From chemistry-request@server.ccl.net Mon Jun 17 08:03:23 2002 Received: from ivory.trentu.ca ([192.75.12.103]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5HC3NH21996 for ; Mon, 17 Jun 2002 08:03:23 -0400 Received: from trentu.ca ([206.248.117.30]) by trentu.ca (PMDF V5.2-32 #37862) with ESMTP id <01KJ13G0SBAI0009G4@trentu.ca> for chemistry@ccl.net; Mon, 17 Jun 2002 08:03:05 EST Date: Mon, 17 Jun 2002 08:05:13 -0400 From: elewars Subject: Hartree-Fock, Pauli To: chemistry@ccl.net Message-id: <3D0DD079.8BCEDB3E@trentu.ca> MIME-version: 1.0 X-Mailer: Mozilla 4.79 [en] (WinNT; U) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en 2002 June 17 Re "Fermi repulsion": that should have been Pauli repulsion, of course (related to the Pauli exclusion principle). E. Lewars ================ From chemistry-request@server.ccl.net Mon Jun 17 10:12:30 2002 Received: from mailer.gwdg.de ([134.76.10.26]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5HECTH24274 for ; Mon, 17 Jun 2002 10:12:29 -0400 Received: from vrlab03.mpibpc.gwdg.de ([134.76.211.99] helo=mpi-bpc.mpg.de) by mailer.gwdg.de with esmtp (Exim 3.33 #11) id 17JxF7-00057y-00 for chemistry@ccl.net; Mon, 17 Jun 2002 16:12:29 +0200 Message-ID: <3D0DEDB2.7010004@mpi-bpc.mpg.de> Date: Mon, 17 Jun 2002 16:09:54 +0200 From: Vlad Cojocaru User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:0.9.4) Gecko/20011126 Netscape6/6.2.1 X-Accept-Language: en-us MIME-Version: 1.0 To: CCL list Subject: visualizing programs Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit I calculated the electron density and electrostatic potential of 2 amino purine using Gaussian 94. I would like to visualize them. Does somebody know any software for Linux that can do that? I am also interested if somebody did the same thing so that I can compare the results. If yes, can you please give me the reference? Thanks a lot, vlad -- Vlad Cojocaru Max Planck Institut for Biophysical Chemistry Deparment: 060 Am Fassberg 11, 37077 Goettingen, Germany tel: ++49-551-201.1389 e-mail: Vlad.Cojocaru@mpi-bpc.mpg.de From chemistry-request@server.ccl.net Mon Jun 17 06:29:24 2002 Received: from mailpost.aist-nara.ac.jp ([163.221.80.20]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5HATNH20865 for ; Mon, 17 Jun 2002 06:29:24 -0400 Received: from mailgate.aist-nara.ac.jp (mailgate.aist-nara.ac.jp [163.221.80.65]) by mailpost.aist-nara.ac.jp (Postfix) with SMTP id BB8A517FA84 for ; Mon, 17 Jun 2002 19:29:21 +0900 (JST) Received: (qmail 23423 invoked from network); 17 Jun 2002 19:29:21 +0900 Received: from tungstenn.aist-nara.ac.jp (HELO tungstenn) (163.221.138.74) by ismailgate.aist-nara.ac.jp with SMTP; 17 Jun 2002 19:29:21 +0900 Message-ID: <009701c215ea$b20b70e0$4a8adda3@tungstenn> From: "dakshanamurthy sivanesan" To: Subject: help Date: Mon, 17 Jun 2002 19:35:27 +0900 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0094_01C21636.21EBECF0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2600.0000 Disposition-Notification-To: "dakshanamurthy sivanesan" X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 This is a multi-part message in MIME format. ------=_NextPart_000_0094_01C21636.21EBECF0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi CCLr's, When I am looking at the literature it seems there are diverse = explanation about the term 'electron correlation'. But I may want to = expect somewhat definition of 'electron correlation', its origin, and = effect. Thanks in advance, -siva ------=_NextPart_000_0094_01C21636.21EBECF0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Hi CCLr's,

When I am looking at the literature it seems there are diverse = explanation=20 about the term 'electron correlation'. But I may want to expect = somewhat=20 definition of 'electron correlation', its = origin, and effect.

