From chemistry-request@www.ccl.net Mon Mar 22 05:34:17 1999 Received: from arnold.chem.uoa.gr (arnold.chem.uoa.gr [195.134.76.50]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id FAA14937 Mon, 22 Mar 1999 05:34:15 -0500 (EST) Received: from localhost (jkerk@localhost) by arnold.chem.uoa.gr (8.8.8/8.8.8) with SMTP id MAA27313 for ; Mon, 22 Mar 1999 12:29:49 +0200 (EET) Date: Mon, 22 Mar 1999 12:29:49 +0200 (EET) From: "I. Kerkines" To: chemistry@www.ccl.net Subject: Summary for MRCI Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII A few days ago I posted the following question On Thu, 11 Mar 1999, I. Kerkines wrote: > > Dear colleagues, > > Does anybody know of any reviews or related papers on second order CI > (SOCI)? > The only answer I got was: Adv. Quant. Chem. 34 (1999) 143 Thanks, ************************************************************ * Ioannis S. Kerkines * * M.Sc. Student in Physical Chemistry * * Department of Chemistry / University of Athens * * Panepistimiopolis Tel: ++30 1 727-4569 * * Zographou, 157 10 FAX: ++30 1 723-3219 * * HELLAS (Greece) Email: jkerk@arnold.chem.uoa.gr * ************************************************************ From chemistry-request@www.ccl.net Mon Mar 22 05:41:24 1999 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id FAA15024 Mon, 22 Mar 1999 05:41:23 -0500 (EST) Received: from chemistry.leeds.ac.uk (chmsun1.leeds.ac.uk [129.11.12.1]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id FAA02993 for ; Mon, 22 Mar 1999 05:40:34 -0500 (EST) Received: from chmibm256 (chmibm256.leeds.ac.uk [129.11.13.165]) by chemistry.leeds.ac.uk (8.8.8/8.8.8) with SMTP id KAA19983; Mon, 22 Mar 1999 10:39:32 GMT Message-Id: <3.0.6.32.19990322103946.007cec80@chmsun1.leeds.ac.uk> X-Sender: wolfgang@chmsun1.leeds.ac.uk X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.6 (32) Date: Mon, 22 Mar 1999 10:39:46 -0800 To: chemistry@ccl.net, g@CCMSD.chem.uga.edu From: Wolfgang Roth Subject: Gaussian 98 has problems with large CASSCF spaces Cc: info@gaussian.com, help@gaussian.com Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear all, I'm trying to proof the the statement from the subject line because I observe a strange behavior of the CASSCF algorithm in Gaussian 98 (Rev. A.4) as reported below: In brief, if you are going to large(r) active spaces of 10 or 12 electrons and more than (approx.) 4000 configuration state functions (CSFs) the energy of the optimized wavefunction is substancially higher (by several hartree) than for the smaller CAS spaces. My geometry optimizations under these conditions always failed after a few step due to convergence problems of the MCSCF wavefunction. As an example, I calculated the single point energy of the molecule 2-H benzotriazole (6 C-, 3 N- and 5 H-atoms) with different active spaces. This molecule has 10 pi-electrons which should be spread over 9 pi-orbitals such that the maximum CASSCF space would be designated as (10, 9). CASSCF( 8, 8,nroot=1) [1764 CSFs, no special selection of orbitals except for pi] yields ITN= 17 MaxIt= 64 E= -393.5116726512 DE=-7.88D-09 Acc= 1.00D-08 Lan= 3 CASSCF(10, 8,nroot=1) [1176 CSFs] yields ITN= 27 MaxIt= 64 E= -393.4877127352 DE=-9.63D-09 Acc= 1.00D-08 Lan= 3 CASSCF( 8, 9,nroot=1) [8001 CSFs} yields ITN= 38 MaxIt= 64 E= -384.7333360567 DE=-9.20D-09 Acc= 1.00D-08 Lan= 1 CASSCF(10, 9,nroot=1) [8001 CSFs} yields ITN= 18 MaxIt= 64 E= -379.8942586656 DE=-4.18D-09 Acc= 1.00D-08 Lan= 1 The HF energy at the same geometry is SCF Done: E(RHF) = -393.396661489 A.U. after 16 cycles As you can see, the two calculations with the (announced) 8001 CSFs are about 9 and 14 hartree higher in energy than the HF claculation. THIS cannot be due to a wrong selection of orbitals. Did anyone else discovered the same observations using Gaussian 98 or may it be traced backed to a problem of our computer (SGI Origin2000 with Irix 6.4 /6.5)? Regards Wolfgang Roth ==W=o=l=f=g=a=n=g==R=o=t=h===========================W=R== University of Leeds School of Chemistry Leeds LS2 9JT UK ===== http://www-public.rz.uni-duesseldorf.de/~rothw ===== From chemistry-request@www.ccl.net Mon Mar 22 05:58:06 1999 Received: from fluor.dechema.de (root@mail.dechema.de [194.162.4.26]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id FAA15094 Mon, 22 Mar 1999 05:58:05 -0500 (EST) Received: from germanium (germanium.dechema.de [194.162.4.114]) by fluor.dechema.de (8.8.8/8.8.8) with SMTP id LAA32269 for ; Mon, 22 Mar 1999 11:23:28 +0100 Message-Id: <199903221023.LAA32269@fluor.dechema.de> From: "Beate Gellermann" To: chemistry@www.ccl.net Date: Mon, 22 Mar 1999 11:22:22 +0100 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: Weiterbildungskurs Molecular Modelling Reply-to: KWI@dechema.de Priority: normal X-mailer: Pegasus Mail for Win32 (v3.01d) Der Kurs Molecular Modelling - Ein Ueberblick fuer Einsteiger findet vom 25-27.10.1999 in Erlangen statt. Er wendet sich Naturwissenschaftler, Chemiker, Mediziner und Pharmazeuten in Forschung und Entwicklung. Themen: Kraftfeldverfahren, Modellierung von Proteinen, Molekuelorbital-Methoden, Protein-Ligand- Wechselwirkungen,QSAR/QSPR. Die Vortraege werden von praktischen Uebungen begleitet. Referenten: T. Clark, H. Lanig (Computer-Chemie-Zentrum der Universitaet Erlangen-Nuernberg) und Referenten aus der Industrie. Teilnahmegebuer: 1.440,-- (incl. Kursunterlagen) Weitere Informationen unter DECHEMA e.V. Weiterbildung Postfach 150104 D-60061 Frankfurt a.M. Tel.: +49/69/7564-253 Fax: +49/69/7564-388 email: KWI@dechema.de http://www.dechema.de/deutsch/veransta/pages/veran4.htm From chemistry-request@www.ccl.net Mon Mar 22 09:50:12 1999 Received: from giasbma.vsnl.net.in (giasbma.vsnl.net.in [202.54.4.