From chemistry-request@server.ccl.net Mon Mar 3 23:21:08 2003 Received: from smtp1.ndsu.NoDak.edu ([134.129.111.146]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h244L7Q23561 for ; Mon, 3 Mar 2003 23:21:08 -0500 Received: from pharm200 (dyn251.sud-118.ndsu.NoDak.edu [134.129.118.251]) by smtp1.ndsu.NoDak.edu (8.11.6/8.11.6) with SMTP id h244L7n06019 for ; Mon, 3 Mar 2003 22:21:08 -0600 Message-ID: <002801c2e205$5b980b00$fb768186@ndsu.nodak.edu> From: "xin Hu" To: Subject: peptide databases Date: Mon, 3 Mar 2003 22:20:15 -0600 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0025_01C2E1D3.10BA7780" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2600.0000 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 This is a multi-part message in MIME format. ------=_NextPart_000_0025_01C2E1D3.10BA7780 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear CCLer, Would you please give me some suggestions on the peptide database = screening? what's kind of peptide databases available? and which docking = program is good at the peptide VS? (FTDock? GRAMM? or small ligand = docking program such as DOCK, AutoDock?) Thank you very much for your help! Xin=20 ------=_NextPart_000_0025_01C2E1D3.10BA7780 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear CCLer,
 
Would you please give me some = suggestions on the=20 peptide database screening? what's kind of peptide databases available? = and=20 which docking program is good at the peptide VS?  (FTDock? GRAMM? = or small=20 ligand docking program such as DOCK, AutoDock?)
 
Thank you very much for your = help!
 
 
Xin
 
------=_NextPart_000_0025_01C2E1D3.10BA7780-- From chemistry-request@server.ccl.net Mon Mar 3 21:48:55 2003 Received: from ns1.scripps.edu ([192.42.82.59]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h242msQ21803 for ; Mon, 3 Mar 2003 21:48:54 -0500 Received: from antigen.scripps.edu (antigen.scripps.edu [137.131.200.100]) by ns1.scripps.edu (8.11.6/TSRI-4.1rx) with SMTP id h242mtL08061 for ; Mon, 3 Mar 2003 18:48:55 -0800 (PST) Received: from relay2.scripps.edu(137.131.200.30) by antigen.scripps.edu via csmap id 1249; Mon, 03 Mar 2003 18:40:58 -0800 (PST) Received: from goliath.scripps.edu (goliath.scripps.edu [137.131.108.88]) by relay2.scripps.edu (8.11.6/TSRI-4.2rAV) with ESMTP id h242mnv19857; Mon, 3 Mar 2003 18:48:49 -0800 (PST) Received: from goliath (goliath [137.131.108.88]) by goliath.scripps.edu (SGI-8.9.3/TSRI-3.0.1) with ESMTP id SAA70684; Mon, 3 Mar 2003 18:48:47 -0800 (PST) Date: Mon, 3 Mar 2003 18:48:47 -0800 From: "Garrett M. Morris" To: "Armin M. Sobhani" cc: CHEMISTRY@ccl.net, 5516@mail.unimo.it, "Garrett M. Morris" Subject: Re: CCL:Database screening with Autodock In-Reply-To: <5.0.2.1.2.20030301210617.00b6b900@pop3.iums.ac.ir> Message-ID: 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 server.ccl.net id h242mtQ21804 Dear Marco, Don't forget that the Olson laboratory now distributes AutoDock for Windows using Cygwin (www.cygwin.com, a free Unix-like system for Windows) as well as a Windows version of AutoDockTools (ADT). ADT is the GUI that lets users set up AutoDock runs, launch them, and analyse the results graphically. There are many molecular graphics options, too, thanks to its foundations of PMV, Michel Sanner's Python Molecular Viewer. We now distribute a Tutorial for