From chemistry-request@server.ccl.net Wed Aug 18 06:02:26 1999 Received: from mail-b.bcc.ac.uk (mail-b.bcc.ac.uk [144.82.100.22]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA12833 for ; Wed, 18 Aug 1999 06:02:26 -0400 Received: from biochem.ucl.ac.uk (actually host bsmori1.biochem.ucl.ac.uk) by mail-b.bcc.ac.uk with SMTP (XT-PP) with ESMTP; Wed, 18 Aug 1999 10:57:07 +0100 Received: from bsmir18.biochem.ucl.ac.uk (bsmir18 [128.40.46.21]) by biochem.ucl.ac.uk (8.9.2/8.9.1) with ESMTP id KAA24312 for ; Wed, 18 Aug 1999 10:58:45 +0100 (BST) Received: from localhost (nobeli@localhost) by bsmir18.biochem.ucl.ac.uk (8.9.3/8.9.3) with SMTP id KAA25965 for ; Wed, 18 Aug 1999 10:58:44 +0100 (BST) X-Authentication-Warning: bsmir18.biochem.ucl.ac.uk: nobeli owned process doing -bs Date: Wed, 18 Aug 1999 10:58:44 +0100 (BST) From: Irene Nobeli X-Sender: nobeli@bsmir18 To: chemistry@ccl.net Subject: Re: Question on LUDI Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Many thanks for all the replies. I'll try them out. Here are the answers: I. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hello Irene, Load your protein/ligand pair into Insight II and use the Unmerge command (in the Modify pulldown) to separate the ligand into a second Insight II object. Then use the Ludi/Score command specifying the protein for the receptor and the new ligand object for the ligand. Best Wishes, Ann Giammona, Ph.D. ann@msi.com Project Manager, Rational Drug Design Molecular Simulations Inc. <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >From m.dooley@mailbox.uq.edu.au Wed Aug 18 00:44:22 1999 Hi Irene, Lesson4 of the online tutorials on ligand design will show you how to do this. Cheers Michael <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Irene, you wrote: > All I want is to be able to use the scoring. That used to be impossible [say 2-3 years ago]. But newer versions may be different. We implemented the scoring function in Sybyl's command language, although it didn't work perfectly. /Leif Norskov Novo Nordisk A/S Copenhagen Denmark LNL@novo.dk <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< From chemistry-request@server.ccl.net Wed Aug 18 08:39:19 1999 Received: from ahnet.net (mail.ahnet.net [207.213.224.25]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA14273 for ; Wed, 18 Aug 1999 08:39:18 -0400 Received: from kae (as1-669.fuse.net [216.68.39.161]) by ahnet.net (8.9.3/8.9.3) with SMTP id FAA34330 for ; Wed, 18 Aug 1999 05:35:23 -0700 (PDT) From: "Jason L. Douglas" To: Subject: Visualize Molecule Viewer; render molecules, surfaces, calculate energies, and geometry optimizations Date: Wed, 18 Aug 1999 08:37:07 -0500 Message-ID: <000401bee97e$c4090870$a12744d8@kae> 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 8.5, Build 4.71.2173.0 Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 I have just released the first major version of Visualize, a free molecule viewer (source code is also available for free) for Win95/98/NT which can open and view PDB and DAS (its own binary, proprietary format) files, build new molecules (using several organic chem sub-units) and proteins (from sequence information), and display these molecules in beautiful 3D (like RasMol or MSI's WebLab Viewer). It can also calculate a wide range of surfaces (electron density contours, electrostatic potential contours, Connolly, fused VDW spheres, full density plots) using RHF wavefunctions, and then map EP or density data to these surfaces using several various color spectrums. It also calculates energies (MNDO, PM3, AM1, RHF, ROHF, UHF, standard force field, and many more), Moller-Plesset 2nd Order and GUGA CI corrections, and solvent energies (PCM, SCRF, and Effective Fragment Potential). It can perform Monte Carlo simulations and geometry optimizations using analytic gradients of the ab initio methods. The graphics system was built using the ScientificGL API. QM calculations were implemented through a PC-GAMESS interface. This is an excellent program for both hobbyists who are looking for a cheap and easy way to explore molecular modeling, or for the professional looking to add to his arsenal-Visualize also has one of the best surfacing systems available for free. For more information and to download Visualize, go to: http://www.compbio.net/downloads/visualize/index.html From chemistry-request@server.ccl.net Wed Aug 18 09:54:20 1999 Received: from mailserv.mta.ca (root@mailserv.mta.ca [138.73.101.