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id JAA16337 Mon, 22 Mar 1999 09:50:02 -0500 (EST) Received: from giasbmc.vsnl.net.in (giasbmc [202.54.4.6]) by giasbma.vsnl.net.in (8.8.8/8.8.8) with SMTP id TAA09349 for ; Mon, 22 Mar 1999 19:25:09 +0500 (IST) Date: Mon, 22 Mar 1999 18:57:52 -0500 (GMT) From: Amit Galande Reply-To: Amit Galande To: CHEMISTRY@www.ccl.net Subject: random screening Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII It has been observed that random approaches are prefered over rational ones when it comes to the sampling of large molecular diversity for screening. But when this set to be screened is selected from MD,randomly, then what all are the constraints or the factors which decides that how many molecules are to be selected randomly from given huge set (of even say combinatorial libraris.) It is obvious that sreening all the molecules is many times not possible hence we look for the set which requisitly represents the entire MD or CL but how large this set should be when random approach is to be used? Thanking you in anticipation Amit From chemistry-request@www.ccl.net Mon Mar 22 11:55:53 1999 Received: from opium.q1.fcen.uba.ar (churca@opium.q1.fcen.uba.ar [157.92.31.21]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id LAA17248 Mon, 22 Mar 1999 11:55:50 -0500 (EST) Received: from localhost (churca@localhost) by opium.q1.fcen.uba.ar (8.8.0/8.8.0) with SMTP id NAA25619; Mon, 22 Mar 1999 13:20:06 -0300 Date: Mon, 22 Mar 1999 13:20:06 -0300 (ARST) From: Adrian Turjanski To: "CHEMISTRY@www.ccl.net" cc: "CHEMISTRY@www.ccl.net" Subject: Xmol software? In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi: does anybody know about Xmol program? Where can i download it? Thank you very much. Adrian Turjanski From chemistry-request@www.ccl.net Fri Mar 19 06:15:49 1999 Sender: daniele@bioem.ing.uniroma1.it Date: Fri, 19 Mar 1999 12:17:01 -0800 From: Daniele Spera To: whole CCL Subject: PCM calc with G94 Dera CCLers, did anyone ever perform PCM calculation using G94 code? I have been running SP jobs over a porphin ring with SCRF+PCM and Nosymm keywords at HF 6-31G(d) level. In some cases I didn't manage to get convergence, yet when I did, there were lines in the output file about a warning message during Tomasi II Approximation: Tomasi Approximation II Iteration number 1 Iteration number 2 MaxDiff 0.148983964393E-01 Iteration number 3 MaxDiff 0.295825718481E-01 Iteration number 4 MaxDiff 0.673842760811E-01 Warning: Deleting charge of infinity. Warning: Deleting charge of infinity. Warning: Deleting charge of infinity. Iteration number 5 MaxDiff 0.154191696315 Warning: Deleting charge of infinity. Warning: Deleting charge of infinity. Iteration number 6 MaxDiff 0.310289858534 Iteration number 7 MaxDiff 0.989697254870E-02 Iteration number 8 MaxDiff 0.135299873542E-02 Does anyone know what it means? Tahnk you Daniele Spera -- _____________ Daniele Spera Universita' di Roma "La Sapienza", Italy E-mail: daniele@bioem.ing.uniroma1.it From chemistry-request@www.ccl.net Fri Mar 19 12:17:13 1999 From: Kim Takita To: "'Computational Chemistry List (CCL)'" Subject: Rational Approaches to Materials Design & Synthesis Date: Fri, 19 Mar 1999 12:19:51 -0500 MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="---- =_NextPart_000_01BE7202.CB17FAC0" ------ =_NextPart_000_01BE7202.CB17FAC0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit International Conference on Rational Approaches to Materials Design & Synthesis May 20-21, 1999 in Philadelphia. see our web site for more information: http://www.knowledgefoundation.com/rational.html or email kmtakita@knowledgefoundation.com with your mailing address and we will mail you a full brochure. Emphasis will be placed on approaches through practical examples on how to effectively: * Target new materials by design * Accelerate discovery through rational design and selective synthesis * Define computational & modeling requirements Just a few organizations represented on program faculty include Universal Oil Products, Eastman-Kodak, Air Products & Chemicals, Symyx Technologies, Exxon Research & Engineering, Mobil Technology as well as leading academic researchers. Please feel free to contact me if you would like further information. Sincerely, Kim ------------------------------------------------ Kim Takita Vice President The Knowledge Foundation, Inc. 101 Merrimac Street Boston, MA 02114 617-367-7979 ext. 202 617-367-7912 (fax) Email: kmtakita@knowledgefoundation.com http://www.knowledgefoundation.com ------ =_NextPart_000_01BE7202.CB17FAC0 Content-Type: application/ms-tnef Content-Transfer-Encoding: base64 eJ8+IjURAQaQCAAEAAAAAAABAAEAAQeQBgAIAAAA5AQAAAAAAADoAAEIgAcAGAAAAElQTS5NaWNy b3NvZnQgTWFpbC5Ob3RlADEIAQ2ABAACAAAAAgACAAEEkAYA8AEAAAEAAAAQAAAAAwAAMAIAAAAL AA8OAAAAAAIB/w8BAAAAhgAAAAAAAAC1O8LALHcQGqG8CAArKlbCFQAAAHjGk9CWGdIRpF8A4JgB 2bHkgwAAAAAAAIErH6S+oxAZnW4A3QEPVAIAAAAAQ29tcHV0YXRpb25hbCBDaGVtaXN0cnkgTGlz dCAoQ0NMKQBJTlRFUk5FVABjaGVtaXN0cnlAY2NsLm9zYy5lZHUAAAAeAAIwAQAAAAkAAABJTlRF Uk5FVAAAAAAeAAMwAQAAABYAAABjaGVtaXN0cnlAY2NsLm9zYy5lZHUAAAADABUMAQAAAAMA/g8G