Thanks in advance,

-siva

------=_NextPart_000_0094_01C21636.21EBECF0-- From chemistry-request@server.ccl.net Mon Jun 17 12:58:16 2002 Received: from hotmail.com ([64.4.14.147]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5HGwFH27556 for ; Mon, 17 Jun 2002 12:58:15 -0400 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Mon, 17 Jun 2002 09:58:10 -0700 Received: from 128.235.249.42 by lw10fd.law10.hotmail.msn.com with HTTP; Mon, 17 Jun 2002 16:58:10 GMT X-Originating-IP: [128.235.249.42] From: "Deepangi Pandit" To: chemistry@ccl.net Date: Mon, 17 Jun 2002 12:58:10 -0400 Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 17 Jun 2002 16:58:10.0304 (UTC) FILETIME=[29096000:01C21620] Hello: I want to learn theory as well as practical examples of Autodock. I did go through Manual but I need some more detailed and user friendly tutorial using, which I can practice whole docking. Please suggest me some good reference or source of tutorial for AutoDock. Thank you, Deepangi _________________________________________________________________ Join the world’s largest e-mail service with MSN Hotmail. http://www.hotmail.com From chemistry-request@server.ccl.net Mon Jun 17 11:46:38 2002 Received: from ucidoor.unitedcatalysts.com ([208.23.162.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5HFkcH26009 for ; Mon, 17 Jun 2002 11:46:38 -0400 Received: by ucidoor.unitedcatalysts.com; (8.8.8/1.3/10May95) id LAA27807; Mon, 17 Jun 2002 11:46:37 -0400 (EDT) Received: from 10.1.0.50 by ucismtp02.unitedcatalysts.com (InterScan E-Mail VirusWall NT); Mon, 17 Jun 2002 11:44:45 -0400 Received: from lvlxch01.unitedcatalysts.com ([10.16.100.88]) by lvlmail.unitedcatalysts.com (PMDF V6.0-24 #41777) with ESMTP id <0GXU001BYWVMU2@lvlmail.unitedcatalysts.com>; Mon, 17 Jun 2002 11:40:35 -0400 (EDT) Received: by lvlxch01.unitedcatalysts.com with Internet Mail Service (5.5.2650.21) id ; Mon, 17 Jun 2002 11:44:02 -0400 Content-return: allowed Date: Mon, 17 Jun 2002 11:43:58 -0400 From: "Shobe, Dave" Subject: RE: help (electron repulsion) To: "'dakshanamurthy sivanesan'" , CHEMISTRY@ccl.net Message-id: <157A51F55AAAD3119CD70008C7B1629D01C15DBC@lvlxch01.unitedcatalysts.com> MIME-version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) 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 g5HFkcH26010 In practice "electron correlation" is a term to describe the inadequacies of the Hartree-Fock (single determinant) model. The best way I can describe the physics is that in the Hartree-Fock model, the repulsion energy between two electrons is calculated between an electron and the average electron density for the other electron. What is unphysical about this is that it doesn't take into account the fact that the electron will push away the other electrons as it moves around. This tendency for the electrons to stay apart diminishes the repulsion energy. --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. -----Original Message----- From: dakshanamurthy sivanesan [mailto:siva@is.aist-nara.ac.jp] Sent: Monday, June 17, 2002 6:35 AM To: CHEMISTRY@ccl.net Subject: CCL:help Hi CCLr's, When I am looking at the literature it seems there are diverse explanation about the term 'electron correlation'. But I may want to expect somewhat definition of 'electron correlation', its origin, and effect. Thanks in advance, -siva From chemistry-request@server.ccl.net Mon Jun 17 12:23:31 2002 Received: from gatekeeper.itqb.unl.pt (qmailr@[193.136.177.1]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g5HGNUH26597 for ; Mon, 17 Jun 2002 12:23:30 -0400 Received: (qmail 9358 invoked from network); 17 Jun 2002 16:23:24 -0000 Received: from mistral.itqb.unl.pt (sgodinho@193.136.176.14) by gatekeeper.itqb.unl.pt with SMTP; 17 Jun 2002 16:23:24 -0000 Received: from localhost (sgodinho@localhost) by mistral.itqb.unl.pt (8.9.3/8.9.3) with ESMTP id RAA12372 for ; Mon, 17 Jun 2002 17:23:24 +0100 Date: Mon, 17 Jun 2002 17:23:23 +0100 (WEST) From: Sofia Godinho To: CCL Subject: Rb 6-31 G* basis set needed Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, I need to perform calculations on molecules containing Rubidium using Gaussian 98 using 6-31G*. As the 6-31 G* basis set is missing for Rubidium I would like some help to find references, web sites or, even better, the basis set itself. May I thank you in advance for your