From yubofan@guomai.sh.cn Sun Dec 14 22:40:21 1997 Received: from guomai.sh.cn for yubofan@guomai.sh.cn by www.ccl.net (8.8.3/950822.1) id WAA16583; Sun, 14 Dec 1997 22:06:29 -0500 (EST) Received: from fgtao (Email-37 [210.0.0.5]) by guomai.sh.cn (8.8.8/8.8.8) with SMTP id LAA07875 for ; Mon, 15 Dec 1997 11:04:55 +0800 (CST) Message-Id: <3.0.3.32.19971215110701.007aa490@guomai.sh.cn> X-Sender: yubofan@guomai.sh.cn (Unverified) X-Mailer: QUALCOMM Windows Eudora Pro Version 3.0.3 (32) Date: Mon, 15 Dec 1997 11:07:01 +0800 To: CHEMISTRY@www.ccl.net From: Yubo Fan Subject: Gaussian 94 option MP2=InCore Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Hi, I tried MP2=InCore option several times in these days. G94W always told me the computer was short of memory. After I changed memory into 8000000 in the file named default.rou, I got the result of short of 8000000. When I changed into 16000000, 16000000 short. What's the problem? Y. Fan From comartin@wicc.weizmann.ac.il Mon Dec 15 04:40:28 1997 Received: from winston.weizmann.ac.il for comartin@wicc.weizmann.ac.il by www.ccl.net (8.8.3/950822.1) id EAA18868; Mon, 15 Dec 1997 04:10:37 -0500 (EST) Received: from localhost by winston.weizmann.ac.il; (5.65v3.2/1.1.8.2/28Jul95-1212AM) id AA03995; Mon, 15 Dec 1997 11:10:04 +0200 Date: Mon, 15 Dec 1997 11:10:04 +0200 (IST) From: "Jan M.L. Martin" X-Sender: comartin@winston.weizmann.ac.il Reply-To: "Jan M.L. Martin" To: CHEMISTRY@www.ccl.net Subject: CCL: PhD/Postdoc position(s) available at Weizmann Institute Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII TWO PH.D. OR POSTDOC POSITIONS AVAILABLE IN QUANTUM/COMPUTATIONAL CHEMISTRY at the Weizmann Institute of Science ============================================================================ The newly established Computational Chemistry research group at the Weizmann Institute of Science (Rechovot, Israel) is looking for two Ph.D. student or postdocs: Position (1): research in the framework of a Minerva project on computational study of organometallic homogenous catalysts, including some light methodological work in the area of ab initio calculations on transition metal complexes. The work involves interaction with a high-profile experimental synthetic group (of Prof. David Milstein, same department). Suitable candidates should either have a background in organometallic chemistry and a willingness to learn computational methods, or be computational chemists interested in working on organometallics. Position (2): methodological research in the area of very accurate ab initio calculations of structural, spectroscopic, and thermodynamic properties of small molecules, including anharmonic force fields. (Some flexibility of research exists for this position.) Suitable candidates should have a background in chemical physics, computational chemistry, or molecular spectroscopy. Programming skills (preferably Fortran) are an asset. Fluency in English (not necessarily mother tongue level) is essential. (Supervisor also speaks French, Dutch, German, and "new immigrant" Hebrew.) Assets for both positions are: * good computer skills (Unix, Macintosh) * aptitude for scientific writing and reporting in English * ability to work creatively and with some degree of independence Applicants for a Ph.D. level position should satisfy the admission requirements to the Ph.D. Program of the Feinberg Graduate School, full details of which are available at http://www.weizmann.ac.il/feinberg/fgs3.html where salary and benefits information can also be found. Ph.D. positions will be for 3 years, with a 1-year trial period and a possible 4th-year extension. Applicants for a postdoctoral position should have obtained a Ph.D. within the last three years. Details of salary and benefits for postdocs at the Institute are available at http://www.weizmann.ac.il/feinberg/wispdoc.html Postdoctoral positions will be for 1 year, extendable by mutual agreement. Applicants with previous postdoc experience may qualify for a higher remuneration scale and will be encouraged to develop their own line of research. Living expenses in Rechovot are relatively low