ADT, along with sample files, to help you get started. Of course, AutoDock and ADT are also available for many other platforms, including Mac OS X, Darwin, Linux, Solaris, and IRIX. We have also processed the National Cancer Institute's Developmental Therapeutics Program's Diversity Set into a format that can be used by AutoDock. These consist of 3D structures generated by Prof. Gasteiger's program CORINA, and then converted using AutoDockTools into PDBQ format with all rotatable bonds defined and partial atomic charges computed, using Gasteiger's PEOE method: these are the charges we used in callibrating AutoDock 3's empirical free energy function. Most of the 1990 compounds passed our quality tests, but there are about 7% that did not. We will be releasing the NCI Diversity Set for AutoDock as soon as possible. Watch http://www.scripps.edu/pub/olson-web/doc/autodock for news when this will be available. Garrett Morris On Sat, 1 Mar 2003, Armin M. Sobhani wrote: > Dear Marco, > > I've succeeded in compiling AutoDock 3.0.5 under Windows 9x/Me/NT/2000/XP. > It only consists of three main executive programs (i.e. autotors, autogrid > and autodock). It lacks all unix shell and awk scripts and that's why I am > working on a graphical front-end for it (named WAD, i.e. Windows AutoDock) > using MFC and Visual C++. In this front-end you can specify several ligand > molecules in HyperChem7 HIN format as input. It's possible to implement > other file formats in the future. In my rough estimate the first working > release would be ready in a two-week period. If you are interested, I will > let you know when it's ready. > > Cheers, > > Armin > > At 11:25 Þ.Ù 2003/02/28 +0100, you wrote: > >my question is about database screening with AUTODOCK3.0.5; > >If possible i would like to screen entire ACD database with autodock, but i'm > >still looking for someone who did it... > >I know there is no a "standard" method to do this, but i think it's possible > >with some shell scripts... > >Have you some information about this question? > > p-----__---_________----____----------------------------------------q > | / \ / _ _ \ / ____\ Armin M. Sobhani, PharmD, PhD | > | / \\ \\ \\ \/\ \___/_ Assitant Prof., Pharmacology Dept. | > | / /\ \\ \\ \\ \ \_____ \ Iran University of Medical Sciences| > | ( ___ \\ \\ \\ \/____/\ \ mailto:armin@iums.ac.ir | > |( \__\_/\__\\__\\__\\__\/\_____/ Tel: +98 (21) 805 2265, Fax: ~64 | > | \/__/ \/__//__//__//__/\/____/ P.O.Box: 14155-6183, Tehran, IRAN | > |~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~| > | Once you understand the universe at the atomic level everything | > | else is easy. -Richard P. Feynman | > b-------------------------------------------------------------------d > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > Garrett ___ Dr Garrett M. Morris, MA, DPhil The Scripps Research Institute, tel: (858) 784-2292 Dept. Molecular Biology, MB-5, fax: (858) 784-2860 10550 North Torrey Pines Road, email: garrett@scripps.edu La Jolla, CA 92037-1000, USA. www.scripps.edu/pub/olson-web/gmm From chemistry-request@server.ccl.net Tue Mar 4 07:04:06 2003 Received: from smtp2.ruc.dk ([130.225.220.70]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h24C45P12083 for ; Tue, 4 Mar 2003 07:04:05 -0500 Received: by smtp2.ruc.dk (Postfix, from userid 