AAAAHgABMAEAAAAlAAAAJ0NvbXB1dGF0aW9uYWwgQ2hlbWlzdHJ5IExpc3QgKENDTCknAAAAAAIB CzABAAAAHwAAAElOVEVSTkVUOkNIRU1JU1RSWUBDQ0wuT1NDLkVEVQAAAwAAOQAAAAALAEA6AQAA AB4A9l8BAAAAIwAAAENvbXB1dGF0aW9uYWwgQ2hlbWlzdHJ5IExpc3QgKENDTCkAAAIB918BAAAA LAAAAL8AAAC1O8LALHcQGqG8CAArKlbCFQAAAHjGk9CWGdIRpF8A4JgB2bHkgwAAAwD9XwEAAAAD AP9fAAAAAAIB9g8BAAAABAAAAAAAAAK6dAEEgAEANAAAAFJhdGlvbmFsIEFwcHJvYWNoZXMgdG8g TWF0ZXJpYWxzIERlc2lnbiAmIFN5bnRoZXNpcwDPEgEFgAMADgAAAM8HAwATAAwAEwAzAAUAQwEB IIADAA4AAADPBwMAEwAMAAUAMQAFADMBAQmAAQAhAAAANzAyODA2ODZFN0RERDIxMUE0NUYwMEUw OTgwMUQ5QjEACAcBA5AGADAHAAAgAAAACwACAAEAAAALACMAAAAAAAMAJgAAAAAACwApAAAAAAAD ADYAAAAAAEAAOQAA47+yLHK+AR4AcAABAAAANAAAAFJhdGlvbmFsIEFwcHJvYWNoZXMgdG8gTWF0 ZXJpYWxzIERlc2lnbiAmIFN5bnRoZXNpcwACAXEAAQAAABYAAAABvnIssp6GBihy3ecR0qRfAOCY AdmxAAAeAB4MAQAAAAUAAABTTVRQAAAAAB4AHwwBAAAAIQAAAGttdGFraXRhQGtub3dsZWRnZWZv dW5kYXRpb24uY29tAAAAAAMABhAD+qLPAwAHEM4DAAAeAAgQAQAAAGUAAABJTlRFUk5BVElPTkFM Q09ORkVSRU5DRU9OUkFUSU9OQUxBUFBST0FDSEVTVE9NQVRFUklBTFNERVNJR04mU1lOVEhFU0lT TUFZMjAtMjEsMTk5OUlOUEhJTEFERUxQSElBU0VFAAAAAAIBCRABAAAA9AMAAPADAADeBQAATFpG dQsvVJIDAAoAcmNwZzEyNRYyAPgLYG4OEDAzM50B9yACpAPjAgBjaArA4HNldDAgBxMCgwBQYwLy ENlUYWgDcQKAfbMKgAjIIDsJbw4wNQKAOQqBdWMAUAsDC7UgSWMCMASRYXRpAiAHQCAZCFBuZgSQ CfBjZSDHAiAH8BemQXBwA2AA0PJoB5F0bwXQF6AGcQdApQQgRAeQaWcDoCYGAH55AjAaAQQACqIK gBpweQIgAdAtMjEsIDGKOR1QIAuAIFBoAxCSYQEAbHAd0GEuHDQHETAYsQhwIHdlYiD7AJAXYCAC EAXABGAJcB2BpyABAMAXsjogAzBjAEEKdQMgaAJAcDovLwJ3ImAua25vd2xNCYBnARAIYG5kF6Mu UQWgbS9yF6UuIfBt/wlQIYABQCHAAUAcQwWwHDSmZQDAAxFrbQGQax/APGFAIq8jtB9gH8BoIE55 HzImYguAZyAeAGS3CXAEEQBwZB9hKLFsAyC/JmMpESnQH/AhwAMgYgNgmxDwCHBlHoUcNEVtHkD2 YRwBKsRiGLALURigKoCVGNFhGaloA2B1ZyjwFxmwANAXsGMX8WV4Yf8tgCeABCAY0RNQB+AaQQER SwWQF7B2HiB5Ohw0Ku0TIXIjEAVAbgfRIOEapZ5iHLABABsyMuZBYxigdyeAJCEYsGQEAAWgMpBy /xywL9YkJjTVKlMRMCeAMmPvH6AbvDNAGxBmC4AYsCPh/HB1AZAXtRuABGIpkwlw+HF1aQlwB4AC MBwlHDR4SnVzBUArsQfRBbBn+QBwaXoXowQgCXAZsAeQ/z0BLsQZsQnAMRAf8ADQIcA2dBywC4Bj CkABACBVqwMANsFzF/FPAxFQA2DuZBYwPSAdIEUtsCTAAHDcLUsEcCbgHSBBPMBC13UbcUMaAG0w okNRBrF5tngTIAWQaCdQCQBnCJD5Q1J4eBjSP9EKwBDwG3E+RQ8gOrEGcQ8gHSBNb/5iAxFGdxyw LbAfYSrxSkH/J4AeACmjMLABAEWRPHFH1PtCQSyrUErxETA+YR4gH/B/CdEaMgWgAjAwcSAwIHFm tStjdwhgbCqAKZBrH+HfCHAb0QXAIJksq1NBgRhh9TKwLBw0SwdwLLgWoRIh4HMxNyAtVQ9WH1b7 71M3EyEm8hw0Vg3gGLBC4C8bIQEAAjAcNFQaACBLuSdWIEYjRx0gF0BjHoV9D0AxBdAEkAUQAMEG AHQzCdFaNUJvPiBcAk1BpSFQMB0AMTQcNDZU0MgtMzZgADc5YGAw4Tx0LhzBDlBfnQ4gICj5QQB4 KS0WJnEhQCa/Iy3/LLUhjyKfZRYlCxZrHDQTsQIAatADABAQAAAAAAMAERAAAAAAAwCAEP////9A AAcwQLrXvCpyvgFAAAgwQLrXvCpyvgELAACACCAGAAAAAADAAAAAAAAARgAAAAADhQAAAAAAAAMA AoAIIAYAAAAAAMAAAAAAAABGAAAAABCFAAAAAAAAAwAFgAggBgAAAAAAwAAAAAAAAEYAAAAAUoUA AHQQAAAeAAmACCAGAAAAAADAAAAAAAAARgAAAABUhQAAAQAAAAUAAAA4LjAyAAAAAAMACoAIIAYA AAAAAMAAAAAAAABGAAAAAAGFAAAAAAAACwATgAggBgAAAAAAwAAAAAAAAEYAAAAADoUAAAAAAAAD ABSACCAGAAAAAADAAAAAAAAARgAAAAARhQAAAAAAAAMAFoAIIAYAAAAAAMAAAAAAAABGAAAAABiF AAAAAAAAHgAlgAggBgAAAAAAwAAAAAAAAEYAAAAANoUAAAEAAAABAAAAAAAAAB4AJoAIIAYAAAAA AMAAAAAAAABGAAAAADeFAAABAAAAAQAAAAAAAAAeACeACCAGAAAAAADAAAAAAAAARgAAAAA4hQAA AQAAAAEAAAAAAAAAHgA9AAEAAAABAAAAAAAAAAMADTT9NwAAG7k= ------ =_NextPart_000_01BE7202.CB17FAC0-- From chemistry-request@www.ccl.net Fri Mar 19 12:59:41 1999 X-Sender: osman@146.202.6.217 (Unverified) X-Mailer: QUALCOMM Windows Eudora Pro Version 4.0.1 Date: Fri, 19 Mar 1999 10:01:03 -0800 To: chemistry@ccl.net From: "Osman F. Guner" Subject: Fwd: Call for Papers - Informatics@Internet Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by www.ccl.net id MAA05505 >Date: Thu, 11 Mar 1999 08:46:40 -0800 >To: chemistry@ccl.net >From: "Osman F. Guner" >Subject: Call for Papers - Informatics@Internet > >WEB-BASED DEPLOYMENT OF INFORMATION MANAGEMENT TOOLS > >CINF Symposium at ACS Fall in New Orleans, August 22-26. > >Please note the deadline of April 15th for submission of your abstracts. Please see http://www.acs.org/meetings/abstract/abinfo.html for information on submitting your abstracts. Alternatively, you can Email me an electronic version. > >Thx..osman -- Osman F. Güner, Ph.D. Sr.Product Manager, Rational Drug Design Molecular Simulations Inc. (619)799-5341 osman@msi.com http://www.msi.com From chemistry-request@www.ccl.net Fri Mar 19 14:22:12 1999 From: Kim Takita To: "'Computational Chemistry List (CCL)'" Subject: Materials Informatics Date: Fri, 19 Mar 1999 12:43:34 -0500 X-Mailer: Microsoft Internet E-mail/MAPI - 8.0.0.4211 MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="---- =_NextPart_000_01BE7214.4A7D7180" ------ =_NextPart_000_01BE7214.4A7D7180 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Thank you to all who provided help and feedback in developing this program. "Effective Data Management for New Materials Discovery: Materials Informatics" June 28-29, 1999 in Boston, MA for more information see our web site: http://www.knowledgefoundation.com/informatics.html or email kmtakita@knowledgefoundation.com and we will mail you a full brochure. The conference covers many of the issues brought up in the group. Some of these questions include: * How to design multiple materials databases to allow transparent acess to all relevant applications throughout the discovery to development phase * How to integrate disparate application software, and provide standardized methods of analyzing data * How to enlist the aid of software and systems providers * How to best access publicly available information sources IN addition, a special session will be