From dobado@ugr.es Mon Jun 21 11:32:06 1993 Date: Mon, 21 Jun 1993 11:32:06 UTC+0200 From: Jose Antonio Dobado Subject: PROAIM/AIMPAC To: chemistry@ccl.net Message-Id: <45*/S=dobado/O=ugr/PRMD=iris/ADMD=mensatex/C=es/@MHS> ----------------------------- Start of body part 1 Dear Netters: Can anybody tell me how I can get PROAIM/AIMPAC programs of Bader ? Thanks in advance. Jose ----------------------------- Start of body part 2 ****************************************************************************** * /\ | Jose Antonio Dobado Jimenez * * / \ | Dept. Quimica Organica * * | G D | Grupo de Modelizacion | Universidad de Granada * * | M M | y Diseno Molecular | 18071 Granada (SPAIN) * * \ / | Tel: + 34 58 243186 * * \/ | Fax: + 34 58 243186 * * | e-mail dobado@ugr.es * ****************************************************************************** ----------------------------- End of body part 2 From rwoods@biop.ox.ac.uk Mon Jun 21 12:21:25 1993 Date: Mon, 21 Jun 1993 11:21:25 +0100 From: rwoods@biop.ox.ac.uk To: chemistry@ccl.net Message-Id: <0096E5AE.AAA66460.5483@biop.ox.ac.uk> Subject: Simulated Annealing Dear Netters: Thanks to everyone who replied to my request for input files for SANDER. I turns out that I had the commands correct, BUT, I had tried to put a comment line between the &cntrl and &end section. The program naturally got confused by this. Perhaps in future releases of SANDER (AMBER) this option will be incorporated as it would certainly aid in keeping track of the meanings of all of the variables. Just a suggestion. One very interesting thing that came out of the replies was that everyone set up the files differently. Some people used one or two lines for everything while others included a seperate line for each cooling increment. Looking at each file, I think they are all equivalent and I prefer the more concise approach. I noted that some people suggested applying a close coupling to the temperature during cooling, while others didn't. All in all I certainly received a great deal of worthwhile advice. Thanks again to everyone, Rob Woods Robert J. Woods, Ph.D. Glycobiology Institute Department of Biochemistry University of Oxford South Parks Road Oxford, OX1 3QU ENGLAND From pis_diez@cpd.uva.es Mon Jun 21 13:41:03 1993 Date: Mon, 21 Jun 1993 13:41:03 UTC+0100 From: Reinaldo Pis Diez Subject: Re: Morokuma's address To: chemistry@ccl.net (confirm) Message-Id: Hi! A visiting professor at the Department of Theoretical Physics, Valladolid, Spain, K. Sen, from India, just told me that prof. Morokuma is currently at Emory University, Georgetown,Washington. I dont know his e-mail address. Sorry. Regards, Reinaldo From HOAREN@CSOVAX.PORTSMOUTH.AC.UK Mon Jun 21 14:48:00 1993 Message-Id: <199306211350.AA08299@oscsunb.ccl.net> Date: Mon, 21 Jun 93 14:48 GMT From: HOAREN@csovax.portsmouth.ac.uk To: CHEMISTRY Subject: Behaviour of ethers in MDS I have performed molecular dynamics on some compounds ( pyrethroid insecticides) using MSI's Quanta/CHARMm and have encountered a problem. Some of the compounds contain what is essentially a diphenyl ether group and the dynamics suggests that the two dihedral bonds centered on the ether O are freely rotating and do not have preferred conformations. This seems to be at odds with what Allinger has said, and he included lone pair effects to ( I believe) MM2. Can anyone suggest how to overcome this problem, if it is in fact a problem ? Thanks, Neil Hoare. From djh@ccl.net Mon Jun 21 06:50:12 1993 From: David Heisterberg Date: Mon, 21 Jun 1993 10:50:12 -0400 Message-Id: <199306211450.AA00294@xipe.ccl.net> To: chemistry@ccl.net Subject: finite element methods I'm beginning to look at finite element methods for atomic hartree-fock and density functional methods and was wondering if anyone else has an interest in this. If so, I'd appreciate hearing from you! I'll see about putting together a bibliography of favorite