12:58:55 -0800 (PST) From: "Osman F. =?ISO-8859-1?Q?G=FCner?=" Subject: Invitation to ISIS Users' discussion forum To: chemind-l@derwent.co.uk, chemistry@ccl.net Message-Id: <01HPAHNHWMV68ZE9CJ@mdli.com> X-Vms-To: IN%"chemind-l@derwent.co.uk", IN%"chemistry@ccl.net" X-Vms-Cc: OSMAN Mime-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Content-Transfer-Encoding: 7BIT --------------------------------------------------------------------------- ISISFORUM-L is an ISIS users' forum for sharing information and experiences about the ISIS software products from MDL. The list is unmoderated. Feel free to post your questions and issues with ISIS, as well as your answers, suggestions, PL applications, and workarounds that you may think the other members of the forum may benefit from. The objective of this forum is to provide an environment where ISIS users can help each other and benefit from each other's experiences. MDL supports this list but does not control its content. To subscribe, please send a message to mailserv@mdli.com with a single line message: subscribe isisforum-l ----------------------------------------------------------------------------- Osman F. Guner, PhD, -- Temporary List Coordinator MDL Information Systems, Inc. (510) 895-1313 Osman@mdli.com From zacarias@PAPALOTL.PQUIM.UNAM.MX Thu Apr 13 16:29:41 1995 Received: from PAPALOTL.PQUIM.UNAM.MX for zacarias@PAPALOTL.PQUIM.UNAM.MX by www.ccl.net (8.6.10/930601.1506) id QAA00539; Thu, 13 Apr 1995 16:21:11 -0400 Received: by PAPALOTL.PQUIM.UNAM.MX (931110.SGI/911001.SGI) for chemistry@ccl.net id AA06723; Thu, 13 Apr 95 14:19:36 -0600 From: "Angelica Garcia Zacarias" Message-Id: <9504131419.ZM6721@PAPALOTL.PQUIM.UNAM.MX> Date: Thu, 13 Apr 1995 14:19:34 -0600 X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: chemistry@ccl.net Subject: relativistic corrections on TM systems Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 Dear CCL's I would appreciate your comments on the use of relativistic corrections on molecular systems containing transition metals. Could you please send me your comments addressing questions like 1) What kind of methods are available right now? 2) How do they compare with respect to each other in the quality of the results? 3) I understand that they are very gross approximations to the exact theories, do they justify to be used? considering that nonrelativistic methods are not precise enough yet for systems containing several electrons. 4) How do the relativistic corrections affect quantities of chemical interest? like geometrical parameters or dissociation energies. 5) Have those methods been validated in any way? 6) For what elements and with what criteria are relativistic corrections "mandatory" or conversely, up to what elements are standard ab initio or DFT nonrelativistic methods applicable? and any other comment that you consider relevant. I will be glad to prepare a summary of the postings if interest arise. Many thanks in advance, With best regards Angelica Zacarias ________________________________ Claudia Angelica Garcia Zacarias Quimica Inorganica, FyQ Teorica DEPg., Facultad de Quimica, UNAM Mexico, D.F. 04510 Tel/Fax: (525) 622 3724 zacarias@papalotl.pquim.unam.mx _________________________________________________ Solo con nuestras flores nos alegramos Solo con nuestros cantos florece nuestra tristeza Nezahualcoyotl From janeou@che.rochester.edu Thu Apr 13 10:10:04 1995 Received: from oz.che.rochester.edu for janeou@che.rochester.edu by www.ccl.net (8.6.10/930601.1506) id KAA22981; Thu, 13 Apr 1995 10:10:02 -0400 Received: by oz.che.rochester.edu (4.1/1.2che) id AA07745; Thu, 13 Apr 95 10:09:59 EDT Date: Thu, 13 Apr 95 10:09:59 EDT From: Jane-Jane Ou Message-Id: <9504131409.AA07745@oz.che.rochester.edu> To: chemistry@ccl.net Subject: Molecular Dynamic Simulation of Liquid Crystals Hi, I am simulating liquid crystal materials. I wrote the program myself with 64 molecules in a box with periodic boundary conditions. I use Alchemy's force field constants to simulate ocb5. The density I got from the simulation is too low, and the order parameters too high. There is not much difference with MM2's exp-6-1 van der Waals and torsion potentials. I also tried Picken et. al. (Liq. Cryst., 1989)'s united atom parameters to simulate cb5. The results I got are: Temperature Order Density 290K 0.48 0.990 300K 0.43 0.970 310K 0.39 0.965 320K 0.36 0.962 Densities are also too low. Is there MD program available somewhere? And what force field programs are available? Please send your opinion, suggestion or advice to my address at janeou@che.rochester.edu. Thank you very much. Sincerely, Jane J. Ou janeou@che.rochester.edu From djh@ccl.net Thu Apr 13 17:29:34 