by Israeli standards. Neither Ph.D. students nor postdocs have teaching assistancy requirements. The positions are available immediately but will remain open until filled by suitable candidates. Send CV, list of publications, and contact information for at least two references to dr. Jan M.L. Martin Department of Organic Chemistry Weizmann Institute of Science IL-76100 Rechovot, Israel Email: comartin@wicc.weizmann.ac.il (preferred) FAX: +972(8) 934-4142 (from abroad), (08)934-4142 (from within Israel) Phone: (08)934-2533 (from within Israel) WWW home page: http://theochem.weizmann.ac.il/ Pre-submission enquiries by Email, FAX, or telephone are welcome. From ccl@www.ccl.net Mon Dec 15 11:40:32 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id LAA20566; Mon, 15 Dec 1997 11:35:45 -0500 (EST) Received: from uscmail.usc.es for qfsaulo@usc.es by bedrock.ccl.net (8.8.6/950822.1) id LAA13444; Mon, 15 Dec 1997 11:35:11 -0500 (EST) Received: from localhost (qfsaulo@localhost) by uscmail.usc.es (8.8.5/8.8.5) with SMTP id RAA02433 for ; Mon, 15 Dec 1997 17:30:38 +0100 (MET) Date: Mon, 15 Dec 1997 17:30:38 +0100 (MET) From: Saulo Vazquez Rodriguez To: CCL CCL Subject: TZ2P basis set Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear netters: I would like to know where I can find the TZ2P basis set for Cl and Br in GAUSSIAN format. Thanks for your help. Saulo Vazquez (qfsaulo@usc.es) From v.gillet@sheffield.ac.uk Tue Dec 16 07:04:05 1997 Received: from pp3.shef.ac.uk for v.gillet@sheffield.ac.uk by www.ccl.net (8.8.3/950822.1) id GAA26594; Tue, 16 Dec 1997 06:15:45 -0500 (EST) Received: from stoat.shef.ac.uk [143.167.2.1] by pp3.shef.ac.uk with smtp (Exim 1.62 #10) id 0xhuyT-0002b2-00; Tue, 16 Dec 1997 11:15:41 +0000 Received: from li1vg by stoat.shef.ac.uk with smtp (Exim 1.73 #1) id 0xhuyS-0000sb-00; Tue, 16 Dec 1997 11:15:40 +0000 Date: Tue, 16 Dec 1997 11:15:39 +0000 (GMT) From: Val Gillet X-Sender: li1vg@stoat Reply-To: Val Gillet To: chemistry@www.ccl.net cc: MOL-DIVERSITY@listserv.arizona.edu, CHMINF-L@LISTSERV.INDIANA.EDU Subject: MGMS/CSA Conference announcement Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII CONFERENCE ANNOUNCEMENT Computational Approaches to the Design and Analysis of Combinatorial Libraries April 14-16th, 1998 Sheffield UK. A joint meeting by the Molecular Graphics and Modelling Society (MGMS) and the Chemical Structure Association (CSA) The conference will emphasise the design of diverse and focussed libraries; algorithms and methods for the selection of database subsets; the representation and searching of combinatorial libraries and analogous virtual databases; the design and use of both in-house and commercial software for diversity analysis; diversity indices; and the integration of diversity analysis with other computational tools, such as docking and QSAR. The meeting will be limited to 110 participants. Speakers include: John Blankley, Mark Bures, Alain Calvet, Keith Daves, Geoff Downs, Johann Gasteiger, Darren Green, Mark Hermsmeir, Robert Jilek, Victor Lobanov, Jonathon Mason, Chris Murray, Nick Pery, Stephen Pickett, Matthias Rarey, Marvin Waldman and Bohdan Waszkowycz. Further information including a Preliminary Programme and Registration Details can be found at: http://panizzi.shef.ac.uk/cisrg/mgms/index.html From chem8@york.ac.uk Tue Dec 16 07:44:32 1997 Received: from pump2.york.ac.uk for chem8@york.ac.uk by www.ccl.net (8.8.3/950822.1) id HAA26796; Tue, 16 Dec 1997 07:05:56 -0500 (EST) Received: from ebor.york.ac.uk (chem8@ebor.york.ac.uk [144.32.129.242]) by pump2.york.ac.uk (8.8.7/8.8.7) with SMTP id MAA28766; Tue, 16 Dec 1997 12:04:44 GMT Date: Tue, 16 Dec 1997 12:04:44 +0000 (GMT) From: John Waite To: Laurence Lavelle cc: chemistry@www.ccl.net Subject: Re: CCL:All-electron basis set higher than 3-21G* for Ni. In-Reply-To: <3.0.32.19971208173550.00a48cc0@mbi.ucla.