504) id 48285941354; Tue, 4 Mar 2003 13:04:05 +0100 (CET) Received: from virgil.ruc.dk (virgil.ruc.dk [130.225.220.110]) by smtp2.ruc.dk (Postfix) with ESMTP id 53068941351; Tue, 4 Mar 2003 13:04:04 +0100 (CET) Received: from VIRGIL/SpoolDir by virgil.ruc.dk (Mercury 1.47); 4 Mar 03 13:04:04 +0100 Received: from SpoolDir by VIRGIL (Mercury 1.47); 4 Mar 03 13:04:01 +0100 From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter To: post@eike-huebner.de Date: Tue, 4 Mar 2003 13:03:43 +0100 Subject: CCL:HOMO/LUMO energy gap Reply-To: spanget@ruc.dk Cc: Chemistry@ccl.net X-Confirm-Reading-To: spanget@ruc.dk X-pmrqc: 1 Priority: normal X-mailer: Pegasus Mail for Windows (v2.23) Message-ID: X-Spam-Status: No, hits=-3.2 required=5.0 tests=QUOTED_EMAIL_TEXT version=2.50 X-Spam-Level: X-Spam-Checker-Version: SpamAssassin 2.50 (1.173-2003-02-20-exp) Eike Huebner: > can anyone point me to a paper where the reasons for the too large > energy gap between calculated (Hartree-Fock) HOMO-LUMO orbitals in > comparison to the longest wavelenght absorbtion is discussed? In > fact I am looking not for a lot of examples or calculations but for > a more general paper (which can be cited aswell) discussing why HF > calculations give much too short longest wavelength absorbtions > compared to the experiment. Dear Eike! The volume by Klessinger and Michl has a Section 1.2 where the use of molecular orbital (MO) models in the description of electronic transitions is explained: Martin Klessinger, Josef Michl: "Lichtabsorption und Photochemie organischer Molekuele", VCH 1989, ISBN 3-527-26085-4 Later editions and in English are available. - Basically, equating a molecular orbital energy difference to an electronic excitation energy is wrong, primarily for two reasons: 1) The energy required to promote an electron from MO i to MO j is not equal to the energy difference e(j) - e(i). The promotion energy E(i-->j) can be expressed as E(i-->j) = e(j) - e(i) - v(i,j) where the term -v(i,j) represents the interaction between a hole in orbital i and an electron in orbital j. This term may be relatively small if the two molecular orbitals are spatially separated, but in general, v(i,j) amounts to several electron volts and is by no means negligible. 2) The wavefunction |i-->j> of an excited electronic configuration is not in general a good approximation to an eigenfunction of the many-electronic Hamilton operator H. Generally, matrix elements corresponding to j|H|k-->l> are not close to zero. Hence, excited configurations tend to interact, and a proper description must include Configuration Interaction, (CI). Of particular importance is the first order CI between near-degenerate configurations of the same symmetry, f.inst. for alternant hydrocarbons where it gives rise to "plus" and "minus" states. - Inclusion of multiply excited configurations (like i,k-->j,l etc.) in the CI formally accounts for electronic correlation effects, thus leading to a description going beyond the orbital picture. However, semiempirical CI-procedures (PPP, CNDO/S, INDO/S, ZINDO, etc.) usually limit the CI expansion to singly excited configurations, and account for correlation effects by empirical adjustment of parameters in the models. Yours, Jens >--< =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= JENS SPANGET-LARSEN Office: +45 4674 2710 Department of Chemistry Fax: +45 4674 3011 Roskilde University (RUC) Mobile: +45 2320 6246 P.O.Box 260 E-Mail: spanget@ruc.dk DK-4000 Roskilde, Denmark http://virgil.ruc.dk/~spanget =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From chemistry-request@server.ccl.net Tue Mar 4 03:13:53 2003 Received: from mx1.ustc.edu.cn ([218.22.21.