held in conjunction with the conference to explore the establishment of an industry consortium for materials informatics. Please feel free to contact me for further information. Sincerely, Kim ------------------------------------------------ Kim Takita Vice President The Knowledge Foundation, Inc. 101 Merrimac Street Boston, MA 02114 617-367-7979 ext. 202 617-367-7912 (fax) Email: kmtakita@knowledgefoundation.com http://www.knowledgefoundation.com ------ =_NextPart_000_01BE7214.4A7D7180 Content-Type: application/ms-tnef Content-Transfer-Encoding: base64 eJ8+IggTAQaQCAAEAAAAAAABAAEAAQeQBgAIAAAA5AQAAAAAAADoAAEIgAcAGAAAAElQTS5NaWNy b3NvZnQgTWFpbC5Ob3RlADEIAQ2ABAACAAAAAgACAAEEkAYA8AEAAAEAAAAQAAAAAwAAMAIAAAAL AA8OAAAAAAIB/w8BAAAAhgAAAAAAAAC1O8LALHcQGqG8CAArKlbCFQAAAHjGk9CWGdIRpF8A4JgB 2bHkgwAAAAAAAIErH6S+oxAZnW4A3QEPVAIAAAAAQ29tcHV0YXRpb25hbCBDaGVtaXN0cnkgTGlz dCAoQ0NMKQBJTlRFUk5FVABjaGVtaXN0cnlAY2NsLm9zYy5lZHUAAAAeAAIwAQAAAAkAAABJTlRF Uk5FVAAAAAAeAAMwAQAAABYAAABjaGVtaXN0cnlAY2NsLm9zYy5lZHUAAAADABUMAQAAAAMA/g8G AAAAHgABMAEAAAAlAAAAJ0NvbXB1dGF0aW9uYWwgQ2hlbWlzdHJ5IExpc3QgKENDTCknAAAAAAIB CzABAAAAHwAAAElOVEVSTkVUOkNIRU1JU1RSWUBDQ0wuT1NDLkVEVQAAAwAAOQAAAAALAEA6AQAA AB4A9l8BAAAAIwAAAENvbXB1dGF0aW9uYWwgQ2hlbWlzdHJ5IExpc3QgKENDTCkAAAIB918BAAAA LAAAAL8AAAC1O8LALHcQGqG8CAArKlbCFQAAAHjGk9CWGdIRpF8A4JgB2bHkgwAAAwD9XwEAAAAD AP9fAAAAAAIB9g8BAAAABAAAAAAAAAK6dAEEgAEAFgAAAE1hdGVyaWFscyBJbmZvcm1hdGljcwBB CAEFgAMADgAAAM8HAwATAAwAKwAiAAUASgEBIIADAA4AAADPBwMAEwAMACUADwAFADEBAQmAAQAh AAAAQUMyODA2ODZFN0RERDIxMUE0NUYwMEUwOTgwMUQ5QjEAJQcBA5AGAGgHAAAgAAAACwACAAEA AAALACMAAAAAAAMAJgAAAAAACwApAAAAAAADADYAAAAAAEAAOQAgkdUCMHK+AR4AcAABAAAAFgAA AE1hdGVyaWFscyBJbmZvcm1hdGljcwAAAAIBcQABAAAAFgAAAAG+cjAC1YYGKK7d5xHSpF8A4JgB 2bEAAB4AHgwBAAAABQAAAFNNVFAAAAAAHgAfDAEAAAAhAAAAa210YWtpdGFAa25vd2xlZGdlZm91 bmRhdGlvbi5jb20AAAAAAwAGEEhE010DAAcQYwQAAB4ACBABAAAAZQAAAFRIQU5LWU9VVE9BTExX SE9QUk9WSURFREhFTFBBTkRGRUVEQkFDS0lOREVWRUxPUElOR1RISVNQUk9HUkFNIkVGRkVDVElW RURBVEFNQU5BR0VNRU5URk9STkVXTUFURVJJQUwAAAAAAgEJEAEAAABFBAAAQQQAAKgGAABMWkZ1 GQKsSAMACgByY3BnMTI1FjIA+Atgbg4QMDMznQH3IAKkA+MCAGNoCsDgc2V0MCAHEwKDAFBjAvIQ 2VRhaANxAoB9swqACMggOwlvDjA1AoD5CoF1YwBQCwMLtRMgEQAQbmsgeQhgIHRvliAHQAMgdxNQ IHADYAR2aQEAZCBoZWwqcBgAbhkAZgngZGJXANAXgAuAIAEAdhkwb+pwC4BnF9BoBAAYggnAmGFt LgqiCoAiRQEgiQWQdGkakCBEYQGQ4wXQAHBhZ2UHgAIwGaB3BbEHwh1QdAZxB0AEIETHBAAFoBqQ cnk6G/QeiBxJbh4BAMAcsGNzIhEb9Ep1bhzgMjgtwDI5LCAxOSKwGjIoQm9zF+BuIoBNQX8b9B4C BGAJcBoxIOUCICBPETAc4AhhGEBlYiVgaakeoDogAzBjAEF1AyCCaAJAcDovL3cnkMAua25vd2wJ gB2QKwIQIfBkJRMuBaBtL+sktyFQLicgbQlQJrABQP8m8AFAHAMFsR2gC3AJUBwDlGttAZBrJkBh QCff/yjkGWMl8BhAAxADICtyF5PtHTBmJvADIGIDYBDwCHD+ZRvlF0Ac4AWgINAEkAnwXmMw8h9x BCADgXkloGY/GxEkkQQQClAEIC/hdWf5JyAgdRlQGkEysgnACGB8cC4GAANwJZEykxEwIN5xMyEl IgQgC4BjCkABAPEftSogSCzAF9IBAACQ+mcDoG0m8BywC1Ac4CER9x61KKEBoGERMAQgF+Q3gn8b sACACrEdwgDQB5A6BiDbCXAs4HYAcDtRcAtQDeB7JRM6AWgzcwhgBUAysmTvHzY3pBqTHbNwEQAR MDb9/wuAHqAboR6gPoIKsUHCPNnzJWAygHR3OxEigBlyGJXPJWABkCiRCyBpehjxB4AfGyAEcAQg MoEdYWx5ev8a4jmCNv0J8D0AI0AyowtwzxkAMoFDZhljc3kjQB2g7xtTGMIRIDb9YjXxO2E7g/xw dQJgDeBGcBgAPIADEH8BoDixJLsIYTuBG/Qb9El6ThgAZD6QJSJD4SVgcP8FkAcxJWEEECUyLpNM ABkS9xkAGkExEWoh8ByhUaMbIPcyozEZR+J4C1AkcjKyNfE7TaEEAGgds0YTGjFkdZ8jQD8BMRFD YAAgaXUuAO8kIx6XKVpPKlAs4DnRGaL/AyADUCWBF+ExEQGQHKBFgX8d8y+QACAZIAXAJLlZ21PX NnExUUZwLBv0SwdwTyqDFmUSIXMxNyAtYa+/Yr9jm193EyEsUhv0Vg3gfRzgUAlwAJABAAIwMHhL uSy2IEYodyKAIMBjG+X9D0AxBdAEkAUQAMEGADqwDwngZtUjKCaAMDIxMYo0G/Q2YXAtMzZsoOw3 OW0AVPF0NNAB0A5QA2w9DiAgKGZheCn9G/RFK3ImcCwfKF1PJSa/vyfPcbYqaxZrG/QTsQB3cAAA AAMAEBAAAAAAAwAREAAAAAADAIAQ/////0AABzBA3tcgL3K+AUAACDBA3tcgL3K+AQsAAIAIIAYA AAAAAMAAAAAAAABGAAAAAAOFAAAAAAAAAwACgAggBgAAAAAAwAAAAAAAAEYAAAAAEIUAAAAAAAAD AAWACCAGAAAAAADAAAAAAAAARgAAAABShQAAdBAAAB4ACYAIIAYAAAAAAMAAAAAAAABGAAAAAFSF AAABAAAABQAAADguMDIAAAAAAwAKgAggBgAAAAAAwAAAAAAAAEYAAAAAAYUAAAAAAAALABOACCAG AAAAAADAAAAAAAAARgAAAAAOhQAAAAAAAAMAFIAIIAYAAAAAAMAAAAAAAABGAAAAABGFAAAAAAAA AwAWgAggBgAAAAAAwAAAAAAAAEYAAAAAGIUAAAAAAAAeACWACCAGAAAAAADAAAAAAAAARgAAAAA2 hQAAAQAAAAEAAAAAAAAAHgAmgAggBgAAAAAAwAAAAAAAAEYAAAAAN4UAAAEAAAABAAAAAAAAAB4A J4AIIAYAAAAAAMAAAAAAAABGAAAAADiFAAABAAAAAQAAAAAAAAAeAD0AAQAAAAEAAAAAAAAAAwAN NP03AADszg== ------ =_NextPart_000_01BE7214.4A7D7180-- From chemistry-request@www.ccl.net Fri Mar 19 20:27:47 1999 From: "yongwen" To: Subject: Ask for biomacromolecular's modelling Date: Sat, 20 Mar 1999 09:21:39 +0800 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_001C_01BE72B3.0F6BFB80" X-Mailer: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 This is a multi-part message in MIME format. ------=_NextPart_000_001C_01BE72B3.0F6BFB80 Content-Type: text/plain; charset="gb2312" Content-Transfer-Encoding: quoted-printable Dear CCLs, I'm a chemistry researcher, but now I'm interested in = biomacromolecular's modelling. That is, I want to predict the secondary = structure, tertiary structure of the proteins, DNA, RNA from their lower = structure.=20 Can anybody give me some reference? Any kindly information I'll be = appreciated. ------=_NextPart_000_001C_01BE72B3.0F6BFB80 Content-Type: text/html; charset="gb2312" Content-Transfer-Encoding: quoted-printable
Dear CCLs,
 
    I'm a chemistry = researcher,=20 but now I'm interested in biomacromolecular's modelling. That is, I want = to=20 predict the secondary structure, tertiary structure of the proteins, = DNA, RNA=20 from their lower structure.
 
    Can anybody give = me some=20 reference? Any kindly information I'll be appreciated.