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi Laurence, Try looking in: EMSL at the www address of the gaussian basis set databank: http://www.emsl.pnl.gov:2080/forms/basisform.html OR, try: Ni (14S9P5D) A Schafer JCP 97,2571(1992) + Diffuse 2S2P2D + 1F Ni 0 S 6 1.0 409347.86899 .21251775671E-03 61355.839255 .16484929893E-02 13964.858128 .85853287121E-02 3956.8598699 .35015333983E-01 1296.0290474 .11427672717 475.27876516 .28015249519 S 2 1.0 188.98838775 .39246284244 76.928736976 .30331302178 S 1 1.0 19.331828730 1.0000000000 S 1 1.0 8.3876399732 1.0000000000 S 1 1.0 2.5894342897 1.0000000000 S 1 1.0 1.0071374699 1.0000000000 S 1 1.0 .12732573122 1.0000000000 S 1 1.0 .46189806319E-01 1.0000000000 S 1 1.0 0.016756221 1.0 S 1 1.0 0.0060786346 1.0 P 3 1.0 2329.8384386 -.18414189988E-02 552.60693015 -.15173689070E-01 178.71193584 -.73004669649E-01 P 3 1.0 67.841750813 -.23224844852 28.028033533 -.43596047040 12.076469199 -.38213785733 P 1 1.0 5.0694186684 1.0000000000 P 1 1.0 1.9911895236 1.0000000000 P 1 1.0 .73006887823 1.0000000000 P 1 1.0 0.267679475 1.0 P 1 1.00 0.098144577 1.0 D 3 1.0 47.088303645 .31522580302E-01 13.144067226 .16855325691 4.4158589541 .40930004652 D 1 1.0 1.4769996640 1.0 D 1 1.0 .43728964755 1.0 D 1 1.0 0.129466675 1.0 D 1 1.0 0.038330703 1.0 F 1 1.0 0.236714939 1.0 **** Ni, TRIPLE ZETA + POLARISATION FUNCTION, FROM WACHTERS (JCP 52,1033,1970) 14S,9P,5D + 1F Ni 0 S 5 1.0 284878.000000 0.000320 41997.900000 0.002460 9627.670000 0.012540 2761.960000 0.049260 920.488000 0.149500 S 1 1.0 341.805000 1.000000 S 1 1.0 138.023000 1.000000 S 1 1.0 59.258700 1.000000 S 1 1.0 20.371200 1.000000 S 1 1.0 8.594000 1.000000 S 1 1.0 2.394170 1.00000 S 1 1.0 0.918169 1.000000 S 1 1.0 0.346000 1.000000 S 1 1.0 0.130176 1.000000 P 4 1.0 1774.180000 0.002950 423.403000 0.023370 138.311000 0.104060 53.170300 0.282260 P 1 1.0 22.387400 1.000000 P 1 1.0 9.928480 1.000000 P 1 1.0 4.116250 1.000000 P 1 1.0 1.710310 1.000000 P 1 1.0 0.672528 1.000000 P 1 1.0 0.264000 1.000000 P 1 1.0 0.104000 1.000000 D 4 1.0 58.730000 0.017529 16.710000 0.100410 5.783000 0.276090 2.064000 0.403480 D 1 1.0 0.675200 1.000000 D 1 1.0 0.182500 1.000000 F 1 1.0 0.182500 1.000000 **** Good computing, John Dr. John Waite, e-mail: chem8@york.ac.uk * or The National Hellenic Research Foundation,* john@john1.eie.gr Organic and Pharaceutical Chemistry Institute, phone: ++30-1-7229811-5 X 1-810 Vas. Konstantinou 48, phone: ++30-1-7247913(secrtry. Mary) Athens 116-35, fax: ++30-1-7247913 Greece or NCRS "Democritos", phone: ++30-1-6503131 c/o Dr. G.Kordas, e-mail john@john.nrcps.ariadne-t.gr Material Science Institute, Aghia Paraskevi, Attikis, Athens 153-10, Greece On Mon, 8 Dec 1997, Laurence Lavelle wrote: > > Hi, > > > I have searched various sources for an all-electron basis set higher than 3-21G* for Ni. > > Does one exist, if so I would appreciate knowing where to find it? > > > Thanks > > Laurence Lavelle > >
> > > """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" > > Laurence Lavelle, Ph.D. > > University of California Los Angeles > > Molecular Biology Institute, and Department of Chemistry & Biochemistry > > Laboratory of Structural Biology & Molecular Medicine > > Los Angeles, CA 90095-1570, USA > > > > Email:LAVELLE@MBI.UCLA.EDU > > Phone (Lab): (310) 206-8270 > > Phone (Office): (310) 825-2083 > > Fax: (310) 267-1957 > > http://www.doe-mbi.ucla.edu/people/lavelle/lavelle.html > > """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" > > > It will be a great day when schools have all the money they need, > > and the military has bake day sales. > > > > > In nature's infinite book of secrecy > > A little I can read. > > >
> > > --- > Administrivia: This message is automatically appended by the mail exploder: > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > --- > > From kharroub@cit.enscm.fr Wed Dec 17 11:40:54 1997 Received: from cit.enscm.fr for kharroub@cit.enscm.fr by www.ccl.net (8.8.3/950822.1) id LAA05339; Wed, 17 Dec 1997 11:21:14 -0500 (EST) Received: from [193.52.205.156] by cit.enscm.fr (AIX 4.1/UCB 5.64/4.03) id AA08766; Wed, 17 Dec 1997 17:08:57 +0100 Message-Id: <3.0.2.32.19971217171847.0090c430@cit.enscm.fr> X-Sender: kharroub@cit.enscm.fr (Unverified) X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.2 (32) Date: Wed, 17 Dec 1997 17:18:47 +0100 To: CHEMISTRY@www.ccl.net From: Kharroubi