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h248DoP27427 for ; Tue, 4 Mar 2003 03:13:51 -0500 Received: from dxl ([202.38.82.79]) by mx1.ustc.edu.cn (8.8.7/8.8.6) with ESMTP id QAA30065 for ; Tue, 4 Mar 2003 16:02:25 +0800 Message-Id: <200303040802.QAA30065@mx1.ustc.edu.cn> Date: Tue, 4 Mar 2003 16:4:39 +0800 From: ¶¡Ñ¸À× Reply-To: dxl@mail.ustc.edu.cn To: CCls Subject: how many k points needed. Organization: Öйú¿Æ´óÑ¡¼ü»¯Ñ§ÊµÑéÊÒ X-mailer: FoxMail 4.0 beta 2 [cn] Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="=====000_Dragon888240703733_=====" This is a multi-part message in MIME format. --=====000_Dragon888240703733_===== Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: base64 RGVhciBDQ2xzo7oNCg0KoaGhoaGhoaEgICAgIFdoZW4gSSBkbyBjYWxjbHVsYXRpb25zIHdpdGgg VkFTUCAsb3IgUFdzY2YsIEkgZG9uJ3Qga25vdyANCglob3cgbWFueSBrIHBvaW50cyBuZWVkZWQu DQoJDQoJY3J5c3RhbCBsYXR0aWNlIDogYSxiLGMoYW5nc3Ryb20pLCBhbmQgayBwb2ludCBudW1i ZXIga2Esa2Isa2MuDQoJSSB0aGluayBhKmthIGFyb3VuZCAyMH4zMCBpcyBvay4gDQoNCg0KICAg IFRoYW5rIHlvdSBmb3IgeW91ciBoZWxwIaGhoaGhoaGhoaGhoaGhoaENCiAJCQkJDQqhoaGhoaGh oaGhoaGhoaGhoaGhoaGhoaGhoaGhRGluZyBYdW5sZWkNCqGhoaGhoaGhoaGhoaGhoaGhoaGhoaGh oaGhoaEyMDAzLTAzLTA0DQpfX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19f X19fX19fDQo= --=====000_Dragon888240703733_===== Content-Type: image/gif; name="LittleBoy(1).GIF" Content-Transfer-Encoding: base64 Content-Disposition: FoxmailIcon; filename="LittleBoy(1).GIF" R0lGODlhIAAgANQAAGCXzwCAgGBnYP/IkPzJmpFjPBsNA2Q8HxQDACIGAk4HADYDAA0AAP///wAA ANPT05KSkm5ubmVlZUZGRiUlJRgYGBEREQ8PDwcHBwMDAwAAAAAAAAAAAAAAAAAAAAAAACH/C05F VFNDQVBFMi4wAwEAAAAh/sJodHRwOi8vd3d3LnJ0bHNvZnQuY29tL2FuaW1hZ2ljLwoKQ3JlYXRl ZCB3aXRoIEFuaW1hZ2ljIEdJRiBWIDEuMjJhCmJ5IFJpZ2h0IHRvIExlZnQgU29mdHdhcmUgSW5j LgoKVG8gc3VwcHJlc3MgdGhpcyBtZXNzYWdlIGluIHRoZSByZWdpc3RlcmVkIHZlcnNpb24KdW5j aGVjayAiT3B0aW9ucyB8IEFuaW1hZ2ljIGNvbW1lbnQgZnJhbWUiCgAh+QQJGQABACwAAAAAIAAg AAAF1mAgjmRpnmiqrqrjvjCLugNsO3LpDPz91rgcggf07XqyYa/nI9ZWytqy6HQGT1HrtEq8mhjc 45b7NImB5DTSrP6py6UoLfweLEwGpuBcJ95LYEANYm5vfyQOeQ4Ng12LfFyHIw5gi41AApdqkiIO CUxdjJppnAGBYYyQBQUERAoleW2QRAWuJFmOfbW1rySnfVy7A70jsV3ARAc8xCO/RXNkC8rDWGGz ZAgpzsgD2Srbfd4rCZ/ALjki5OXWXjKWoz2D6AEvooM2ojEtAADvqfz+BgE0EQIAIfkECRkAAQAs AAAAACAAIAAABc5gII5kaZ5oqq6q474wi7oDbDty6Qz8/da4HIIH9O16smGv5yPWVsrasuh0Bk9R 67RKvJoY3OOW+zSJgeQ00qz+qculKC38HixMhum5TryXwFKBVHV+JA55R2KJhGZgMFt7XIUjDglM XZhvkyKAYW5OBQUERAoleW2RRAWkJFldqVWrq6UknXxcsgO0I6eZtwMHPLsjtkVzZAvBulievwgp xb8DzyrRfNQrCZa3Ljki2tueXjIODeaR5eMrL+bnNu0xLQAA5e0NDvP18PkmIQAh+QQJGQABACwA AAAAIAAgAAAF02AgjmRpnmiqrqrjvjCLug9sO3LpPPz91rgchgf07XqyYa/nI9ZWytqy6HQGT1Hr tEq8mjLc45b7NImB5DTSrP6py6UoLfx+VEwWpuRcJ95LYEANYm5vfyQOeQ4Ng12LfFyHIw5gi41A EpdqkiIOF0xdjJppnAGBYYyQERFOFCV5bZBErDyuI1mOfaystiOnfVy7D70isF3ARBO1X1U2m8rD WGGyZBgpv8g81irYwNsrF5/ALjki4eLTXjKWoz2D5QEvooM2ojEtEBDsqfn7g/0mQgAAOw== --=====000_Dragon888240703733_=====-- From chemistry-request@server.ccl.net Tue Mar 4 09:54:12 2003 Received: from mail-a.bcc.ac.uk ([144.82.100.21]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h24EsBP17474 for ; Tue, 4 Mar 2003 09:54:11 -0500 Received: from pop-b.ucl.ac.uk by mail-a.bcc.ac.uk with SMTP (Mailer) with ESMTP; Tue, 4 Mar 2003 14:54:09 +0000 Received: from chem135 (chem135.chem.ucl.ac.uk [128.40.76.135]) by pop-b.ucl.ac.uk (8.11.6+Sun/8.9.3) with SMTP id h24Es6O14823 for ; Tue, 4 Mar 2003 14:54:06 GMT Message-ID: <005601c2e25e$77ecb540$874c2880@chem.ucl.ac.uk> Reply-To: Carole Ouvrard From: Carole Ouvrard To: ccl list Subject: DFT population density with g98 Date: Tue, 4 Mar 2003 14:58:08 -0000 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 X-UCL-MailScanner: Found to be clean Dear All, I am using Gaussian98 to run population analysis calculations on whether MP2 or B3LYP optimised structures. For each method I would like to get the density which is available with MP2 using Density=MP2 or current. For DFT, it seems that the density is calculated using the SCF procedure. Does anyone know if it uses the results of Kohn-Sham, or if it is calculated from HF ones. In other words is it the "true " dft density that we get ? If it is not, is there any other way to get it ? Many thanks for your help. carole -------------------------------------------------------------------------- Dr Carole Ouvrard Centre for Theoretical and Computational Chemistry University College London 20 Gordon Street LONDON - WC1H 0AJ U.K. http://www.ucl.ac.uk/~ucca17p/ Email: c.ouvrard@ucl.ac.uk Tel: (0) 20 7679 4665 --------------------------------------------------------------------------- From chemistry-request@server.ccl.net Tue Mar 4 10:21:36 2003 Received: from gatekeeper.tripos.com ([192.160.145.62]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h24FLaP18499 for ; Tue, 4 Mar 2003 10:21:36 -0500 Received: (from uucp@localhost) by gatekeeper.tripos.com (8.11.6+Sun/8.11.6) id h24FJMG22098 for ; Tue, 4 Mar 2003 09:19:22 -0600 (CST) Received: from cairo.tripos.com(172.20.176.21) by gatekeeper.tripos.com via csmap (V6.0) id srcAAASCaikR; Tue, 4 Mar 03 09:19:21 -0600 Received: (from nmalcolm@localhost) by cairo.tripos.com (SGI-8.9.3/8.9.3) id PAA44709; Tue, 4 Mar 2003 15:32:14 GMT Date: Tue, 4 Mar 2003 15:32:14 GMT Message-Id: <200303041532.PAA44709@cairo.tripos.com> X-Authentication-Warning: cairo.tripos.com: nmalcolm set sender to nmalcolm@tripos.com using -f From: "Nathaniel O.J. Malcolm" To: c.ouvrard@ucl.ac.uk CC: chemistry@ccl.net In-reply-to: <005601c2e25e$77ecb540$874c2880@chem.ucl.ac.uk> (message from Carole Ouvrard on Tue, 4 Mar 2003 14:58:08 -0000) Subject: Re: CCL:DFT population density with g98 Sender: nmalcolm@tripos.com Reply-To: nmalcolm@tripos.com Organization: Tripos UK Ltd. References: <005601c2e25e$77ecb540$874c2880@chem.ucl.ac.uk> Carole, Yes this will be the DFT density. Noj >>Dear All, >> >>I am using Gaussian98 to run population analysis calculations on whether MP2 >>or B3LYP optimised structures. For each method I would like to get the >>density which is available with MP2 using Density=MP2 or current. For DFT, >>it seems that the density is calculated using the SCF procedure. Does anyone >>know if it uses the results of Kohn-Sham, or if it is calculated from HF >>ones. In other words is it the "true " dft density that we get ? >>If it is not, is there any other way to get it ? >>Many thanks for your help. >>carole >> >>-------------------------------------------------------------------------- >>Dr Carole Ouvrard >>Centre for Theoretical and Computational Chemistry >>University College London >>20 Gordon Street >>LONDON - WC1H 0AJ >>U.K. >>http://www.ucl.ac.uk/~ucca17p/ >>Email: c.ouvrard@ucl.ac.uk >>Tel: (0) 20 7679 4665 >>--------------------------------------------------------------------------- -- -------------------------------- Dr. N.O.J. Malcolm Software Support Scientist Tripos UK Ltd nmalcolm@tripos.com Tel +44 (0)1908 650020 Fax +44 (0)1908 650001 -------------------------------- Sybyl, Unity and other products are exclusive property of Tripos & are protected trademarks, copyrights, & patents as appropriate The information in this e-mail is confidential and may have associated legal obligations. It is intended for the exclusive attention of the addressee stated above and should not be copied or disclosed to any other. If you have received this transmission in error, please contact the sender. From chemistry-request@server.ccl.net Tue Mar 4 13:48:24 2003 Received: from nature.Berkeley.EDU ([128.32.175.19]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h24ImNR02224 for ; Tue, 4 Mar 2003 13:48:23 -0500 Received: from localhost (localhost [127.0.0.1]) by nature.Berkeley.EDU (Postfix) with ESMTP id 9A9CE261261 for ; Tue, 4 Mar 2003 10:48:22 -0800 (PST) Received: from nature.Berkeley.EDU ([127.0.0.1]) by localhost (nature.Berkeley.EDU [127.0.0.1:10024]) (amavisd-new) with ESMTP id 23214-08 for ; Tue, 4 Mar 2003 10:48:21 -0800 (PST) Received: from nature.berkeley.edu (localhost [127.0.0.1]) by nature.Berkeley.EDU (Postfix) with SMTP id 2322026126B for ; Tue, 4 Mar 2003 10:48:21 -0800 (PST) Received: from 128.32.27.14 (SquirrelMail authenticated user moconnor) by nature.Berkeley.EDU with HTTP; Tue, 4 Mar 2003 10:48:21 -0800 (PST) Message-ID: <2283.128.32.27.14.1046803701.squirrel@nature.Berkeley.EDU> Date: Tue, 4 Mar 2003 10:48:21 -0800 (PST) Subject: crystal modelling From: "Dr. Mary V. O'Connor" To: "computational chemistry" X-Priority: 3 Importance: Normal X-Mailer: SquirrelMail (version 1.2.11) MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Virus-Scanned: by amavisd-new Hello, CCLers: Does anyone have any specific book references that deal with computational modelling of crystals and solids? The more detailed, the better! Thanks, Mary Mary V. O'Connor, Ph.D. Rm. 235 Hilgard Hall University of California Berkeley, CA 94704 From chemistry-request@server.ccl.net Tue Mar 4 13:25:38 2003 Received: from evans.univer.kharkov.ua ([80.92.225.132]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h24IPWR01809 for ; Tue, 4 Mar 2003 13:25:33 -0500 Received: from spin.univer.kharkov.ua (spin.univer.kharkov.ua [192.168.213.252]) by evans.univer.kharkov.ua (8.12.6/8.12.5) with SMTP id h24IPRfS030378 for ; Tue, 4 Mar 2003 20:25:27 +0200 Received: by spin.univer.kharkov.ua with Microsoft Mail id <01C2E28B.9F34E2D0@spin.univer.kharkov.ua>; Tue, 4 Mar 2003 20:21:21 +0200 Message-ID: <01C2E28B.9F34E2D0@spin.univer.kharkov.ua> From: "sergey i. kotelevskii" To: "'CCL community'" Subject: GAMESS error Date: Tue, 4 Mar 2003 20:21:20 +0200 MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h24IPcR01810 Dear All, Could someone explain the error message generated by PC GAMESS? The program treats molecular symmetry in a strange way: it produces new atoms as if Unique Atoms were only presented while full molecular frame is really given. Attached is an example of the Furan molecule (9 atoms, 6 Unique Atoms, C2v (i.e. Cnv 2) group of symmetry). INPUT (in Cartesians): ********************************************************************************************************* !MCSCF=CASSCF optimization !