 
------=_NextPart_000_001C_01BE72B3.0F6BFB80-- From chemistry-request@www.ccl.net Sat Mar 20 00:27:21 1999 From: "Kalju Kahn" Date: Fri, 19 Mar 1999 21:21:43 -0800 X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: chemistry@www.ccl.net Subject: SUMMARY: BSSE in calc. of activation energies Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hello, everyone. Is about month now from the day I posted my initial question. Thanks for good responses, I think I learned a lot about this subject. Sorry to be so slow in responding, had to wait to get some literature and then wait even more until I understood some problems with BSSE. Of course, as many of you noticed, my original equation was incorrect because I assumed that there is no geometrical changes in reactant geometries during the TS formation. Kalju. Original question was: ######################################################### From: Kalju Kahn kalju@bioorganic.ucsb.edu ########################## I realize there has been some controversy about basis set superposition error (BSSE), and that the current consensus favors the view that full counterpoise procedure (CP) of Boys and Bernardini is a good way to correct for BSSE. (e.g. van Duijneveldt et. al. in Chem. Rev, 1994, 94, 1873-1885) My question concerns application of BSSE correction via CP to bimolecular reactions. Let's take gas phase SN2 displacement as an example. Here we have a two reactants, A and B, forming first a bimolecular "reactants complex" (RC), followed by transition state (TS): A + B -> (A...B)[RC] -> A-B[TS] The activation barrier can be defined as an energy difference between TS and RC. What is the correct way to calculate this energy difference? (Assuming Born-Oppenheimer approximation, and dealing with size-consistent methods, e.g. HF level of theory) My own answer would be: If one accepts a view that energies of both RC and TS (relative to isolated reactants) are affected by BSSE, one should correct both according to the CP scheme, and now: E_act = E(TS,TS_basis_in_TS_geometry)-E(RC,RC_basis_in_RC_geometry)- E(A,TS_basis_in_TS_geometry) -E(B,TS_basis_in_TS_geometry)+ E(A,RC_basis_in_RC_geometry) +E(B,RC_basis_in_RC_geometry) Obviously, the number of basis functions in TS_basis and RC_basis is the same, but the geometrical position of ghost orbitals relative to partner molecule are different in TS_geometry and RC_geometry. So, the last four terms do not cancel out. This seems a right way to account for BSSE, but the above method was quoted as "misinterpretation of the BSSE concept" by Dr. J. A. Sordo in "Comment on "Ab initio investigation of internal rotation in the ethylene-sulfur dioxide dimer"" (J. Chem. Phys., 106(14), 6204). Could somebody kindly explain me how do I misinterpret the BSSE concept here? Or do we need to be concerned about BSSE when calculating ab initio activation barriers? %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Summary of answers, stripped off from headers and tails: ########################################################################## From: Frank Jensen ##################### I am not familiar with that paper, but my opinion is similar to yours, there is always a BSSE present when comparing calculations using different geometries. For non-bonded interactions, as your RC, the CP procedure is well-defined. For bonded species, however, the CP procedure is much less clear. You may be interested in the results in Chem. Phys. Lett. 261, 633. Frank ########################################################################## From: Pr. Xavier Assfeld assfeld@host23.lctn.u-nancy.fr ############################## To be rigorous, you forget to take into account the energy of geometrical deformation, i.e. : Your_formula + E(A,A_basis_in_TS_geometry) - E(A,A_basis_in_RC_geometry) + E(B,B_basis_in_TS_geometry) - E(B,B_basis_in_RC_geometry) Moreover, Pr. Sordo et al. publish some papers about BSSE for this kind of systems, showing that Delta_E_act is almost BSSE free : 1] J. A. Sordo, J. Chem. Phys. 1997, 106, 6204 2] V. M. Rayon, and J. A. Sordo, J. Phys. Chem. 1997, 107, 7591 3] D. Suarez, and J. A. Sordo, Chemical Communications, 1998, 3, 385 I also would like to point out that there are other (better) methods to evaluate BSSE than couterpoise. For exemple have a look at the work of Istvan MAYER about the Chemical Hamiltonian Approach. There is plenty of papers dealing with that but here is a "recent" reference : I. Mayer, and P. Valiron, J. Chem. Phys. 1998, 109, 3360. ######################################################################### From: Huub van Dam h.j.j.vandam@chem.ruu.nl ######################## COUNTERPOISE recipe for complexes of monomers with internal geometry Ra : geometry of monomer A in complex Rae : geometry of monomer A in its equilibrium Rb : geometry of monomer B in complex Rbe : geometry of monomer B in its equilibrium R, distance (geometrical parameters) between A and B e.g. Ea(R,Ra,Rb)(AB) is the energy of A at geometry defined by (R,Ra,Rb) and the basis of AB Generally a complete counterpoise corrected interaction energy is : Delta E = Eab(R,Ra,Rb)(AB) - Ea(R,Ra,Rb)(AB) - Eb(R,Ra,Rb)(AB) + Ea(Ra)(A) - Ea(Rae)(A) + Eb(Rb)(B) -Eb(Rbe)(B) The first line gives the counterpoise corrected interaction energy as it would be for rigid monomers; The second gives the correction for the deformation of the monomers Applying this to a transition state (TS) and reaction complex (RC) gives for a interaction energy with respect to isolated monomers for both : Delta E-TS= Eab(R-TS,Ra-TS,Rb-TS)(AB) - Ea(R-TS,Ra-TS,Rb-TS)(AB) - Eb(R-TS,Ra-TS,Rb-TS)(AB) + Ea(Ra-TS)(A) - Ea(Rae)(A) + Eb(Rb-TS)(B) -Eb(Rbe)(B) Delta E-RC= Eab(R-RC,Ra-RC,Rb-RC)(AB) - Ea(R-RC,Ra-RC,Rb-RC)(AB) - Eb(R-RC,Ra-RC,Rb-RC)(AB) + Ea(Ra-RC)(A) - Ea(Rae)(A) + Eb(Rb-RC)(B) -Eb(Rbe)(B) To get the barrier one have to substract the two : Delta E-TS - Delta E-RC = Eab(R-TS,Ra-TS,Rb-TS)(AB) - Eab(R-RC,Ra-RC,Rb-RC)(AB) - Ea(R-TS,Ra-TS,Rb-TS)(AB) - Eb(R-TS,Ra-TS,Rb-TS)(AB) + Ea(R-RC,Ra-RC,Rb-RC)(AB) + Eb(R-RC,Ra-RC,Rb-RC)(AB) + Ea(Ra-TS)(A) + Eb(Rb-TS)(B) - Ea(Ra-RC)(A) - Eb(Rb-RC)(B) Where the last two lines (the extra part) is due to a different deformation in transition state and reaction complex See : F.B. van Duijneveldt "Basis Superposition Error" in : S. Scheiner (ed.) , "Molecular Interactions" Wiley (1997) ########################################################################## From: Tanja van Mourik T.vanMourik@ucl.ac.uk ##################### I think that your way to correct for BSSE is correct, assuming at least that BSSE is only important *between* (and not within) A and B, as it is in my ArHF example below. If you would calculate your energy difference simply as: E_act = E(TS,TS_basis_in_TS_geometry)-E(RC,RC_basis_in_RC_geometry) then you would not correct for BSSE at all! Assuming the BSSE within the monomers can be neglected, you can compare with a diatomic AB (like He2, for example). In this case, you also have to correct for BSSE at each individual point of the potential energy curve. Simply substracting two AB dimer energies does not produce a BSSE-free energy difference, since the uncorrected potential energy curve will be distorted. Also in this case, for each different interatomic distance the ghost orbitals are at different geometrical positions. As another example: For ArHF, which has 2 linear minima and a T-shaped TS, the correct way to compute the stationary points would be, in my opinion, to substract from the dimer energy the Ar and HF energies computed in the ArHF basis set, and you would do this for the 2 different minima (Ar...HF and Ar...FH), as well as for the TS. The barrier height is then the difference between the minimum and TS interaction energy. This of course assumes that the BSSE within HF can be neglected. For this example, I can reference 2 papers (I must confess I am on the author list of both): JCP 107, 2451 (1997) and Adv. Quant. Chem. 