Mohamed Subject: Summary : Bond Dissociation Energies Cc: CHEMISTRY@www.ccl.net Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Hi! As requested, please find below the list of the CCLer's who have contacted me. Please do not hesitate to informe me if you have got more information. I thank you by advance. Joyeuses fetes et Bonne annee Mohamed KHARROUBI ============================================================================ 1/ Maybe this is not quite what you want, but a book on computational thermochemistry will be published in the ACS Symposium Series in January. ---------------------------------------------- Dr. Karl K. Irikura Physical and Chemical Properties Division National Institute of Standards and Technology NIST 221/A111 Gaithersburg, MD 20899 voice: 301-975-2510 fax: 301-869-4020 e-mail: karl.irikura@nist.gov ---------------------------------------------- ============================================================================ 2/ Hi, Kharroubi, I would try give a answer. Which BDEs in the molecules are you interested in? I have an approach for predicting the BDEs of organic, organometllic and biologically active species. Now the values of trillions of BDEs can be estimated easily by my method and a calculator (not computer so far). Please draw the molecular structure you are interested in and send a fax to me. I would give you the answers ASAP. By the way, please tell me if you know a company wants to consider an electronic version of my method. Yu-Ran Luo, Ph.D. Fax: 813-553-1189 (USA) E-mail: luo@seas.marine.usf.edu ============================================================================ 3/ Mohamed, we've calculated a few simple BDE's check out, J.Phys.Chem. A 101(1997)8119 - and ref.s therein noj -- Dr. Noj Malcolm Theory Group, Dept. of Chemistry, University of Manchester, Oxford Road, Manchester. M13 9PL e-mail noj.malcolm@man.ac.uk ============================================================================ 4/ Hello Mohamed, one of the methods I know is the Transition State Method from T. Ziegler and A. Rauk : T. Ziegler , A. Rauk Theoret. Chim. Acta (Berl.) 46, 1-10 (1977) which is originally a method for the calculation of bonding energies within the Hartree Fock Slater method, but it can be extended to the more advanced DFT methods. I hope this is of any help to you. Greetings. Raf --  Raf Bruyndonckx Department of Inorganic Chemistry Univ Fribourg (Suisse) Perolles Tel: ++41 26 300 87 49 Fax: ++41 26 300 97 38 mailto:Raf.Bruyndonckx@unifr.ch http://sgich1.unifr.ch/ac/phd/rbruyn/ ============================================================================ 5/ Mohamed, You may want to look at the following papers dealing with BDE calculations. Regards, Ashutosh ------------------------------------------------------------------ 1. Benson, S. W. J. Chem. Educ. 1965, 42, 502. 2. Szwarc, M. Chem. Rev. 1950, 47, 75. 3. Golden, D. M.; Benson, S. W. Chem. Rev. 1969, 69, 125. 4. Benson, S. W.; O'Neal, H. E. Free Radicals; Wiley: New York, 1973; Vol. 2. 5. Kerr, J. A. In Handbook of Chemistry and Physics; CRC Press: Boca Raton, Fl.; 1981, pp F-222. 6. Baghal-Vayjooee, M. H.; Colussi, A. J.; Benson, S. W. J. Am. Chem. Soc. 1978, 101, 3214. 7. Baghal-Vayjooee, M. H.; Benson, S. W. J. Am. Chem. Soc. 1979, 101, 2838. 8. Baghal-Vayjooee, M. H.; Colussi, A. J.; Benson, S. W. Int. J. Chem. Kinet. 1979, 11, 147. 9. Robinson, P. J.; Holbrook, K. A. Unimolecular Reactions; Wiley: New York, 1972. 10. Bogan, D.; Setser, D., N. Fluorine-Containing Free Radicals: Kinetics and Dynamics of Reactions; Am. Chem. Soc.: Washington, D. C., 1978. 