references and various tips and tricks. Dave Heisterberg From jas@medinah.atc.ucarb.com Mon Jun 21 05:54:40 1993 Message-Id: <9306211455.AA22418@medinah.atc.ucarb.com> Date: Mon, 21 Jun 1993 10:54:40 -0500 To: Jose Antonio Dobado From: jas@medinah.atc.ucarb.com (Jack Smith) Subject: Re: PROAIM/AIMPAC > >Can anybody tell me how I can get PROAIM/AIMPAC programs of Bader ? > According to the GAMESS documentation (which has an AIMPAC output option), just send an e-mail request to Richard Bader at bader@sscvax.cis.mcmaster.ca. I did so just last week, and I already got an acknowledgement from Bader that the code is on its way. -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= JACK A. SMITH ...................................................................... Union Carbide Corp. || Phone: (304) 747-5797 Catalyst Skill Center || FAX: (304) 747-5571 P.O. Box 8361 || S. Charleston, WV 25303 || Internet: jas@medinah.atc.ucarb.com -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From mlorenz@ecn.purdue.edu Mon Jun 21 04:55:33 1993 Date: Mon, 21 Jun 93 09:55:33 -0500 From: mlorenz@ecn.purdue.edu (Michael Lorenz) Message-Id: <9306211455.AA13509@cn.ecn.purdue.edu> To: CHEMISTRY@ccl.net Subject: MOPAC:IRC Dear Netters, Awhile back I submitted a question to the network concerning using IRC to find the path (of lowest energy) between minima. Many of you responded (THANKS!) with lots of suggestions and I am finally getting around to implementing them (before I was using the 4.0 version, we just recently installed the 6.0). I have located and optimized the TS for ortho-Terphenyl and also have done a force calculation as a precursor to the IRC. I was under the impression that MOPAC would also give me the internal coordinates (for those i flagged) for those energy points calculated along the reaction path. I am obviously mistaken I noticed that the output gives me, among other things, REF% and MOVEMENT. Not to sound totally ignorant (too late for that, i guess) What exactly is this "MOVEMENT" referring to? Do I need to try a different approach to get this specific information? I recall somemone suggested a GRID calculation; would that be more appropriate in this case? Any comments or suggestions would be appreciated. Thanks, Mike Lorenz Purdue Graduate Student From eastonpl@pore.dnet.dupont.com Mon Jun 21 07:45:21 1993 Date: Mon, 21 Jun 93 11:45:21 -0400 Message-Id: <9306211545.AA08312@esds01.es.dupont.com> From: eastonpl@pore.dnet.dupont.com (PHILLIP L. EASTON) To: "CHEMISTRY@ccl.net"@esds01.dnet.dupont.com Subject: Oklahoma ACS Meeting 38th Annual Pentasectional Meeting Oklahoma Section of the American Chemical Society Saturday, August 7th, 1993 at Conoco Inc., Ponca City, Oklahoma CALL FOR PAPP CALL FOR PAPERS Planned Symposia Molecular Modeling On-line Analysis Spectroscopy Environmental Chemistry Kinetics/Catalysis Cyanide Analysis/Treatment plus general sessions in: analytical, organic, physical & inorganic. send max 200 word abstract (camera ready) by JULY 16, 1993 to: Program Chair Dr. Hary W. Keen Conoco Inc. P.O. Box 1267 - 346RE Ponca City, OK 74602-1267 (405) 767-2468 Those interested in the Molecular Modeling symposium can also contact: Dr. Phillip Easton e-mail: eastonpl@pore.dnet.dupont.com phone: (405) 767-5707 From rpm@wag.caltech.edu Mon Jun 21 03:03:41 1993 Date: Mon, 21 Jun 1993 10:03:41 -0700 From: "Richard P. Muller" Message-Id: <199306211703.AA01542@bach.wag.caltech.edu> To: chemistry@ccl.net Subject: Tamm-Dankoff method for CI singles Could anyone give me a reference to the Tamm-Dankoff method for CI singles. I have done a keywords search of journals in the past 5 years without luck. I will summarize anything I receive. Thanks in advance. -- Rick Muller rpm@wag.caltech.edu Caltech 139-74 818.397.2722 Pasadena, CA 91125 818.585.0918 FAX From evi@tiberius.tc.cornell.edu Mon Jun 21 09:11:36 1993 Message-Id: <9306211711.AA91488@tiberius.tc.cornell.edu> To: chemistry@ccl.net Subject: Morokuma's address Date: Mon, 21 Jun 93 13:11:36 -0400 From: Evi Goldfield Although I know that address hunting is discouraged on the list, I will give Prof. Morokuma's address since I cannot remember who originally asked for it. Emory is in Atlanta, not in Washington DC. - Evi Goldfield Prof Keiji Morokuma Dept. of Chemistry Emory University Atlanta, GA 30322 From blonski@alumina.rutgers.edu Mon Jun 21 09:30:22 1993 Date: Mon, 21 Jun 93 13:30:22 EDT From: blonski@alumina.rutgers.edu (Slawomir Blonski) Message-Id: <9306211730.AA01997@alumina.rutgers.edu> To: chemistry@ccl.net Subject: simulations of solid-solid phase transitions Dear netters: I work on molecular dynamics simulations of alumina crystals. Modeling a solid-state phase transition from gamma-Al2O3 to alpha-Al2O3 is one of my goals which, however, seems to be difficult to accomplish. Do you know about successful simulations of the solid-solid phase transitions ? Any references ? I found only those: "Isothermal-isobaric molecular dynamics simulation of polymorphic phase transitions in alkali halides" I. Ruff, A. Baranyai, E. Spohr, & K. Heinzinger J. Chem. Phys. 91 (1989) 3148 "Rigid Unit Modes in the Molecular Dynamics Simulation of Quartz and the Incommensurate Phase Transition" F.S. Tautz, V. Heine, M.T. Dove, & X. Chen Phys. Chem. Minerals 18 (1991) 326 I shall also appreciate any comments on the problem. Slawomir Blonski From h.rzepa@ic.ac.uk Mon Jun 21 18:45:37 1993 Message-Id: <9306211747.AA09016@cscmgb.cc.ic.ac.uk> Date: Mon, 21 Jun 1993 18:45:37 +0000 To: CHEMISTRY@ccl.net From: h.rzepa@ic.ac.uk (Henry Rzepa) (Henry Rzepa) Subject: Image processing In the interests of establishing how images may be disseminated, I have mounted some unusual ones in the following gopher server argon-fddi.ch.ic.ac.uk, sub directory photo-CD_rzepa. You will need turbogopher 1.06b5, and JPEGViewer 2.0 (or Teachtext). Any other suggestions for getting to know eachother are welcome! PS, no it is not our garden. I believe it belongs to our Royal Family! On a general point, have many people tried the Kodak photo-CD format yet? PS for Jan; Does this follow the rules, or should I hastily remove the files? Dr Henry Rzepa, Dept. Chemistry, Imperial College, LONDON SW7 2AY; rzepa@ic.ac.uk via Eudora 1.3.1, Tel:+44 71 225 8339, Fax:+44 71 589 3869. From jas@medinah.atc.ucarb.com Mon Jun 21 09:25:39 1993 Message-Id: <9306211827.AA27504@medinah.atc.ucarb.com> Date: Mon, 21 Jun 1993 14:25:39 -0500 To: chemistry@ccl.net From: jas@medinah.atc.ucarb.com (Jack Smith) Subject: Analytic Solution for Hyperbolic Paraboloid I have six points that I want to fit to a quadratic surface (more specifically, a hyperbolic paraboloid, i.e., looks like a saddle point or TS, although this is not for a PE surface). The problem is that I want to do this repeatedly in a simple scripting language where it's not plausible (easy, that is) to do matrix inversion or call a subroutine from a package. Does anyone perchance have the analytic solution to this fit. Perhaps someone with a solver (Mathematica, etc.) that would be willing to crank this out. It would also be quite useful to have a simple analytic solution for transforming these same six points to the inertial frame (i.e., principle axes of inertia) before the fit. -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= JACK A. SMITH ...................................................................... Union Carbide Corp. || Phone: (304) 747-5797 Catalyst Skill Center || FAX: (304) 747-5571 P.O. Box 8361 || S. Charleston, WV 25303 || Internet: jas@medinah.atc.ucarb.com -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From cqsimpson@halnet.com Mon Jun 21 10:17:17 1993 Date: Mon, 21 Jun 1993 15:17:17 -0500 From: cqsimpson@halnet.com (Charlie Simpson) Message-Id: <9306212017.AA24535@cre2> To: chemistry@ccl.net Subject: rs6k graphics to PCs Howdy Netters! Thanks