help. Sofia Sofia Godinho, PhD CFMC, University of Lisbon, Portugal Email: sgodinho@itqb.unl.pt From chemistry-request@server.ccl.net Mon Jun 17 20:27:15 2002 Received: from cdanc02.nc.rd.canon.com ([146.184.1.62]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5I0RBH10597 for ; Mon, 17 Jun 2002 20:27:15 -0400 content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Subject: Photinics West 2003 Integrated Optics Call for Papers X-MimeOLE: Produced By Microsoft Exchange V6.0.5762.3 Date: Mon, 17 Jun 2002 17:27:11 -0700 Message-ID: <5A2DAADC74A1C847B3EA24ECCA028A00115C22@cdanc02.nc.rd.canon.com> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: Photinics West 2003 Integrated Optics Call for Papers Thread-Index: AcIWXuNINS+KOlzFTTmFTOKey8hGNg== From: "Thoms, Travis" To: "Computational Chemistry List (E-mail)" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g5I0RFH10600 Greetings: If you do modeling of materials or device design in the field of integrated optics, please consider presenting a talk or poster at Photonics West 2003. To save space, I will only post the part of the Call pertinent to modeling: The goal of this conference is to provide an interdisciplinary update and review of innovations in IO materials, devices and applications, manufacturing technologies, and theoretical and experimental tools that support these innovations. The conference includes, but is not limited to, the following topics (WG: waveguide, IO: integrated optics, NL: nonlinear): * Theory and Modeling: Numerical modeling methods and design tools Novel IO devices Propagation phenomena in special WG structures (e.g., photonic band-gap structures) Optical guided-wave circuit design Etc. If you would like a full version of the "Call for Papers", or if you have any questions, please let me know. Sincerely, Travis Thoms Canon Development Americas travis.thoms@cda.canon.com From chemistry-request@server.ccl.net Mon Jun 17 16:13:04 2002 Received: from f04n07.cac.psu.edu ([128.118.141.35]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5HKD4H31580 for ; Mon, 17 Jun 2002 16:13:04 -0400 Received: from ra.chem.psu.edu (ra.chem.psu.edu [128.118.199.40]) by f04n07.cac.psu.edu (8.9.3/8.9.3) with ESMTP id QAA337118 for ; Mon, 17 Jun 2002 16:13:01 -0400 Content-Type: text/plain; charset="us-ascii" From: Rajarshi Guha Reply-To: rajarshi@presidency.com To: CCL Subject: conversion of a 3d image of a molecule to 2d Date: Mon, 17 Jun 2002 16:11:07 -0400 X-Mailer: KMail [version 1.4] MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Message-Id: <200206171611.12570.rajarshi@presidency.com> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi, does anybody know of any freeware programs that will convert a 3d molecular structure (from a hin or MDL mol file) to a 2D represenation suitable for printing/saving as a gif et al? TIA, - -- - ------------------------------------------------------------------- Rajarshi Guha | email: rajarshi@presidency.com 417 Davey Laboratory | web : http:// www.jijo.cjb.net Dept. Of Chemistry | ICQ : 123242928 Pennsylvania State University | AIM : LoverOfPanda - ------------------------------------------------------------------- GPG Fingerprint: DCCB 4D1A 5A8B 2F5A B5F6 1F9E CDC4 5574 9017 AF2A Public Key : http://pgp.mit.edu/ - ------------------------------------------------------------------- Breadth-first search is the bulldozer of science. -- Randy Goebel -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.0.6 (GNU/Linux) Comment: For info see http://www.gnupg.org iD8DBQE9DkJgzcRVdJAXryoRAv4cAJkBVVvyfqtbSfqERGZeAu6svSAfXgCggydc TFladPuZ6Y7O3gULK6gkBZE= =N517 -----END PGP SIGNATURE----- From chemistry-request@server.ccl.net Mon Jun 17 14:06:34 2002 Received: from hotmail.com ([64.4.15.110]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5HI6YH28819 for ; Mon, 17 Jun 2002 14:06:34 -0400 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Mon, 17 Jun 2002 11:06:28 -0700 Received: from 128.235.249.42 by lw10fd.law10.hotmail.msn.com with HTTP; Mon, 17 Jun 2002 18:06:23 GMT X-Originating-IP: [128.235.249.42] From: "Deepangi Pandit" To: chemistry@ccl.net, garrett@scripps.edu, csaba@ovrisc.mdche.u-szeged.hu, zhang@biokemi.su.se, zhang@server.biokemi.su.se Date: Mon, 17 Jun 2002 14:06:23 -0400 Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 17 Jun 2002 18:06:28.0546 (UTC) FILETIME=[B3C77A20:01C21629] Hello: After going through Archives of CCL ,I feel you all can help me. I have just started using AutoDock 3.0 and I am starting with HIV gp120 and small molecule for docking. Please suggest me sources, references in which basics and applications of AutoDock with reference to HIV gp120 or protein and small ligand is discussed. Thank you very much, Deepangi _________________________________________________________________ Chat with friends online, try MSN Messenger: http://messenger.msn.com From chemistry-request@server.ccl.net Mon Jun 17 19:04:25 2002 Received: from webshield01.net.kent.edu ([131.123.75.125]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5HN4PH03714 for ; Mon, 17 Jun 2002 19:04:25 -0400 Received: from localhost (unknown [127.0.0.1]) by webshield01.net.kent.edu (Postfix on SuSE Linux) with ESMTP id BD7DE22B177 for ; Mon, 17 Jun 2002 21:59:15 +0000 (UTC) Received: from sergio (sergio.chem.kent.edu [131.123.232.24]) by webshield01.net.kent.edu (Postfix on SuSE Linux) with ESMTP id D2BC522B16B for ; Mon, 17 Jun 2002 17:59:14 -0400 (EDT) Message-ID: <004201c21653$4ac02c00$18e87b83@ligquim.ffclrp.usp.br> Reply-To: "Sergio Emanuel Galembeck" From: "Sergio Emanuel Galembeck" To: Subject: G98: vizualize orbitals in TD-DFT Date: Mon, 17 Jun 2002 19:04:10 -0400 Organization: =?Windows-1252?Q?Universidade_de_S=E3o_Paulo?= MIME-Version: 1.0 Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2600.0000 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 X-Virus-Scanned: by AMaViS perl-11 Dear Netters, I am interested in a graphical program to analyse molecular orbitals calculated by TD-DFT and printed using iop(5/33=2). I tried Molden and Molekel without result. Best regards, Sergio ============================================================== Sergio Emanuel Galembeck Assistant Professor in Physical Chemistry Laboratorio de Modelagem Molecular Departamento de Quimica Faculdade de Filosofia, Ciencias e Letras de Ribeirao Preto Universidade de Sao Paulo Av Bandeirantes, 3900 Ribeirao Preto, SP Brasil phone: +55-16-602-37-65 fax: +55-16-633-81-51 e-mail: segalemb@usp.br ============================================================== From chemistry-request@server.ccl.net Mon Jun 17 23:36:47 2002 Received: from rwcrmhc52.attbi.com ([216.148.227.88]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5I3alH15215 for ; Mon, 17 Jun 2002 23:36:47 -0400 Received: from C1353359A ([12.228.187.177]) by rwcrmhc52.attbi.com (InterMail vM.4.01.03.27 201-229-121-127-20010626) with SMTP id <20020618033642.JJBF2751.rwcrmhc52.attbi.com@C1353359A>; Tue, 18 Jun 2002 03:36:42 +0000 Reply-To: From: "Mark Thompson" To: "Sergio Emanuel Galembeck" , Subject: RE: G98: vizualize orbitals in TD-DFT Date: Mon, 17 Jun 2002 20:39:34 -0700 Message-ID: <000001c21679$c3595260$0300a8c0@attbi.com> MIME-Version: 1.0 Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2911.0) X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4807.1700 Importance: Normal In-Reply-To: <004201c21653$4ac02c00$18e87b83@ligquim.ffclrp.usp.br> Try ArgusLab http://www.arguslab.com It will plot grid data that Gaussian saves to cube files. Mark ================================= Mark Thompson, Ph.D. Planaria Software Seattle, WA. http://www.arguslab.com ================================= > -----Original Message----- > From: Computational Chemistry List [mailto:chemistry-request@ccl.net]On > Behalf Of Sergio Emanuel Galembeck > Sent: Monday, June 17, 2002 4:04 PM > To: chemistry@ccl.net > Subject: CCL:G98: vizualize orbitals in TD-DFT > > > Dear Netters, > > I am interested in a graphical program to analyse molecular orbitals > calculated by TD-DFT and printed using iop(5/33=2). I tried Molden and > Molekel without result. > > Best regards, > > Sergio > > ============================================================== > Sergio Emanuel Galembeck > Assistant Professor in Physical Chemistry > Laboratorio de Modelagem Molecular > Departamento de Quimica > Faculdade de Filosofia, Ciencias e Letras de Ribeirao Preto > Universidade de Sao Paulo > Av Bandeirantes, 3900 > Ribeirao Preto, SP > Brasil > > phone: +55-16-602-37-65 > fax: +55-16-633-81-51 > e-mail: segalemb@usp.br > ============================================================== > > > > > -= 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 > > > > > >