31, 105, 1999. You already mentioned the review article by van Duijneveldt et al. ########################################################################## From: Qadir K. Timerghazin qt@chat.ru ########################## See good article on this subj: Some difficulties in computing BSSE-corrected potential surfaces of chemical reactions. G. Lendvay 1 , I. Mayer Chemical Physics Letters 297 1998 365–373 May be you'll find there some answers on questions you put. ########################################################################## From: liang@wavefun.com ####################### The AE is calculated between the TS1 and P1 structures, using the SAME basis set (Sordo's eq1), therefore no CP is needed. CP is needed when calculating, say, the P1(A..B) energy relative to the fragments (A and B) where P1 has the functions on BOTH fragments. ########################################################################## From: Steven.Creve Steven.Creve@dsm-group.com ########################## Hello, Maybe it would be interesting to come to a generalized view of BSSE procedures, and summarize that to the list. ########################################################################## %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% This is almost all, neglecting two private responses. What follows is my attept to come up with a generalized view on BSSE and CP correction in particular. I am not competent to discuss methods which exclude BSSE a priori (Chemical Hamiltonian Approach and Symmetry Adapted Perturbation Theory), and these apparently are not applicable for activation energies. 0. BSSE is not specific to molecular complexes. It affects geometries and energies of individual molecules when nuclei-centered basis sets are used. The effects on bond lengths are small but BSSE could affect the conformation of flexible molecule (Extra stabilization occurs when ends of the chain are next to each other) 1. The energy difference between the reactant complex and the transition state is affected by BSSE. I am not convinced that Delta_E_act is almost BSSE free. 2. The interaction energy can be partitioned into two components: (i) intermolecular interaction energy between two deformed reactants (ii) energy associated with deformation of isolated reactants. My initial equation neglected deformatiion energy, this is equal to assuption that reactants do not change geometry upon formation of reactant complex or transition state. While deformation of monomers may be negligable in reactant complex, it is very significant in the transition state. Assuming that there is no BSSE associated with deformation of monomers, the CP equation is: E_act = E(TS,TS_basis_in_TS_geometry)- E(RC,RC_basis_in_RC_geometry)- E(A,TS_basis_in_TS_geometry) - E(B,TS_basis_in_TS_geometry) + E(A,RC_basis_in_RC_geometry) + E(B,RC_basis_in_RC_geometry) + E(A, A_basis_in_TS_geometry) - E(A, A_basis_in_RC_geometry) + E(B, B_basis_in_TS_geometry) - E(B, B_basis_in_RC_geometry) or, rearranged: E_act = E(TS,TS_basis_in_TS_geometry)- E(RC,RC_basis_in_RC_geometry)+ E(A, A_basis_in_TS_geometry) - E(A,TS_basis_in_TS_geometry) + E(B, B_basis_in_TS_geometry) - E(B,TS_basis_in_TS_geometry) + E(A,RC_basis_in_RC_geometry) - E(A, A_basis_in_RC_geometry) + E(B,RC_basis_in_RC_geometry) - E(B, B_basis_in_RC_geometry) It is not clear how important is BSSE in the deformation process E_def(A) = E(A,A_basis_in_TS_geometry) - E(A,A_basis_in_RC_geometry) Neither it is clear how to calculate BSSE for a deformation process. And, Rayon and Sordo (Theor. Chem. Acc. 99, 68-70(1998) have argued that when geometrical changes in fragments are large (as they are in formation of TS), then one should be careful when performing CP. 3. There appear to be serious conceptual difficulties when applying two-body CP correction to bimolecular reaction where group or atom is being transfered. The paper by Lendvay and Mayer (Chem. Phys.Lett. 297, 365-373) points out that assignement of transferred group to reactants becames ambiguous in TS, and different assignements will generally give different results. 4. From a practical point of view it could be better to ignore BSSE completery in calculation of activation energies. The arguments in favour of this neglect are: 1) There are conceptual probles with performing BSSE correction (BSSE in deformation energies and p.3) 2) The BSSE may not be too big compared to the current accuracy of describing transition states. This is probably fine when E_act is large. 3) Correcting for BSSE by CP scheme involves four additional calculations using the large basis set and four additional calculations using smaller basis sets. No correction requires only two calculations with large basis sets (RC and TS). 5. Ignoring BSSE in TS calculations is expected to yield too tight transition states (in analogy with too short intermolecular distances on uncorrected potential energy surfaces between two reactants). Does anybody know of BSSE free (Chemical Hamiltonian Approach, or very large basis set LCAO) determinations of TS structures to evaluate this statement? 6. Ignoring BSSE in TS calculations is expected to yield too low activation energies. BSSE in TS is larger than BSSE in RC since the two fragments are closer. I have very crude estimate for the MP2/AUG-cc-pVDZ basis set and RCl-HOH system, according to this BSSE near RC is about 0.6 kcal/mol and near TS about 2.6 kcal/mol. So the activation energy is underestimated by about 2 kcal/mol. (Note: these numbers have nothing to do with Sn2 displacement reaction, I havn't studied it). This underestimation is not terrible at HF level, since RHF activation energies are generally overestimated. 7. Some recent papers about BSSE: *Introduction to Computational Chemistry, pg. 172, Frank Jensen, Wiley, 1999 *Basis set superposition error, F.B. van Duijneveldt, in "Molecular Interactions", ed. S. Scheiner, Wiley, 1997 (These two still disagree whether CP is an approximate way or the method to deal with BSSE in weakly interacting molecular complexes) *Ab initio Calculations on Uracil-Water, van Mourik et al, J. Phys. Chem. A 103, 1611-1618 (1999). (Neat example of manual optimization to get a BSSE-free potential energy surface). *Comparison of basis set superposition error corrected perturbation theories for calculating intermolecular interaction energies. J. Comp. Chem. 20(2):274-283, 1999 (BSSE is significant at correlated levels) *On the validity of the counterpoise correction for the basis set superposition error including fragment relaxation terms Rayon & Sordo, Theor. Chem. Acc, 99, 68-70 (1998) (CP not valid) *Some difficulties in computing BSSE-corrected potential surfaces of chemical reactions. Lendvay & Mayer, Chem. Phys. Lett. 297, 365-373 (1998) (CP correction results in discontinuous PES) ****************************************************************** Kalju Kahn kalju@bioorganic.ucsb.edu Chemistry Department tel: (805)-893-7158 University of California Santa Barbara Santa Barbara, CA 93106 ################################################################## From chemistry-request@www.ccl.net Sat Mar 20 03:37:19 1999 From: "yongwen" To: Subject: MOL2 file format Date: Sat, 20 Mar 1999 16:37:04 +0800 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0028_01BE72EF.E30EC9E0" X-Mailer: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 This is a multi-part message in MIME format. ------=_NextPart_000_0028_01BE72EF.E30EC9E0 Content-Type: text/plain; charset="gb2312" Content-Transfer-Encoding: quoted-printable Dear CCLs, =20 Does anybody know the file format of SYBYL MOL2? I hope the detailed = document. Thanks in advance. sincerely, yongwen (yyw_j@263.net) ------=_NextPart_000_0028_01BE72EF.E30EC9E0 Content-Type: text/html; charset="gb2312" Content-Transfer-Encoding: quoted-printable
Dear CCLs,
 
    Does anybody know the file format = of SYBYL=20 MOL2? I hope the detailed document. Thanks in advance.