to all who responded to my question last week concerning how to transfer rs6k graphics to PCs. I've included all of the responses below. The most useful to date has been the AVS center at NCSC. If you use AVS for anything, this site is worth checking out. They have a lot of software that doesn't appear to be included with the standard issue. Thanks again, Charlie ****************************** Hello: Have tried xv? It can grab a portion of your graphics and save it various formats suitable for pc. You can ftp xv from export.lcs.mit.edu:contrib/ regards pedro -- ============================================================================= Pedro A. M. Vazquez | Caixa Postal 6154 | FONE: 55 192 39 7253 Depto de Fisico Quimica | CEP 13081 | FAX : 55 192 39 3805 Instituto de Quimica | SP/BRASIL | UNICAMP | |vazquez@iqm.unicamp.br ============================================================================= ****************************** The anonymous ftp site at the International AVS Center has modules that convert images to just about every graphics format imaginable (at least to a non-graphics programmer). They are found at avs.ncsc.org (128.109.178.23) in the avs_modules/data_output directory. The set includes a write_tiff_image module. If you have any questions about using them or accessing them, you can contact the IAC by sending mail to avs@ncsc.org. ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ || Kevin Moore North Carolina Supercomputing Center || || Scientific Support Analyst 3021 Cornwallis Rd. || || (919) 248-1179 Research Triangle Park, NC 27709 || ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ****************************** Yep, try GHOSTSCRIPT v2.5... This will take a POSTSCRIPT file that your program generates, and convert it to .BMP, .PCX and .GIF (+ others). Failing that, try CorelDRAW!.. Ghost script is available via anonymous FTP from places such as Simtel. Cheers, Mark Baker ****************************** There are quite a few modules available from the Nat. AVS center to convert the output from AVS into various formats. Have you already checked out this option? wdc ****************************** We use the AVS Chemistry Viewer as well. I would suggest that you look into some sort of postscript viewer or encapsulated postscript viewer for your PCs, something from gnu perhaps. Or you can check on the archives of the international AVS center at NCSC -- there are over 600 modules there and I know that there are quite a few which do file format conversions. Doug Douglas A. Smith Assistant Professor of Chemistry The University of Toledo Toledo, OH 43606-3390 voice 419-537-2116 fax 419-537-4033 email dsmith@uoft02.utoledo.edu ****************************** Charlie, You should be able to use the 'xwd' program to capture an X-Windows screen dump. There is a suite of programs known as PBM that can then translate from xwd to the "ppm" format, and from that format out to any of dozens of other formats. The PBMPLUS programs are available via anonymous FTP from wuarchive.wustl.edu and probably several other sites as well, but I don't recall the exact directory. Regards, Bob Funchess -- Dr. Robert B. Funchess Molecular Simulations Inc. Technical Support Scientist 16 New England Executive Park bobf@msi.com Burlington, MA 01803-5297 (617) 229-9800 x202 FAX (617) 229-9899 ================================================================================ Charlie Simpson Ph.D. cqsimpson@halnet.com Halliburton Services P.O. Box 1431 Phone 405/251-4564 Duncan, OK 73536-0444 Fax 405/251-3218 Life for him was an adventure, and perilous indeed, but men were not made for safe havens. -- Edith Hamilton on Aeschylus ================================================================================ From MOSES@CMCHEM.CHEM.CMU.EDU Mon Jun 21 14:03:04 1993 Date: Mon, 21 Jun 1993 18:03:04 EDT From: MOSES@CMCHEM.CHEM.CMU.EDU (David J. Moses / 412-279-6700) Message-Id: <930621180304.202018b7@CMCHEM.CHEM.CMU.EDU> Subject: Reminder about Gaussian e-mail list To: chemistry@ccl.net --------------------------------------------------------------------- GAUSSIAN, INC. Carnegie Office Park Building 6 Pittsburgh, PA 15106 USA PHONE - 412-279-6700 FAX - 412-279-2118 E-MAIL - info@gaussian.com Subj: Reminder about Gaussian Mailing Lists (both e-mail and regular post) In addition to our regular mailing list, we at Gaussian have assembled an electronic mailing list for those interested in news regarding the Gaussian system of programs. Both mailing lists help us keep users updated on new versions of the program, improvements and enhancements to the program, and upcoming Gaussian workshops and user meetings. We invite any interested parties to subscribe to either or both lists. If you would like to subscribe to the electronic mailing list, please send your e-mail address to info@gaussian.com. If you would like to subscribe to our regular mailing list (to receive our newsletter, Gaussian NEWS), please include your full mailing address along with your electronic mail address in the e-mail message. We also welcome any comments or suggestions you might have. Sincerely, David J. Moses info@gaussian.com --------------------------------------------------------------------- This notice is sent without warranty of any kind, expressed or implied. Gaussian is a trademark of Gaussian, Inc. From pitman@SECS.UCSC.EDU Mon Jun 21 08:14:16 1993 Date: Mon, 21 Jun 1993 15:14:16 PDT From: Mike Pitman To: chemistry@ccl.net Message-Id: <0096E5CF.31D17540.2607@SECS.UCSC.EDU> Subject: summary: transition states with DFT Hello, Here is the summary of responses for my question about finding transition states with DFT. Most of the responses were requests for the responses, only three responses were substantive. Sorry it took me so long to post the summary. The question concerned my orals exam and I felt it best to wait until after the exam was over. ;) Thanx much to those who responded Mike Pitman Dept. of Chemistry Santa Cruz, CA 95060 Univ. of California, Santa Cruz email: pitman@secs.ucsc.edu Original Posting ____________________________________________________________________________ Hello, I was wondering about the state of development for methods of finding transition states with Density Functional Theory. More specifically, how much will programs like DGauss or Dmol give you, and how much do you have to do yourself? Can they calculate normal vibrational modes? Can they do any type of saddle point searching? Pointers to literature, On-line docs, or words of experience from those in the know would be greatly appreciated. Thanks in advance. Mike Pitman Dept. of Chemistry Univ. of California, Santa Cruz email: pitman@secs.ucsc.edu Responses ____________________________________________________________________________ From: David Heisterberg In a very brief look at Diels-Alder transition states with DMol, I've run into some problems. First, DMol doesn't specifically know anything about transition states, though that shouldn't necessarily be a problem. Second, the BFGS method doesn't work well with the systems I was looking at -- this was a problem with Mopac, Gaussian 92, and DMol. The conjugate gradient optimizer did work, sort of. After a couple hours on a YMP it eventually gave me norbornene, having run right through the transition state! I ran into some similar problems with G92 unless an analytic hessian was generated; this would be a nice feature to have in DMol. Calculations were done with the DND basis and just JMW local functional. -- David J. Heisterberg (djh@ccl.net) Gee, it's so beautiful, I gotta The Ohio Supercomputer Center give somebody a sock in the jaw. Columbus, Ohio -- Little Skippy (Percy Crosby) ____________________________________________________________________________ From: jas@medinah.atc.ucarb.com (Jack Smith) > I was wondering