From chemistry-request@server.ccl.net Sun Jul 8 00:09:17 2001 Received: from ilion.bio.sunysb.edu ([129.49.94.22]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6849H517091 for ; Sun, 8 Jul 2001 00:09:17 -0400 Received: from presario (080-023.dialup.sunysb.edu [129.49.80.23]) by ilion.bio.sunysb.edu (SGI-8.9.3/8.9.3) with SMTP id AAA38595 for ; Sun, 8 Jul 2001 00:09:15 -0400 (EDT) From: "Guanglei Cui" To: Subject: compile gaussian98 for Redhat 7.1 with pgf77 Date: Sun, 8 Jul 2001 00:09:05 -0400 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 Dear CCLers, Perhaps this's the question that has been asked so many times. I first tried to scan the CCL archive, but couldn't get an answer. I have PGI compiler and BLAS library and blas-f2c.a as recommended by Gaussian's website. But I still have errors while compiling. Most of the errors are caused by ml0.F and util.F. Here's a shortened version: -- ml0.o: In function `MAIN_': ml0.o(.text+0x296): undefined reference to `gauabt_' ml0.o(.text+0x330): undefined reference to `gauabt_' ml0.o(.text+0x402): undefined reference to `gauabt_' ml0.o(.text+0x4dc): undefined reference to `gauabt_' ml0.o(.text+0x619): undefined reference to `gauabt_' ml0.o(.text+0x63c): undefined reference to `fixinout_' ml0.o(.text+0xe47): undefined reference to `ggeten_' ml0.o(.text+0xea8): undefined reference to `getexen_' ml0.o(.text+0x112c): undefined reference to `gsyst_' util.so: undefined reference to `writwa_' util.so: undefined reference to `closwa_' util.so: undefined reference to `asynwa_' util.so: undefined reference to `erfcx_' util.so: undefined reference to `fixstdin_' util.so: undefined reference to `gaufls_' util.so: undefined reference to `fixenv_' util.so: undefined reference to `ifalph_' util.so: undefined reference to `ntrsiz_' util.so: undefined reference to `guname_' util.so: undefined reference to `openwa_' util.so: undefined reference to `envfil_' util.so: undefined reference to `gfree_' util.so: undefined reference to `gauexec_' -- I'll really appreciate if someone can point me what I'm missing. Best regards, Guanglei Cui From chemistry-request@server.ccl.net Sat Jul 7 08:41:01 2001 Received: from mum.mans.eun.eg ([193.227.50.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f67Cex510362 for ; Sat, 7 Jul 2001 08:41:00 -0400 Received: by mum.mans.eun.eg with Internet Mail Service (5.5.2650.21) id <33F9K7P0>; Sat, 7 Jul 2001 15:44:28 +0300 Message-ID: <4EF2E03A9B67D2119E2E0000F805349942755D@mum.mans.eun.eg> From: Tarek Mamoun El-Gogary To: "'CHEMISTRY@ccl.net'" Subject: INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY Date: Sat, 7 Jul 2001 15:44:27 +0300 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C106E2.8F22AEF8" This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. ------_=_NextPart_001_01C106E2.8F22AEF8 Content-Type: text/plain Hi Netters, Could any one, kindly, refere me to any information about: INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, i.e., web site, editorial board, .....etc. Thank you in advance Tarek ------_=_NextPart_001_01C106E2.8F22AEF8 Content-Type: text/html Content-Transfer-Encoding: quoted-printable INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY

Hi Netters,
Could any one, kindly, refere me to = any information about: INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, = i.e., web site, editorial board, .....etc.