11. Luo, Y. R.; Holmes, J. L. J. Mol. Struct. (Theochem) 1993, 281, 123. ------------------------------------------------------------------------ **************************************************** Ashutosh Misra, Ph.D. Phone: 972-995-7552 Air Liquide Electronics Fax : 972-995-3204 Chemicals & Services, Inc. Pager: 972-598-1274 13546 N. Central Expressway M/S 301, Dallas, TX 75243 =========================================================================== :::::::::::::::::::::::::::::::::::::::: :: :: :: Mohamed KHARROUBI :: :: LCA UPRSA-5076 :: :: ENSCM :: :: 8, rue de l'Ecole Normale :: :: F-34296 MONTPELLIER CEDEX 5 :: :: FRANCE :: :: tel: 04.67.14.72.06 :: :: fax: 04.67.14.72.20 :: :: e-mail: kharroub@cit.enscm.fr :: :: :: :::::::::::::::::::::::::::::::::::::::: From chaudash@helios.aston.ac.uk Thu Dec 18 06:41:05 1997 Received: from hermes.aston.ac.uk for chaudash@helios.aston.ac.uk by www.ccl.net (8.8.3/950822.1) id GAA09543; Thu, 18 Dec 1997 06:35:31 -0500 (EST) Message-Id: <199712181135.GAA09543@www.ccl.net> Received: from Pharm33.aston.ac.uk by hermes.aston.ac.uk with SMTP (PP); Thu, 18 Dec 1997 11:40:17 +0000 Comments: Authenticated sender is From: chaudash@aston.ac.uk Organization: aston.ac.uk To: chemistry@www.ccl.net Date: Thu, 18 Dec 1997 11:44:45 +0000 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: Re: calculating cavity free volumes. Reply-to: chaudash@aston.ac.uk X-Confirm-Reading-To: chaudash@aston.ac.uk X-pmrqc: 1 Return-receipt-to: chaudash@aston.ac.uk Priority: normal X-mailer: Pegasus Mail for Windows (v2.54) Hi ccler's, I need help!!! I have undertaken several PM3 calculations on bidentate complexes of Al (3:1), using GAMESS, and viewing the minimised molecule in chemx. What I would like to do is xtract the central Al ion and measure the cavity produced. Is this possible? If so how? many thanks Shaqil From jmadura@jaguar1.usouthal.edu Fri Dec 19 11:41:25 1997 Received: from jaguar1.usouthal.edu for jmadura@jaguar1.usouthal.edu by www.ccl.net (8.8.3/950822.1) id LAA15701; Fri, 19 Dec 1997 11:34:17 -0500 (EST) Received: by jaguar1.usouthal.edu (SMI-8.6/SMI-SVR4) id KAA10474; Fri, 19 Dec 1997 10:43:07 -0600 Date: Fri, 19 Dec 1997 10:43:07 -0600 (CST) From: "Jeffry D. Madura" To: CHEMISTRY@www.ccl.net Subject: Postdoctoral Position: Biomolecular Modelling Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Colleagues, Applications for a post-doc position in my lab at Duquesne University are being sought. Research projects fall under the general area of biomolecular dynamics. Specific projects include the study of antifreeze proteins at the ice/water interface, binding of oligosaccharides to glycosyl hydrolases, development of coupled Possion-Boltzmann electrostatics to molecular dynamics. Other projects areas are possible. The position is open now and is good for 1 year with the possibility of a second year. If you are interested please send via e-mail a CV which includes a description of research interests and 3 names of references to me as soon as possilbe. Best Regards, Jeffry D. Madura >>>>>>>>>> NEW ADDRESS AFTER Dec. 31, 1997 <<<<<<<<<< Address: Department of Chemistry and Biochemistry Duquesne University 600 Forbes Ave. Pittsburgh, PA 15282-1503 Phone: (412) 396-4129 FAX: (412) 396-5683 e-mail: madura@space1.chemistry.duq.edu Until then.... Address: Department of Chemistry University of South Alabama Mobile, AL 36688 Phone: (334) 460-7430 FAX: (334) 460-7359 e-mail: jmadura@jaguar1.usouthal.edu From MAILER-DAEMON@www.ccl.net Sat Dec 20 04:39:55 1997 Received: from ms for MAILER-DAEMON@www.ccl.net by www.ccl.net (8.8.3/950822.1) id DAA00797; Sat, 20 Dec 1997 03:56:21 -0500 (EST) Received: by ms (8.8.4/961001-gatekeeper) with ESMTP id RAA23907; Sat, 20 Dec 1997 17:53:45 +0900 (JST) Message-Id: <199712200853.RAA23907@ms> To: CHEMISTRY@www.ccl.net Cc: hiro@ms Subject: amber4.1 parallelization From: Hiroyuki Takahashi X-Mailer: Mew version 1.66 on Emacs 19.28.1 / Mule 2.3 Mime-Version: 1.0 Content-Type: Text/Plain; charset=us-ascii Content-Transfer-Encoding: 7bit Date: Sat, 20 Dec 1997 17:53:44 +0900 Sender: hiro@ms Dear CCLers, I compiled sander of amber4.1 programs on Sun microsystems UltraEnterprise10000 (64nodes) with MPI library. But it does not run well. So does anyone know amber MACHINE file for Sun Multiprocessor machines using MPI library? I will summrized and post it. Thank you, Hiroyuki Takahashi -- Hiroyuki Takahashi Bioinformation Engineering Laboratory E-mail: hiro@ms.dr7w.saitama-u.ac.jp From Jurisic@akcomba.oci.uni-heidelberg.de Mon Dec 22 04:16:51 1997 Received: from akcomba.oci.uni-heidelberg.de for Jurisic@akcomba.oci.uni-heidelberg.de