 
sincerely,
yongwen (yyw_j@263.net)
------=_NextPart_000_0028_01BE72EF.E30EC9E0-- From chemistry-request@www.ccl.net Sat Mar 20 05:37:50 1999 Date: Sat, 20 Mar 1999 12:40:06 +0200 From: mehmet kabak X-Mailer: Mozilla 4.5 [en] (Win98; I) X-Accept-Language: tr MIME-Version: 1.0 To: Computational chemistry List Subject: How to import your HPGL files to Microsoft Office Progs. References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL's I hope importing HPGL files into your document would be profitable for MS users. First download the HPGL32.EXE files from the Microsoft ftp site via ftp or other methods (ftp.microsoft.com/Softlib/MSLFILES/HPGL32.EXE) to your location(s). Then double click (or run) the HPGL32.EXE file from your Windows Explorer (or from the Start button) and follow the information (accept Microsoft Licence agreement). Put your extracted graphic filters files under the "Program Files\Common Files\Microsoft Shared\Grphflt\" directory. Then from the "Start" button select "Run" and call the "Regedit" program and select the "Registery File/Import Registry File" from the menu. Go directly in to the files which were you located "C:\Program Files\Common Files\Microsoft Shared\Grphflt\". Follow the instruction and then exit from the registry editor. Now the Microsoft programs are ready for the filtering the HPGL graphic files. Best regards, Mehmet Kabak e-mail : kabak@science.ankara.edu.tr PS: For any questions please mail me and I will not accept any responsibility for any damage to your Windows programs and system. From chemistry-request@www.ccl.net Sat Mar 20 15:39:46 1999 Message-Id: <3.0.32.19990320173856.00947aa0@lua.ifi.unicamp.br> X-Sender: dasf@lua.ifi.unicamp.br X-Mailer: Windows Eudora Pro Version 3.0 (32) Date: Sat, 20 Mar 1999 17:38:57 -0300 To: CHEMISTRY@www.ccl.net From: "=?iso-8859-1?Q?=22Dem=E9trio_A._da_Silva_Filho=22?=" Subject: MOLDEN AND G94 OUTPUTS Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by www.ccl.net id PAA10051 Dear CCLers, I'm trying to read the G94 outputs using MOLDEN and although I have several geometries MOLDEN just show me one (single point). I already add the keywork gfinput and IOP(6/7=3) as MOLDEN requires but I didn't have success. Any hints will be appreciated. Thanks, Demétrio Filho _____________________________________ Demetrio A. da Silva Filho UNICAMP - IFGW Prédio D - Sala 17 CEP 13083-970 C.Postal 6165 Campinas - SP - Brasil _____________________________________ "The time it takes to complete a scientific project is given by the equation t = 2a + b where a is the original estimate, 2 is a correction factor, and b is a number large compared to 2a." From chemistry-request@www.ccl.net Sat Mar 20 17:23:57 1999 Sender: xiaomei@ne059.cm.utexas.edu Message-Id: <36F41D9A.41C6@usa.net> Date: Sat, 20 Mar 1999 16:13:46 -0600 From: Xiaomei Yang Organization: Dept of Chem & Biochem X-Mailer: Mozilla 3.01Gold (X11; I; AIX 2) Mime-Version: 1.0 To: CCL Subject: Summary: convert PDB to CHARMm Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, CCLers, My original question on how to convert PDB file to CHARMm format seemed ridiculous, but I was in a situation without QUANTA/CHARMm in hand. Anyway, many thanks to all the people who answered my question and gave me helpful information. Now the summary. How to convert PDB files to CHARMm format ========================================= 1. CHARMm 2. QUANTA 3. RasMol 4. Babel 5. your own code 1. CHARMm itself can read PDB files and convert to CRD/PSF format. <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< as suggested by G. Matthias Ullmann Ryszard Czerminski dmacks@sas.upenn.edu (Daniel E. Macks) Shobana Sundaram ) ------------------------------------------------ open read unit 12 card name "1rie.protein.pdb" read sequ pdb unit 12 generate 1rie setup rewind unit 12 read coor pdb unit 12 close unit 12 But you should read only one straint at once. If you have more than one straint, repeat the command like this: open read unit 12 card name "1rie.hetero.pdb" read sequ pdb unit 12 generate fes setup rewind unit 12 read coor pdb unit 12 appe close unit 12 You have to edit the PDB file a little bit, so that it look like ATOM 1 N THR 53 15.450 0.804 17.223 1.00 15.05 1rfs ATOM 2 CA THR 53 14.080 0.730 16.642 1.00 15.16 1rfs ATOM 3 C THR 53 14.002 1.723 15.471 1.00 14.32 1rfs ATOM 4 O THR 53 14.581 2.805 15.549 1.00 14.38 1rfs ATOM 5 CB THR 53 13.011 1.058 17.715 1.00 16.16 1rfs ATOM 6 OG1 THR 53 13.161 2.411 18.160 1.00 18.16 1rfs ATOM 7 CG2 THR 53 13.171 0.139 18.916 1.00 16.08 1rfs ATOM 8 1H THR 53 15.677 1.830 17.297 1.00 0.00 1rfs ATOM 9 2H THR 53 15.484 0.373 18.153 1.00 0.00 1rfs ATOM 10 3H THR 53 16.137 0.366 16.590 1.00 0.00 1rfs ATOM 11 HG1 THR 53 13.847 2.552 18.821 1.00 0.00 1rfs The string in the last column has to be the segid. Otherwise you can not read the coordinates properly. ----- End of Example 1. Example 2: ========== (by Shobana Sundaram ) ----------------------------------------------------- open read card unit 10 name a.pdb ('your filename') read coor pdb unit 10 close unit 10 if you want only the coordinates to be written open write unit 11 card name a.crd write coor unit 11 card * title * and if you want to write in psf format which included connectivities etc.. write psf card name a.psf * title * ----- End of Example 2 2. QUANTA - the Graphical User Interface for CHARMm can of course do this. <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< as suggested by dmacks@sas.upenn.edu (Daniel E. Macks) Istvan Enyedy" Shobana Sundaram 3. RasMol can read both PDB and CHARMm formats <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< as suggested by Rick Venable RasMol can export the current image to various graphical formats, such as gif, bmp, ps; but it is not clear if it can re-write the structure into any formats other than the input one. (Xiaomei) 4. Babel reads both PDB and CHARMm formats but doesn't write to CHARMm format. <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< 5. Write you own code <<<<<<<<<<<<<<<<<<<<< as suggestd by Themis Lazaridis (aldo jongejan) Themis gave me his little code that helped me to accomplish my job in time. Thanks. Example 3: ========== (by Themis Lazaridis ) ----------------------------------------------- Themis Lazaridis Department of Chemistry phone (212) 650-8364 City College of New York fax (212) 650-6107 Convent Avenue & 138th St. email: themis@sci.ccny.cuny.edu New York, NY 10031 http://www.sci.ccny.cuny.edu/~themis ---------------------- c Reads PDB file, writes out charmm file c Uses a temp file c PDB format c text IATOM TYPE RES IRES X Y Z W c A6 I5 2X A4 A4 I5 4X 3F8.3 6X F6.2 c charmm format c ATOMNO RESNO RES TYPE X Y Z SEGID RESID Weighting c I5 I5 1X A4 1X A4 F10.5 F10.5 F10.5 1X A4 1X A4 F10.5 c c character*80 infile,outfile,line character*4 str1,type,res,code,segid,resid,residold,resold character*1 chain logical loxt(1000) write (6,*) 'Give input PDB files, output will be .crd' 1 read (5,'(a)') infile i=1 2 i=i+1 if (infile(i:i).eq.' ') then outfile=infile(1:i-1)//'.crd' else goto 2 endif open (unit=11, file=infile, status='old') open (unit=12, file='temppdb', status='unknown') open (unit=13, file=outfile, status='new') write (13,'(a80)') '* converted from '//infile write (13,'(a)') '*' do 4 i=1,1000 4 loxt(i)=.false. nss=0 ires=0 iat=0 residold=' ' resold=' ' do 100 i=1,100000 read (11,'(a80)',end=1000) line read (unit=line,fmt=500) str1 if (str1.eq.'SSBO') then nss=nss+1 goto 100 else if (str1.eq.'ATOM') then iat= iat+1 read (unit=line,fmt=500) str1,iatom,type,res,chain,resid, & x,y,z,a,w,code 500 format (a4,2x,i5,2x,a4,a4,a1,a4,4x,3f8.3,2f6.2,6x,a4) if ((resid.ne.residold).or.(res.ne.resold)) ires=ires+1 residold=resid resold= res if (chain.ne.' ') then segid=chain//code elseif (code.ne.' ') then segid=code else segid='MAIN' endif if (type.eq.'CD1 ') then if (res.eq.'ILE ') type='CD ' elseif (type.eq.'OCT1') then type='OT1 ' elseif (type.eq.'OCT2') then type='OT2 ' elseif (type.eq.'OXT ') then type='OT2 ' loxt(ires)=.true. endif c fluch resid left 5 if (resid(1:1).eq.' ') then resid=resid(2:4)//' ' goto 5 endif write (12,600) iat,ires,res,type,x,y,z,segid,resid,w 600 format (I5,I5,1X,A4,1X,A4,3F10.5,1X,A4,1X,a4,F10.5) else goto 100 endif 100 continue 1000 write (6,*) 'Disulfide bonds', nss nres=ires write (13,'(i5)') iat close (unit=12) open (unit=12,file='temppdb',status='old') do 200 i=1,100000 read (12,'(a80)',end=2000) line read (unit=line,fmt=600) iatom,ires,res,type,x,y,z,segid,resid,w if (loxt(ires).and.