Thank you in advance
Tarek

------_=_NextPart_001_01C106E2.8F22AEF8-- From chemistry-request@server.ccl.net Sat Jul 7 15:29:30 2001 Received: from mail-b.bcc.ac.uk ([144.82.100.22]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f67JTU514765 for ; Sat, 7 Jul 2001 15:29:30 -0400 Received: from socrates-a.ucl.ac.uk by mail-b.bcc.ac.uk with SMTP (Mailer); Sat, 7 Jul 2001 20:29:29 +0100 From: uccatvm Message-Id: <5429.200107071929@socrates-a.ucl.ac.uk> Subject: Re: CCL:BSSE on Dimers To: dasf@u.arizona.edu (Demetrio Antonio da Silva Filho) Date: Sat, 7 Jul 2001 20:29:29 +0100 (BST) Cc: CHEMISTRY@ccl.net In-Reply-To: <5.1.0.14.0.20010706124722.024390a0@deimos.email.arizona.edu> from "Demetrio Antonio da Silva Filho" at Jul 06, 2001 12:52:21 PM X-Mailer: ELM [version 2.5 PL3] MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi Demetrio, > I am doing some MP2/6-311G(2d,2p) canculation on > anthracene dimers (using Gaussian'98) and I want to > know how I can eliminate the BSSE (basis set > superposition error) using the counterpoise method > for that system of two equal molecules. > > I wonder if someone can point me to articles or > a scheme in order to do that using Gaussian'98. If you calculate a binding energy De as: De = E{AB} -E{A} - E{B} Using counterpoise, you calculate the monomer energies E{A} and E{B} also in the complete dimer basis set. In Gaussian, you do this by setting the nuclear charge of the second dimer (B for E{A} and A for E{B}) to zero. This is done by the Massage keyword; see the examples in the Gaussian manual (www.gaussian.com/00000452.htm). (but don't believe what the manual says about counterpoise only providing "a crude estimate" - see papers below). Depending on how much your monomer geometries change upon complexation, you may also have to take into account the monomer deformation energies (the energy it takes to bring an anthracene molecule to the geometry it has in the complex). Some references: - F.B. van Duijneveldt, J.G.C.M. van Duijneveldt-van de Rijdt, and J.H. van Lenthe, Chem. Rev. 94, 1873, 1994 (on counterpoise theory) - S. Simon, M. Duran, J.J. Dannenberg, J. Chem. Phys. 105, 1996 (on geometry optimizations on BSSE-corrected potential energy surfaces). - F.B. van Duijneveldt, "Basis Superposition Error" in "Molecular Interactions" S. Scheiner (ed.), Wiley (1997) - T. van Mourik, A.K. Wilson, K.A. Peterson, D.E. Woon, T.H. Dunning, Jr., Adv. Quant. Chem. 31, 105, 1999 (showing BSSE effects on interaction energies, distances, and frequencies). You may also want to search the ccl archives; there have been a few disussions on counterpoise the last few years. Hope that helps, Tanja -- ===================================================================== Tanja van Mourik Royal Society University Research Fellow Chemistry Department University College London phone: +44 (0)20-7679-4663 20 Gordon Street e-mail: work: T.vanMourik@ucl.ac.uk London WC1H 0AJ, UK home: tanja@netcomuk.co.uk http://www.chem.ucl.ac.uk/people/vanmourik/index.html ===================================================================== From chemistry-request@server.ccl.net Sun Jul 8 06:04:51 2001 Received: from mail.shcnc.ac.cn ([202.127.16.22]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f68A4j506255 for ; Sun, 8 Jul 2001 06:04:50 -0400 Received: from PC18 ([202.127.19.225]) by mail.shcnc.ac.cn (8.9.3/8.9.3) with SMTP id SAA09160 for ; Sun, 8 Jul 2001 18:03:38 +0800 (CDT) Message-Id: <200107081003.SAA09160@mail.shcnc.ac.cn> Date: Sun, 8 Jul 2001 17:57:47 +0800 From: bxiong To: "chemistry@ccl.net" Subject: X-mailer: FoxMail 3.0 beta 2 [cn] Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="=====_Dragon843488127631_=====" This is a multi-part message in MIME format. --=====_Dragon843488127631_===== Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: 7bit hello,all members: I want