by www.ccl.net (8.8.3/950822.1) id DAA07932; Mon, 22 Dec 1997 03:29:21 -0500 (EST) Received: by akcomba.oci.uni-heidelberg.de with Internet Mail Service (5.0.1457.3) id ; Mon, 22 Dec 1997 09:29:50 +0100 Message-ID: <719D7972C359D111958D008048E15C0D015C2F@akcomba.oci.uni-heidelberg.de> From: Pero Jurisic To: Peter Comba Cc: "'chemistry@www.ccl.net'" Subject: AW: volume of molecule Date: Mon, 22 Dec 1997 09:29:47 +0100 X-Priority: 3 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.0.1457.3) Content-Type: text/plain > ---------- > Von: Dr. Bruno Manunza[SMTP:bruno@antas.agraria.uniss.it] > Gesendet: Sunday, December 14, 1997 6:21 PM > An: Pang Siu Kwong > Cc: chemistry@www.ccl.net > Betreff: CCL:volume of molecule > > > > > On Sat, 13 Dec 1997, Pang Siu Kwong wrote: > > > How are you? Do you know how to estimate the volume of molecule if > the > > molecule is assumed to be a hard sphere? Is there any literature > about > > that? If the geometry of molecule is known from X-ray > crystallography > > method or ab initio method, is it possible to assume that the radius > of > > hard sphere is equal to the maximum distance between two atoms > inside a > > molecule? For example, the radius of water molecule is equal to the > > > distance between two hydrogen atoms. Thank you for your attention. > > > > Patrick Pang > > > > Dear Patrick, > you'll found some useful link to software computing molecular > volume on our software page at http://antas.agraria.uniss.it > Hope it helps > regards > Bruno > > > Dr Bruno Manunza > DISAABA (Dept. of Agricultural Environm. Sci) > University of Sassari > V.le Italia 39 > 07100 Sassari, ITALY > phone: 39 79 229215 > fax: 39 79 229276 > e-mail: bruno@antas.agraria.uniss.it > e-mail: bruno@tharros.dipchim.uniss.it > e-mail: gx6bot81@cray.cineca.it > web: http://antas.agraria.uniss.it > > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: bruno@antas.agraria.uniss.it > -- Original Sender From: Address: bruno@antas.agraria.uniss.it > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: > Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: > www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive > search > Web: http://www.ccl.net/chemistry.html > > > > Dear Patrick, > there is also another interesting side for you which contains > a program for computing molecular volumes. It works on unix and on > windows. It`s called STERIC and you can download it from > ftp://hobbes.gh.wits.ac.za/pub/steric > regards > Pero > > Jurisic Pero > University of Heidelberg > Germany > From cyrillo@ifi.unicamp.br Mon Dec 22 16:15:34 1997 Received: from ifi.unicamp.br for cyrillo@ifi.unicamp.br by www.ccl.net (8.8.3/950822.1) id PAA10616; Mon, 22 Dec 1997 15:32:32 -0500 (EST) Received: from dfa01.ifi.unicamp.br (dfa01 [143.106.6.152]) by ifi.unicamp.br (8.8.8/8.8.8) with ESMTP id SAA14177 for ; Mon, 22 Dec 1997 18:34:03 -0200 (BDB) Received: (from cyrillo@localhost) by dfa01.ifi.unicamp.br (8.6.9/8.6.9) id TAA04152 for CHEMISTRY@www.ccl.net; Mon, 22 Dec 1997 19:39:36 -0200 From: Marcio Cyrillo - pos Message-Id: <199712222139.TAA04152@dfa01.ifi.unicamp.br> Subject: Software annoucement -> HyperSpin. To: CHEMISTRY@www.ccl.net (Lista de Quimica) Date: Mon, 22 Dec 1997 19:39:36 -0200 (BDB) X-Mailer: ELM [version 2.4 PL24] Content-Type: text Dear CCLers, The following is the readme of my software. I hope you will enjoy it as well as send me suggestions and comments. Nice holidays for you all, Marcio Cyrillo =-------------------------------------------------= Marcio Cyrillo - http://www.ifi.unicamp.br/~cyrillo Graduate Student State University of Campinas - Unicamp Campinas - SP - Brazil Applied Physics Department room 51 - phone +55 19 788 2364 Alternative e-mail: mcyrillo@yahoo.com =-------------------------------------------------= -- HyperSpin 2.0 (32-bit) for Windows 95 ------------------------------------- 2.0.4 December 1997 ===================================================================== Written by Marcio Cyrillo - cyrillo@ifi.unicamp.br This software was developed as part of my master thesis project under the supervision of