1995 Received: from xipe.ccl.net for djh@ccl.net by www.ccl.net (8.6.10/930601.1506) id RAA01682; Thu, 13 Apr 1995 17:17:26 -0400 From: David Heisterberg Received: for djh@ccl.net by xipe.ccl.net (8.6.9/920428.1525) id RAA04145; Thu, 13 Apr 1995 17:17:25 -0400 Date: Thu, 13 Apr 1995 17:17:25 -0400 Message-Id: <199504132117.RAA04145@xipe.ccl.net> To: chemistry@ccl.net Subject: fda: a C++ atomic code Content-Length: 977 FDA, a finite difference C++ atomic structure code is available from the CCL ftp server in pub/chemistry/software/SOURCES/Cpp/atomic-DF FDA is an "object inclined" (it may be stretching it to call it object oriented) program for density functional atomic structure calculations. It bears a striking similarity to Herman and Skillman's 1963 code (and in its initial release doesn't push the level of theory any farther). However, FDA does have some nice features: a simple input form, but one that allows for pretty complete control of grid generation, convergence, functional calculation, and orbital occupation; a total energy and energy breakdown; a simple dump file that can be used to extract additional orbital-related quantities, or generate basis sets suitable for Fenske-Hall or Ellis' DVXA; a reasonably easy to follow source code that should build without difficulty on most platforms. -- Dave Heisterberg The Ohio Supercomputer Center From brett@si.fi.ameslab.gov Thu Apr 13 17:44:34 1995 Received: from si.fi.ameslab.gov for brett@si.fi.ameslab.gov by www.ccl.net (8.6.10/930601.1506) id RAA01996; Thu, 13 Apr 1995 17:30:51 -0400 Received: by si.fi.ameslab.gov (AIX 3.2/UCB 5.64/4.03) id AA43547; Thu, 13 Apr 1995 16:33:56 -0500 From: brett@si.fi.ameslab.gov (Brett Bode) Message-Id: <9504132133.AA43547@si.fi.ameslab.gov> Subject: Re: CCL:ab-initio on Power Mac(& GAMESS WWW home page) To: chemistry@ccl.net (Computational Chemistry List) Date: Thu, 13 Apr 1995 16:33:55 -0500 (CDT) X-Mailer: ELM [version 2.4 PL24] Content-Type: text Content-Length: 1774 Adrian Roitberg asked if there where any ab initio programs available for the PowerMacintosh. The answer is Yes! My group (Mark Gordon's research group at Iowa State University) has recently ported our ab initio quantum code GAMESS (General Atomic and Molecular Electronic Structure System) to the PowerMac. At this point we simply have it running in a similar way to any other system. ie. you have to create text input files and retrieve your output from .log and .dat files, but it is a fully functional copy of GAMESS capable of using as much or as little memory and disk as you can give it. If you are interested you can get more information from myself via email (brett@si.fi.ameslab.gov) or the WWW from the GAMESS home page: http://www.msg.ameslab.gov/GAMESS/GAMESS.html or via FTP: ag.fi.ameslab.gov or las3.iastate.edu user: anonymous.bmbode password: you email address At the above WWW site you can also find information about the regular version of GAMESS, including the current version and a new PostScript version of the GAMESS manual, and information about our Graphics programs for visualizing GAMESS output including my own program for the Macintosh, MacMolPlt. In the next version (due out next month) MacMolPlt will add the ability to read GAMESS log and IRC files directly and create animations of IRC's, DRC's, optimizations and enhance the current ability to animate Normal Modes. As with the regular version of GAMESS, MacGAMESS and MacMolPlt are free of charge. Let me know if I can provide more assistance... Brett Bode brett@si.fi.ameslab.gov ______________________________________________ Brett Bode 201 Spedding Hall Iowa State University Ames, Iowa 50011 ______________________________________________ From chburger@aci.unizh.ch Thu Apr 13 19:30:09 1995 Received: from rzusuntk.unizh.ch for chburger@aci.unizh.ch by www.ccl.net (8.6.10/930601.1506) id TAA03222; Thu, 13 Apr 1995 19:25:34 -0400 Received: from [130.60.152.42] (acipc3.unizh.ch) by rzusuntk.unizh.ch (4.1/SMI-4.1.9) id AA02331; Fri, 14 Apr 95 01:25:28 +0200 Date: Fri, 14 Apr 95 01:26:07 CST From: "peter burger" Message-Id: <17132.chburger@rzuaix.unizh.ch> X-Minuet-Version: Minuet1.0_Beta_11 X-Popmail-Charset: English To: Chemistry@ccl.net Subject: Opinion on Gaussian92/DFT for Windows Dear CCL'ers since we are considering to purchase Gaussian92/DFT for Windows, we would appreciate to gather some opinions (pro's/con's, performance etc.) >from users of the program. Many thanks in advance, Peter Burger _________________________________ Peter Burger Anorg.-Chem. Institut Universitaet Zuerich Winterthurerstr. 190 8057 Zuerich Switzerland PHONE:+41 1 257 4692 (work) +41 1 252 1793 (home) FAX: +41 1 364 0191 E-mail:chburger@aci.unizh.ch