$CONTRL SCFTYP=MCSCF CITYP=ALDET RUNTYP=OPTIMIZE COORD=CART $END $CONTRL SCFTYP=RHF CITYP=ALDET RUNTYP=ENERGY COORD=CART $END $CONTRL EXETYP=CHECK $END $BASIS GBASIS=N311 NGAUSS=6 NDFUNC=2 NPFUNC=2 $END $BASIS DIFFSP=.TRUE. $END $SCF DIRSCF=.TRUE. $END $DATA Furan.inp Cnv 2 C 6.0 -0.71644 0.95625 -0.00037 C 6.0 -1.09404 -0.34564 0.00026 O 8.0 0.00000 -1.15854 0.00000 C 6.0 1.09404 -0.34564 -0.00026 C 6.0 0.71644 0.95625 0.00037 H 1.0 -2.04794 -0.83980 0.00039 H 1.0 2.04794 -0.83981 -0.00038 H 1.0 -1.37052 1.81029 -0.00065 H 1.0 1.37052 1.81029 0.00065 $END $GUESS GUESS=HUCKEL $END !$GUESS GUESS=MOREAD $END $MCSCF CISTEP=ALDET FORS=.TRUE. $END $DET NCORE=3 NACT=6 NELS=6 $END ******************************************************************************************************** OUTPUT: ******************************************************************************************************** 1 ****************************************************** * GAMESS VERSION = 6 MAY 1998 * * FROM IOWA STATE UNIVERSITY * * M.W.SCHMIDT, K.K.BALDRIDGE, J.A.BOATZ, S.T.ELBERT, * * M.S.GORDON, J.H.JENSEN, S.KOSEKI, N.MATSUNAGA, * * K.A.NGUYEN, S.J.SU, T.L.WINDUS, * * TOGETHER WITH M.DUPUIS, J.A.MONTGOMERY * * J.COMPUT.CHEM. 14, 1347-1363(1993) * ********Intel x86 (WIN32, OS/2, DOS32) VERSION******** * PC GAMESS version 5.3, build number 1637 * * Compiled on Thursday, 01-07-1999, 01:10:20 * * Intel specific optimization, bug fixes, * * code changes, and additional functionality - * * copyright (c) 1994, 1999 by Alex. A. Granovsky, * * Laboratory of Chemical Cybernetics, * * Moscow State University, Moscow, Russia. * * PC GAMESS URL: * * http://classic.chem.msu.su/gran/gamess/index.html * * E-mail: gran@classic.chem.msu.su * * This program should not be redistributed * * without special permission of its developers. * ****************************************************** (Intermediate, omitted) BASIS OPTIONS ------------- GBASIS=N311 IGAUSS= 6 POLAR=POPN311 NDFUNC= 2 DIFFSP= T NPFUNC= 2 DIFFS= F SPLIT2= 2.00000000 0.50000000 RUN TITLE --------- Furan.inp THE POINT GROUP OF THE MOLECULE IS CNV THE ORDER OF THE PRINCIPAL AXIS IS 2 THE MOMENTS OF INERTIA ARE (AMU-ANGSTROM**2) IXX= 53.285 IYY= 54.255 IZZ= 107.540 ERROR! YOUR CART/ZMT/ZMTMPC INPUT GENERATED 16 ATOMS, BUT ONLY 9 ATOMS WERE PRESENT IN YOUR $DATA. THIS MEANS THERE IS A MISTAKE IN YOUR COORDINATES, OR YOUR CHOICE OF GROUP. ADIOS, MY FRIEND!! AFTER PRINCIPAL AXIS TRANSFORMATION, THE PROGRAM HAS CHOSEN THE FOLLOWING ATOMS AS BEING UNIQUE: C 6.0 0.0003734749 -0.7164190483 0.9844888517 C 6.0 -0.0002544974 -1.0940467557 -0.3173931127 O 8.0 0.0000003185 -0.0000240533 -1.1303163939 H 1.0 -0.0003797960 -2.0479572719 -0.8115328135 H 1.0 0.0003703369 2.0479227307 -0.8116299743 H 1.0 0.0006565188 -1.3704808727 1.8385427704 EXECUTION OF GAMESS TERMINATED ABNORMALLY AT 18:19:09 LT 4-MAR-2003 CPU TIME: STEP = 0.12 , TOTAL = 0.2 SECONDS ( 0.0 MIN) WALL