Prof. Dr. D.S. Galvao (galvao@ifi.unicamp.br) at Gleb Wataghin Institute of Physics, State University of Campinas, Brazil. Supported by the Brazilian Agency CNPq ===================================================================== What's HyperSpin? ----------------- HyperSpin is a full 32-bit DDE client for HyperChem and allows conformational search of one or more selected dihedrals. The full phase space of three dihedrals can be analyzed with xyz text files and Mathematica(TM) notebooks to visualize the surfaces being generated. Minimization of a selected variable is automatically done with interpolation. With Molecular Mechanics it is possible to view on-line graphing of specified variables. HyperSpin development started in April 1997. The version zero was written using Pascal for DOS. Then I moved to Visual Basic 3 and wrote version 1.0 which is a 16-bit interface that can run over Windows 3.11; However this version has been abandoned with many unfixed bugs since I moved to VB 5.0 (professional) which resulted in the present 32-bit version. System requirements: -------------------- Windows 95 (any language) with English set as default language on the control panel. Resolution 800x600 or greater. HyperChem installed. Tests were done with HyperChem 3, 4 and 5.02. The full features are for HC 5.02 (Thanks to evaluation copy provided by HyperCube). Attention: ---------- HyperSpin is totally free of charge and I intend to keep it so for all HyperChem users under the condition of proper acknowledgments. If you publish any material using HyperSpin please cite the following: Real Time Graphical Interface Add-on to HyperChem(TM) (HyperSpin). M. Cyrillo and D.S. Galvao, to be published. How to get a copy of it? ------------------------ You can request the software via e-mail: cyrillo@ifi.unicamp.br (subject: "HyperSpin request") or download it directly from the following web sites: - www.hyper.com/support/software/Other/other_index.html - www.ifi.unicamp.br/~cyrillo/hyperspin/hspin.html In order to provide all bug reports and new releases to potencial HyperSpin users, please provide the following information: Name: e-mail: homepage: address: (full) pc model: HyperChem version: and send it by e-mail to cyrillo@ifi.unicamp.br with the message subject "HyperSpin user". I would appreciate very much if you could send me a postcard from where you are to the following home address: Marcio Cyrillo R. Luzitana 1482 apto 23 Centro, Campinas, SP, Brazil CEP 13015.122 Package Components: ------------------- HyperSpin package is composed of 5 components that can be accessed from "Start/Programs/HyperSpin 2.0 (32-bit)" folder on Windows 95 desktop: 1. Script Editor ---------------- It is the first program you have to run, because it sets some important ini files to other package components. With Script Editor you can set all information to generate scripts and set HyperChem to do a conformational search. In its window you can see three "folders" named as the following: 1. Setup HyperSpin calculation 2. Setup HyperChem calculation 3. Setup scripts. Let us name them Script Editor Folders (SEFs). Click on a SEF to switch to it. All information within these folders can be saved in HSE files that are simply text files saved with the option "Edit/Save HSE file" and loaded with "Edit/Open HSE file". The getting started section of this file will explain how to use HyperSpin asking the user to open some HSE files found in the directory "c:\hspin\samples" and study their effects. The only thing you have to do in order to get HyperChem ready for HyperSpin calculations is to fill in all the required fields and click the "Go" button (3rd SEF) 2. HyperGraph ------------- It is available for Molecular Mechanics calculations only. As HyperSpin executes scripts and calculations are being done, one is able to see on-line plotting of two selected energy variables. It has options to manipulate the graphic and HyperSpin results. In order to use it one has two alternatives: 1. By checking the option "Prepare HyperGraph" on the third SEF. When Script Editor is done, it will automatically run HyperGraph and connect it to HyperChem 2. By running it directly and connecting it to HyperChem manually just before starting any calculation in HyperChem. 