about the state of development for methods of finding >transition states with Density Functional Theory. More specifically, how much >will programs like DGauss or Dmol give you, and how much do you have to do >yourself? Can they calculate normal vibrational modes? Can they do any type >of saddle point searching? > > Pointers to literature, On-line docs, or words of experience from >those in the know would be greatly appreciated. Mike: I use DMol quite regularly, but have had only limited success in locating transition states. The current gradient technique can minimize to a saddle point, but you have to be pretty close to start with. DMol will do a force calculation and normal coordinate analysis to help confirm a transition state, but you can not follow a specific mode to make sure it actually connects products to reactants. I believe that analytical gradients and a more robust optimizer are in the works, but you should probably check with Biosym for details. One of the more frustrating things about DMol with regard to reaction modeling is the lack of internal coordinates, and in particular, the inability to optimize along an internal coordinate (except, perhaps, for a simple bond formation/breaking, where one can align the reaction coordinate along a particular axis and manually use the 'onlyopt' feature for a series of points along the axis). I look forward to the day when one can study reaction paths with DMol as easily as one can now with MOPAC/AMPAC (and certain ab initio programs, if you can afford it). I'd like to see a posting of a summary of your responses. -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= JACK A. SMITH ...................................................................... Union Carbide Corp. || Phone: (304) 747-5797 Catalyst Skill Center || FAX: (304) 747-5571 P.O. Box 8361 || S. Charleston, WV 25303 || Internet: jas@medinah.atc.ucarb.com -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= _____________________________________________________________________________ From: chengteh@himalia.cray.com (Chengteh Lee) There are some results in literature about transition states seraches using density functional methods. For example, see the work by Ziegler and coworkers in JCP 92, 3645(1990) and Chem. Rev. 91, 651(1991). Dgauss does give you saddle point optimizations, but the computations are based on a finite difference numerical methods and an initial Hessian input is required. Analytical methods for generating the second derivatives will be available in the near future. Applications of transition state searches using DGauss can be found in: JCP 98, 8004(1993), IJQC (Submitted). p.s. Pople and co-workers have also made a lot of progress in this area. Chengteh Lee UniChem Cray Research, Inc. 612-683-3653 From wiedeman@altair.acs.uci.edu Mon Jun 21 09:03:30 1993 To: chemistry@ccl.net Subject: Re: Morokuma's address Date: Mon, 21 Jun 93 16:03:30 -0700 Message-Id: <2615.740703810@altair.acs.uci.edu> From: Lyle Wiedeman >> A visiting professor at the Department of Theoretical >> Physics, Valladolid, Spain, K. Sen, from India, just told me that >> prof. Morokuma is currently at Emory University, Georgetown,Washington. >> I dont know his e-mail address. Sorry. Regards, Well, Emory U. is in Georgia, not Georgetown. Netfind provides: MAIL FOR Keiji Morokuma IS FORWARDED TO morokuma@emory.edu NOTE: this is a domain mail forwarding arrangement - so mail intended for "morokuma" should be addressed to "morokuma@emory.edu". SYSTEM: emory.edu Login name: morokuma In real life: Keiji Morokuma Directory: /home/emoryu1/emu/morokuma Shell: /bin/ksh Last login Thu Dec 3, 1992 on ttyp8 from 128.140.6.13 New mail received Sun Apr 4 17:13:24 1993; unread since Tue Nov 17 15:32:10 1992 No Plan. Lyle Wiedeman Office of Academic Computing wiedeman@uci.edu Univ. Calif. Irvine wiedeman@UCI.BITNET Irvine, CA 92717 (714) 856-8718 FAX (714) 725-2069