to use the AMBER to simulation of the small molecule. but I do not have the FF parameters of this molecule.Can you suggest the parameters for me? If I pubish the paper ,I will thank you in the paper . the molecule is in pdb file format.thanks very much!!! (any suggestion will be helpful and if I get something, I will send to the pharmacy.man.ac.uk/amber ,which is the AMBER parameter database. Best regards! bxiong@mail.shcnc.ac.cn Xiong Bin Shanghai Institute of Materia Medica, C.A.S. phone:021-64311833-222(office) --=====_Dragon843488127631_===== Content-Type: application/octet-stream; name="extractlig.pdb" Content-Transfer-Encoding: base64 Content-Disposition: attachment; filename="extractlig.pdb" UkVNQVJLICAgTVNJIFdlYkxhYiBWaWV3ZXIgUERCIGZpbGUNClJFTUFSSyAgIENyZWF0ZWQ6ICBT dW4gSnVsIDA4IDE3OjUzOjUxINbQufqx6te8yrG85CAyMDAxDQpBVE9NICAgICAgMSAgUzEgIE1P TCAgICAgMSAgICAgIDEwLjgwNSAgIDkuMjg4ICAtOS4zMzYgIDEuMDAgIDAuMDAgICAgICAgICAg ICAgIA0KQVRPTSAgICAgIDIgIE4xICBNT0wgICAgIDEgICAgICAgNy44NzIgIDEzLjM0OCAgLTUu ODk2ICAxLjAwICAwLjAwICAgICAgICAgICAgICANCkFUT00gICAgICAzICBOMiAgTU9MICAgICAx ICAgICAgMTIuNTQ2ICAgOS4zOTkgIC05LjA5OCAgMS4wMCAgMC4wMCAgICAgICAgICAgICAgDQpB VE9NICAgICAgNCAgTzEgIE1PTCAgICAgMSAgICAgIDE0LjAyMyAgIDkuOTExIC0xMS45NDMgIDEu MDAgIDAuMDAgICAgICAgICAgICAgIA0KQVRPTSAgICAgIDUgIE80ICBNT0wgICAgIDEgICAgICAx 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LTMuNzQwICAxLjAwICAwLjAwICAgICAgICAgICAgICANCkFUT00gICAgIDUxICBIMyAgQ1lTICAg ICAxICAgICAgIDkuNjAxICAgOS44MDkgIC0zLjg5MCAgMS4wMCAgMC4wMCAgICAgICAgICAgICAg DQpURVINCg== --=====_Dragon843488127631_=====-- From chemistry-request@server.ccl.net Fri Jul 6 23:52:22 2001 Received: from lacebark.ntu.edu.au ([138.80.63.12]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f673qK525099 for ; Fri, 6 Jul 2001 23:52:20 -0400 Received: (qmail 15965 invoked by uid 200); 7 Jul 2001 13:01:39 +0930 Date: Sat, 7 Jul 2001 13:01:38 +0930 From: Brian Salter-Duke To: "'CCL'" Subject: Re: CCL:aromaticity w/o orbitals Message-ID: <20010707130138.A17484@lacebark.ntu.edu.au> Mail-Followup-To: 'CCL' References: <157A51F55AAAD3119CD70008C7B1629DDAB043@lvlxch01.unitedcatalysts.com> Mime-Version: 1.0 Content-Type: text/plain; charset=IBM-850 Content-Disposition: inline Content-Transfer-Encoding: 8bit User-Agent: Mutt/1.3.10i In-Reply-To: <157A51F55AAAD3119CD70008C7B1629DDAB043@lvlxch01.unitedcatalysts.com>; from dshobe@sud-chemieinc.com on Fri, Jul 06, 2001 at 12:08:59PM -0400 On Fri, Jul 06, 2001 at 12:08:59PM -0400, Shobe, Dave wrote: > Another question in the philosophical debate about orbitals. > > The explanation of aromaticity and the 4n+2 rule that I was taught was very > dependent on the idea of orbitals. In fact, it was usually presented in > terms of the Huckel orbitals derived from the molecular graph of the pi > system. My question is, is it possible to explain the Huckel 4n+2 rule > without appealing to orbitals? How does one do it? Why would you want to? First, the orbitals are actually determined by the symmetry of the planar cyclic ring systems, not by the Huckel apprimations. Second, a molecular orbital approximation to the correct wave function is not that bad. It is likely to be getting correct that the 4n+2 systems are closed shell and stable and the 4n systems are triplet ground states with little stability. To answer some questions you do not need an exact wave function or even a post-Hartree-Fock wavefunction. Cheers, Brian. > --David Shobe > Süd-Chemie Inc. > phone (502) 634-7409 > fax (502) 634-7724 > email dshobe@sud-chemieinc.com > > Don't bother flaming me: I'm behind a firewall. > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > -- Associate Professor Brian Salter-Duke (Brian Duke) b_duke@lacebark.ntu.edu.au Chemistry, School of BECS, SITE, NT University, Darwin, NT 0909, Australia. Phone 08-89466702. Fax 08-89466847. http://www.smps.ntu.edu.au/