3. Last Calculation Results --------------------------- It simply shows information about the last calculation you have done with HyperSpin. 4. LogViewer ------------ It is an application to monitor HyperChem logfiles showing their contents as soon as any changes occur. You can execute it directly or by checking the item logfile on the 2nd SEF and then by clicking the button with the image of "windows explorer" icon in the up toolbar. 5. HyperRemote -------------- Its main window is also composed of three "folders", now let us name them HRF. In the first HRF you have what I think is a fundamental tool for HyperChem interface developers: the full control of ALL hyperchem 5.02 DDE messages (future updates can be made in the file "c:\hspin\remote.ini"). One can read HyperChem variables and execute DDE commands by simply dbl clicking an element in the list box that contains DDE messages previously selected in menus that mimic all HyperChem default menus. In the second HRF you have a picture of HyperChem settings and for versions greater than 4.5 it is possible to on-line monitor all HyperChem energy variables. In the third HRF it is shown the HyperSpin settings. If you are doing a 2D conformational search for example, it will be possible to view the values for the dihedrals as they change. Warning: -------- All these "modules" are still under test. please Report bugs to: cyrillo@ifi.unicamp.br (subject: "bug report") Getting started: ---------------- You are going to use HSE files to explore HyperSpin potential. Althogh HyperSpin is capable to detect many HyperChem initialization status, I recommend oppening HyperChem and loading some molecule in its workspace before starting HyperSpin Script Editor. This will be avoid many undesirable communication problems. The molecule we are going to work on is "c:\hspin\samples\hyperspin.zmt" but you do not need to load it. It will be loaded when you load a HSE file. As said before you have to fill in the fields and click the "Go" button on the 3rd SEF in order to set HyperChem to HyperSpin calculations. One way to do that is by loading a HSE file and then clicking "Go". To get in touch with HyperSpin capabilities, try out the following HSE files found in the "c:\hspin\samples" directory: 1. One dihedral search with HyperGraph viewing ---------------------------------------------- c:\hspin\samples\hspin.hse 2. Three dihedral search, one each time. (1D search) --------------------------------------------------- c:\hspin\samples\1D.hse 3. Two dihedrals in full phase space search. (2D search) -------------------------------------------------------- c:\hspin\samples\2D.hse 4. Three dihedrals in full phase space search. (3D search) ---------------------------------------------------------- c:\hspin\samples\3D.hse 5. One dihedral search with all conformers being saved ------------------------------------------------------ c:\hspin\samples\conformers.hse Load them using menu "Edit/Open HSE file" and then click the "Go" button. In the final of each calculation a HyperSpin window will appear giving the calculation results and allowing data viewing. Read carefully all information provided by it because it will tell you where to find all files generated by the program in each situation. From the author: ---------------- I would like to say that I hope you will enjoy the software as well as feel free to ask me about anything related to it. Please notice that this is a very preliminary manual version, in a near future a more complete manual will be available. Acknowledgments: ---------------- I am very thankful to Douglas S. Galvao who has brought me into the fascinating world of theoretical Chemistry since March 1997 and encouraged me to develop the softwares we are using in our research group. I would like to thank also Sand Yates from University of Edinburgh (UK) who first tested the software for me and Krassimir Stavrev from HyperCube staff for his efforts to make HyperSpin available in HyperChem web page.