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA14681 for ; Wed, 18 Aug 1999 09:54:20 -0400 Received: from m0612.mta.ca (host-22-237.mta.ca [138.73.22.237]) by mailserv.mta.ca (8.9.3/8.9.3) with SMTP id KAA25728 for ; Wed, 18 Aug 1999 10:50:25 -0300 (ADT) Message-Id: <3.0.5.32.19990818105421.007b0c70@mailserv.mta.ca> X-Sender: mculf@mailserv.mta.ca X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.5 (32) Date: Wed, 18 Aug 1999 10:54:21 -0300 To: chemistry@ccl.net From: Miroslava Culf Subject: Equations on the internet Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear all, I would like to find out what is the best way in your opinion to publish equations on Internet? What programs do you use for publishing documents with equations on the web. Thanks to all that answer, Mira p.s.1. This is only remotely related to computational chemistry and I apologize but as there are many nice web sites for comp.chem. with equations I am sure that many of you have experience with such programs. p.s.2. If there is interest I will summarize answers. ____________________________________________________________ Miroslava Culf, Ph.D. 65 York St. Computer Services Department/Chemistry Department Mount Allison University Sackville, NB E4L 1E4 Canada e-mail: mculf@mta.ca tel. 506-364-2411 www.mta.ca ____________________________________________________________ From chemistry-request@server.ccl.net Mon Aug 16 11:33:55 1999 Received: from risky3.thchem.siu.edu (risky3.thchem.siu.edu [131.230.89.13]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA26865 for ; Mon, 16 Aug 1999 11:33:54 -0400 Received: from localhost (tapas@localhost) by risky3.thchem.siu.edu (AIX4.3/UCB 8.8.8/8.7) with SMTP id KAA11968; Mon, 16 Aug 1999 10:35:38 -0500 Date: Mon, 16 Aug 1999 10:35:38 -0500 (CDT) From: Tapas Kar To: Ruth Tanner cc: chemistry@ccl.net Subject: Re: CCL:Frequency Scaling Factors In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII B3LYP calculations with cc-pVDZ basis set: stretches involving hydrogen: 0.96 other vibrations: 0.976 JML Martin, Chem. Phys. Lett. 262, 97-104 (1996); see also Martin et al., J. Phys. Chem. 100, 15358-15367 (1996). J. Phys. Chem., 100, 15056, 1996 On Fri, 13 Aug 1999, Ruth Tanner wrote: > Date: Fri, 13 Aug 1999 18:38:27 -0400 (EDT) > From: Ruth Tanner > To: chemistry@ccl.net > Subject: CCL:Frequency Scaling Factors > > > Earlier someone was asking about scaling factors for B3LYP cc-pVTZ > frequency calculations. Could anyone give me a good reference for scaling > factors for B3LYP cc-pVDZ, MP2 cc-pVDZ and cc-pVTZ? > > thank you, > Ruth > > ----------------------------------------------------------------------------- > Ruth Tanner rtanner@uoguelph.ca > M.Sc. Candidate in Physical Chemistry University of Guelph > ----------------------------------------------------------------------------- > "Women and cats will do as they please, and men and dogs should relax > and get used to the idea." --Robert A. Heinlein > ============================================================================= > > > -= 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 > > > > > > -------------------------------------------- Tapas Kar, Ph. D Department of Chemistry Southern Illinois University at Carbondale Illinois 62901-4409 Fax: (618) 453 6408 Tel: (618) 453 6433(Lab) 6485(Office) -------------------------------------------- From chemistry-request@server.ccl.net Mon Aug 16 23:44:38 1999 Received: from out4.ibm.net (out4.ibm.net [165.87.194.239]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id XAA03839 for ; Mon, 16 Aug 1999 23:44:38 -0400 From: jerome.f.baker@ibm.net Received: from jerry---mary (slip-32-100-227-93.ny.us.ibm.net [32.100.227.93]) by