CLOCK TIME: STEP = 0.26 , TOTAL = 0.3 SECONDS ( 0.0 MIN) CPU UTILIZATION: STEP = 46.22%, TOTAL = 80.89% 100000 WORDS OF DYNAMIC MEMORY USED STOP IN ABRT ******************************************************************************************************* One another run (with Gaussian Z-matrix) led to similar results. What does it mean? Thanks for your attention. Serghey. ****************************** Serghey I. Kotelevskii, Department of Theoretical Chemistry and Astrochemistry, Research Institute for Chemistry, Kharkiv VNKarazin National University, Svobody Square 4, UA-61077 Kharkiv, UKRAINE E-mail: kotelevskiy@univer.kharkov.ua From chemistry-request@server.ccl.net Tue Mar 4 15:02:53 2003 Received: from aguila.dti.udec.cl ([152.74.16.63]) by server.ccl.net (8.11.6/8.11.0) with SMTP id h24K2rR03976 for ; Tue, 4 Mar 2003 15:02:53 -0500 Received: (qmail 31949 invoked from network); 4 Mar 2003 20:02:53 -0000 Received: from andes.dpi.udec.cl (HELO udec.cl) ([127.0.0.1]) (envelope-sender ) by 0 (qmail-ldap-1.03) with SMTP for ; 4 Mar 2003 20:02:53 -0000 Message-ID: <3E65066C.4020802@udec.cl> Date: Tue, 04 Mar 2003 17:02:52 -0300 From: "Dr. Antonio Buljan" User-Agent: Mozilla/5.0 (Macintosh; U; PPC; en-US; rv:1.0.1) Gecko/20020823 Netscape/7.0 X-Accept-Language: en,pdf MIME-Version: 1.0 To: chemistry@ccl.net Subject: G98w in DOS Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Dear All.. Someone knows as can be runed gaussian98w under the interface MS-DOS of a PC? I tries the following alternative: g98 < file.gjf > file.out g98w < file.gjf > file.out but no works Some suggestions? Thanks in advances for your kind replies. Dr. Antonio Buljan Facultad de Ciencias Quimicas Universidad de Concepcion CHILE From chemistry-request@server.ccl.net Tue Mar 4 16:32:35 2003 Received: from zephyr.meteo.McGill.CA ([132.206.43.13]) by server.ccl.net (8.11.6/8.11.0) with SMTP id h24LWZR06617 for ; Tue, 4 Mar 2003 16:32:35 -0500 Received: from kinetic.Meteo.McGill.CA by zephyr.meteo.McGill.CA (AIX 4.1/UCB 5.64/4.03) id AA21880; Tue, 4 Mar 2003 16:26:57 -0500 Date: Tue, 4 Mar 2003 16:31:29 -0500 From: Andrew Ryzhkov X-Mailer: The Bat! (v1.61) Reply-To: Andrew Ryzhkov Organization: Dep. of Atm. & Oc. Sci. McGill Univ. X-Priority: 3 (Normal) Message-Id: <19214134156.20030304163129@zephyr.meteo.mcgill.ca> To: "Dr. Antonio Buljan" Cc: chemistry@ccl.net Subject: Re: CCL:G98w in DOS In-Reply-To: <3E65066C.4020802@udec.cl> References: <3E65066C.4020802@udec.cl> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Dr. Antonio Buljan, DAB> Someone knows as can be runed gaussian98w DAB> under the interface MS-DOS of a PC? DAB> I tries the following alternative: DAB> g98 < file.gjf > file.out DAB> g98w < file.gjf > file.out DAB> but no works DAB> Some suggestions? Just try the following command c:\g98\g98.exe file.gjf The output file will be "file.out" Note that this will work only under Windows, in DOS box, not in native DOS. Best regards, Andrew Dr. Andrei Ryjkov Departments of Chemistry, and Atmospheric and Oceanic Sciences, McGill University, 805 Sherbrooke St. West #808 Montreal, Quebec, CANADA, H3A 2K6. -------------------------------------- Phone: +1(514)398-8867 Fax: +1(514)398-6115 -------------------------------------- E-mail: Andrew@Zephyr.Meteo.McGill.Ca Internet: http://RedAndr.tripod.com