(type.eq.'O ')) type='OT1 ' write (13,600) iatom,ires,res,type,x,y,z,segid,resid,w 200 continue 2000 close (unit=11) close (unit=12) close (unit=13) goto 1 end ----- End of Example 3 -----End of Summary ////////////////////// Xiaomei Yang, Postdoc Dept of Chem & Biochem Univ of Texas at Austin Austin, 78712 TX, USA Tel: +1-512-471-4671 (O) xiaomei@ne059.cm.utexas.edu ///////////////////////////// From chemistry-request@www.ccl.net Mon Mar 22 16:38:46 1999 Received: from iacgu7.chemie.uni-mainz.de (root@iacgu7.Chemie.Uni-Mainz.DE [134.93.136.23]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id QAA05082 Mon, 22 Mar 1999 16:38:40 -0500 (EST) Received: from localhost (renee@localhost) by iacgu7.chemie.uni-mainz.de (8.8.5/8.8.5) with SMTP id TAA12436 for ; Mon, 22 Mar 1999 19:34:59 +0100 Date: Mon, 22 Mar 1999 19:34:58 +0100 (CET) From: Renee Dillinger To: chemistry@www.ccl.net Subject: G xyz to Z-matrix conversion Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I have a set of cartesian coordinates describing a molecule in C2h symmetry. In order to perform a Potential energy surface scan in Gaussian I have to convert the cartesian coordinates to a Z-Matrix. When I do that using different programs the resulting Z-Matrix is always C1 symmetry. So How can I convert the cartesian coordinates to a Z-Matrix with conservation of symmetry ?? Greetings Renee --- ****************************************************** Renee Dillinger Inst. f. Anorg. und Analyt. Chemie Universitaet Mainz Staudinger Weg 9 55099 Mainz Tel. 49-06131-393250 Fax. 49-06131-392990 From chemistry-request@www.ccl.net Mon Mar 22 16:57:18 1999 Received: from alchemy.chem.utoronto.ca (alchemy.chem.utoronto.ca [142.150.224.224]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id QAA05148 Mon, 22 Mar 1999 16:57:07 -0500 (EST) Received: (from elewars@localhost) by alchemy.chem.utoronto.ca (8.9.3/8.9.3) id NAA28022 for chemistry@www.ccl.net; Mon, 22 Mar 1999 13:42:41 -0500 (EST) Date: Mon, 22 Mar 1999 13:42:41 -0500 (EST) From: "E. Lewars" Message-Id: <199903221842.NAA28022@alchemy.chem.utoronto.ca> To: chemistry@www.ccl.net Subject: CBS AND G2 FAILURE-SUMMARY; THANKS 1999 March 22 CBS and G@ METHODS FAILING Thankd to all who replied to my question (below) about problems with CBS and G2 methods. I give a summary of the answers Again, thank you all. E Lewars ================== THE QUESTION: 1999 March 14 Hello, I find that the high-accuracy G2-type (G2, G2MP2 etc) and CBS (CBS-4, CBS-Q) methods, as implemented in Gaussian 94 and Gaussian 98, useful as they are, fairly frequently fail because of convergence problems. G92MP2 fails in step 5, and CBS-Q and CBS-4 in step 4, that is, after wasting hours on several previous steps. If others have had this problem with G2 and CBS methods and found a solution, I would very much appreciate hearing what it is. Thank you. E. Lewars ========================== THE ANSWERS #1 Mar 14 Giovanni Scalmani (52) Re: CCL:G:G2 AND CBS METHODS: CONVECommand: Read MessageMessage 3/10 from Giovanni Scalmani Mar 14 '99 at 6:28 pm X-Sender: Giovanni@jack.umh.ac.be Subject: Re: CCL:G:G2 AND CBS METHODS: CONVERGENCE FAILURES On Sun, 14 Mar 1999, E. Lewars wrote: > I find that the high-accuracy G2-type (G2, G2MP2 etc) and CBS (CBS-4, > CBS-Q) methods, as implemented in Gaussian 94 and Gaussian 98, useful as they > are, fairly frequently fail because of convergence problems. G92MP2 fails in > step 5, and CBS-Q and CBS-4 in step 4, that is, after wasting hours on several > previous steps. Hi! You are not talking about the SVD (singular value decomposition) in link 803, aren't you? (I don't remenber the exact sequence of steps). Anyway, once I had problems with CBS-Q and - even worse - with CBS-APNO. They failed "after wasting hours" during SVD. So I modified the code to use the LAPACK SVD routine (DGESVD) instead of the original one and since then I never had a new failure (at least in l803.exe). Hope this help. Giovanni PS: Let me know if this is your case. I may provide you the modification to l803.F ---------------------------------------------------------------------- Scalmani Giovanni Giovanni@averell.umh.ac.be Service de Chimie des Materiaux Nouveaux Centre de Recherche en Electronique et Photonique Moleculaires Universite' de Mons-Hainaut Place du Parc, 20 Phone: ++32-(0)65-373361 B-7000 Mons (Belgium) Fax: ++32-(0)65-373367 ---------------------------------------------------------------------- ============== #2 Subject: RE: G:G2 AND CBS METHODS: CONVERGENCE FAILURES Date: Mon, 15 Mar 1999 08:38:44 +1000 Greetings,... >I find that the high-accuracy G2-type (G2, G2MP2 etc) and CBS (CBS-4, >CBS-Q) methods, as implemented in Gaussian 94 and Gaussian 98, useful as they >are, fairly frequently fail because of convergence problems. G92MP2 fails in >step 5, and CBS-Q and CBS-4 in step 4, that is, after wasting hours on several >previous steps. I'm not sure what 'Step 5' is in a 'G2' calculation as implemented in G94, however, I suspect it is the QCISD calculation, something I have much experience with (convergence problems that is). The best alternative is to replace the QCISD(T) with CCSD(T). Regards,... Brian. ________________________________________________________________ | Dr Brian J. Smith | | Research Scientist | | Biomolecular Research Institute | | 343 Royal Parade Ph: +61-3-9662-7289 | | Parkville, VIC 3052, Fax: +61-3-9662-7347 | | Australia WWW http://www.bioresi.com.au/index.htm | |________________________________________________________________| ============= #3 X-Sender: theis@kalium.kiku.dk X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.6 (32) Date: Mon, 15 Mar 1999 09:44:48 +0100 To: elewars@alchemy.chem.utoronto.ca Subject: CBS and G2 Dear Prof. Lewars, In problem cases I usually run the jobs separately. For G2(MP2) method this gives me the possibility of converging the SCF (using SCF=qc) in the MP2/6-311+(3df,2p) calculation. On the other hand, the CBS extrapolation convergence problems appear to be hard ware dependent, switching to different hard ware brand have helped in all my problem cases. In the end I collect the results in a spread sheet. When the implemented method crashes in the final step, the results from the earlier steps can also be extracted in this manner. Thus, re-running the job can be avoided. Cheers, Theis ** ** ** ** Mr. Theis Ivan Solling ** ** ** ** ** Department of Chemistry ****** ****** University of Copenhagen ** ** ** DK-2100 Copenhagen ** ** ** Ph. 45-3532-0187/Fax. 45-3532-0212 =========== From chemistry-request@www.ccl.net Mon Mar 22 20:07:02 1999 Received: from oxmail.ox.ac.uk (oxmail3.ox.ac.uk [163.1.2.9]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id UAA06183 Mon, 22 Mar 1999 20:06:58 -0500 (EST) Received: from ermine.ox.ac.uk ([163.1.2.13]) by oxmail.ox.ac.uk with esmtp (Exim 2.10 #1) id 10P3aK-0005MM-00 for CHEMISTRY@www.ccl.net; Mon, 22 Mar 1999 12:13:36 +0000 Received: from oums0054 (helo=localhost) by ermine.ox.ac.uk with local-smtp (Exim 2.12 #1) id 10P3aK-0003zK-00 for CHEMISTRY@www.ccl.net; Mon, 22 Mar 1999 12:13:36 +0000 Date: Mon, 22 Mar 1999 12:13:35 +0000 (GMT) From: "Ivan I. Oleinik" To: CHEMISTRY@www.ccl.net Subject: Gaussian-98 efficiency for DFT calculations Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, I am a novice user of Gaussian and want to have a good advice from experts on tuning Gaussian-98 options to get best performance in terms of CPU time. Some specific information: 1. Molecular system: medium-size hydrocarbon clusters (20-30 carbon atoms) 2. Method: DFT (standard LSDA + Becke-Perdew-Wang gradient corrections). 3. Task: energy and forces with moderate accuracy. 4. System: SGI O2K machine with plenty of memory available. I can get trivial speedup by using several processors in parallel mode, but I want to tune the execution on the level of single processor first. Also the effect of the basis set size is also obvious and predictable. Since I have to sample quite a large number of configurations studying transition states, I have to count every CPU minute. But I according to my little experience Gaussian is still slow as compared to MSI DMOL. I will summarize responses, Ivan Oleinik. ------------------------------------------------------------------------ Ivan I. Oleinik E-mail : ivan.oleinik@materials.ox.ac.uk Department of Materials University of Oxford Parks Road Oxford OX1 3PH Tel : +44 (0)1865 283325 United Kingdom Fax : +44 (0)1865 273764 ------------------------------------------------------------------------