out4.ibm.net (8.8.5/8.6.9) with ESMTP id DAA92212 for ; Tue, 17 Aug 1999 03:41:00 GMT Message-ID: <000801bee863$6a4ead60$5de36420@jerry---mary> Reply-To: "jerome f. baker" To: Subject: docking of lig. with hydrophobic grps. Date: Mon, 16 Aug 1999 22:48:46 -0500 MIME-Version: 1.0 Content-Type: text/plain; charset="utf-7" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.72.3155.0 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3155.0 Dear CCL subscribers, We are trying to do docking simulations between an enzyme (for which a good crystal structure exists), and a ligand which is charged, has several hydrophobic groups, and is very conformationaly flexible. Both charge and hydrophobicity appear to be important in the binding interactions. Does anyone have any suggestions for appropriate programs and/or approaches to a docking problem in which charge and hydrophobicity are both important factors? We will soon have Dock, AutoDock, and DockVision available to us. Thanks very much for any suggestions or ideas... Sincerely, Jerry Baker jfbaker+AEA-ibm.net From chemistry-request@server.ccl.net Wed Aug 18 11:26:24 1999 Received: from bacchus.pc1.uni-duesseldorf.de (root@bacchus.pc1.uni-duesseldorf.de [134.99.152.11]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA15321 for ; Wed, 18 Aug 1999 11:26:22 -0400 Received: from bacchus.pc1.uni-duesseldorf.de (jochen@localhost [127.0.0.1]) by bacchus.pc1.uni-duesseldorf.de (8.8.7/8.8.7) with SMTP id RAA23266; Wed, 18 Aug 1999 17:21:55 +0200 From: Jochen Reply-To: jochen@bacchus.pc1.uni-duesseldorf.de Organization: Heinrich-Heine-Universität To: Miroslava Culf , chemistry@ccl.net Subject: Re: CCL:Equations on the internet Date: Wed, 18 Aug 1999 17:20:35 +0200 X-Mailer: KMail [version 1.0.28] Content-Type: text/plain References: <3.0.5.32.19990818105421.007b0c70@mailserv.mta.ca> In-Reply-To: <3.0.5.32.19990818105421.007b0c70@mailserv.mta.ca> MIME-Version: 1.0 Message-Id: <99081817215404.15477@bacchus.pc1.uni-duesseldorf.de> Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id LAA15322 On Mit, 18 Aug 1999 Miroslava Culf wrote: >I would like to find out what is the best way in your opinion to publish >equations on Internet? >What programs do you use for publishing documents with equations on the web. I usually use LaTeX to do the writing, and the produce html or PDF by latex2html or pdfLaTeX, repsectivly. Esp. the second alternative gives _very_ nice results. -- Jochen From chemistry-request@server.ccl.net Wed Aug 18 18:39:36 1999 Received: from proxy4.ba.best.com (root@proxy4.ba.best.com [206.184.139.15]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA17288 for ; Wed, 18 Aug 1999 18:39:35 -0400 Received: from acc7 (dynamic58.pm02.san-mateo.best.com [205.149.174.122]) by proxy4.ba.best.com (8.9.3/8.9.2/best.out) with SMTP id PAA20832 for ; Wed, 18 Aug 1999 15:35:11 -0700 (PDT) Message-ID: <007a01bee9ca$0a911b20$099d18d1@vip.best.com> From: "Nicholas Sobb" To: Subject: Prediction of physico-chemical parameters online Date: Wed, 18 Aug 1999 15:35:13 -0700 Organization: Comgenex 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 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 You can predict pKa, logP and logD using your browser, without installing any software, by accessing CompuDrug's online prediction service at www.compudrug.com . The 1st 20 predictions are free of charge. Nicholas Sobb CompuDrug International www.compudrug.com (650)246-1470 From chemistry-request@server.ccl.net Wed Aug 18 19:22:33 1999 Received: from alchemy.chem.utoronto.ca (alchemy.chem.utoronto.ca [142.150.224.224]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id TAA17481 for ; Wed, 18 Aug 1999 19:22:33 -0400 Received: (from elewars@localhost) by alchemy.chem.utoronto.ca (8.9.3/8.9.3) id TAA04765 for chemistry@ccl.net; Wed, 18 Aug 1999 19:18:31 -0400 (EDT) Date: Wed, 18 Aug 1999 19:18:31 -0400 (EDT) From: "E. Lewars" Message-Id: <199908182318.TAA04765@alchemy.chem.utoronto.ca> To: chemistry@ccl.net Subject: C-13 NMR SHIFT AND CHARGE ON THE ATOM (?) 1999 August 18 Hello, I would appreciate it if someone could give me a reference to a paper or two showing the relationship between C-13 chemical shift (exp. or calc.) and the calculated charge (electrostatic potential, Lowdin, Mulliken, whatever) on the atom (if you plot NMR shift vs. calc. charge do you get a straight line, a hopeless scatter, or what?). Thanks very much E. Lewars =============================== From chemistry-request@server.ccl.net Wed Aug 18 12:16:34 1999 Received: from dedalus.lcc.ufmg.br (dedalus.lcc.ufmg.br [150.164.65.10]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA15595 for ; Wed, 18 Aug 1999 12:16:32 -0400 Received: from localhost (amolive@localhost) by dedalus.lcc.ufmg.br (8.9.3/8.9.3) with SMTP id NAA68501; Wed, 18 Aug 1999 13:11:52 -0300 Date: Wed, 18 Aug 1999 13:11:52 -0300 (BSC) From: andre mauricio de oliveira To: jerome.f.baker@ibm.net cc: chemistry@ccl.net Subject: Re: CCL:docking of lig. with hydrophobic grps. In-Reply-To: <000801bee863$6a4ead60$5de36420@jerry---mary> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Mon, 16 Aug 1999 jerome.f.baker@ibm.net wrote: Dear Dr Baker, Could you please tell me where have you gotten DockVision program(URL)? Thank you. > Dear CCL subscribers, > > We are trying to do docking simulations between an enzyme (for which a good > crystal structure exists), and a ligand which is charged, has several > hydrophobic groups, and is very conformationaly flexible. Both charge and > hydrophobicity appear to be important in the binding interactions. > > Does anyone have any suggestions for appropriate programs and/or approaches > to a docking problem in which charge and hydrophobicity are both important > factors? > > We will soon have Dock, AutoDock, and DockVision available to us. > > Thanks very much for any suggestions or ideas... > > Sincerely, > > Jerry Baker jfbaker+AEA-ibm.net > > > > > > > -= 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 > > > > > > Andre Mauricio de Oliveira VOICE +55-031-374-1325 +55-031-499-5765 FAX +55-031-499-5700 Laboratorio de QSAR e Modelagem Molecular Nucleo de Estudos em Quimica Medicinal (NEQUIM) NEQUIM's Homepage: http://www.qui.ufmg.br/~nequim Departamento de Quimica ICEx Federal University of Minas Gerais Av Antonio Carlos 6627 Pampulha ZIP CODE 31270-901 Belo Horizonte MG Brazil From chemistry-request@server.ccl.net Wed Aug 18 16:34:04 1999 Received: from server (bay2-43.la.ziplink.net [208.196.123.57]) by server.ccl.net (8.8.7/8.8.7) with SMTP id QAA16802; Wed, 18 Aug 1999 16:34:00 -0400 From: homebus@netcom.com Subject: Homeworkers needed. 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From chemistry-request@server.ccl.net Wed Aug 18 17:39:47 1999 Received: from uscmail.usc.es (uscmail.usc.es [193.144.75.8]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA17045 for ; Wed, 18 Aug 1999 17:39:46 -0400 Received: from qogolem (qogolem.usc.es [193.144.74.235]) by uscmail.usc.es (8.9.1/8.9.1) with SMTP id XAA18869 for ; Wed, 18 Aug 1999 23:35:46 +0200 (MET DST) From: "Armando Navarro" To: Subject: printing cas configurations Date: Wed, 18 Aug 1999 23:36:48 +0200 Message-ID: <01bee9c1$c7256830$eb4a90c1@qogolem.usc.es> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0006_01BEE9D2.8AAE3830" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 This is a multi-part message in MIME format. ------=_NextPart_000_0006_01BEE9D2.8AAE3830 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear All How can I print the weight of all configurations in a casscf calculation = in Gaussian98? Thanks in Advance Armando Navarro Departamento de quimica organica Facultade de quimica=20 Universidade de Santiago de Compostela e-mail qoajnv@uscmail.usc.es ------=_NextPart_000_0006_01BEE9D2.8AAE3830 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear All
How can I print the = weight of all=20 configurations in a casscf calculation in Gaussian98?
Thanks in = Advance
Armando = Navarro
Departamento de quimica = organica
Facultade de quimica =
Universidade de = Santiago de=20 Compostela
e-mail qoajnv@uscmail.usc.es
 
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