From chemistry-request@server.ccl.net Fri Aug 18 09:17:09 2000 Received: from gollum.med.harvard.edu ([134.174.168.173]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA07487 for ; Fri, 18 Aug 2000 09:17:09 -0400 Received: from hms.harvard.edu (localhost [127.0.0.1]) by gollum.med.harvard.edu (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id JAA07615 for ; Fri, 18 Aug 2000 09:15:46 -0300 (EST) Sender: jeremy@hms.harvard.edu Message-ID: <399D28F2.526ADF20@hms.harvard.edu> Date: Fri, 18 Aug 2000 09:15:46 -0300 From: Jeremy Jenkins Organization: Harvard Medical School X-Mailer: Mozilla 4.07C-SGI [en] (X11; I; IRIX64 6.5 IP28) MIME-Version: 1.0 To: chemistry@ccl.net Subject: AutoDock library screening? Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear AutoDock users: Is it possible to dock a virtual chemical library in .sdf format or any other format using AutoDock? Has anyone done it and are there references? Incidentally, a dumb question: why are binding free energies so high in docking scores compared to protein-protein delta Gs? Jeremy Jenkins Research Fellow Harvard Medical School jeremy_jenkins@hms.harvard.edu From chemistry-request@server.ccl.net Thu Aug 17 22:38:22 2000 Received: from exconnect.levels.unisa.edu.au (exconnect.levels.unisa.edu.au [130.220.36.204]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id WAA04096 for ; Thu, 17 Aug 2000 22:38:19 -0400 Received: by exconnect.levels.unisa.edu.au with Internet Mail Service (5.5.2650.21) id ; Fri, 18 Aug 2000 12:07:03 +0930 Message-ID: <5DA42F8A3C18D111979400AA00DD609D035F34E4@exstaff3.levels.unisa.edu.au> From: Phuong-Cac Nguyen To: "'chemistry@ccl.net'" Subject: ab initio method for organic compounds Date: Fri, 18 Aug 2000 12:07:04 +0930 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-Type: text/plain Dear CCLers, I wish to calculate LUMO and HOMOs for N-Allyl-O-Alkyl thiocarbamate molecules using an ab initio method. These are straight chain molecules containing C, O, N, H and C=C, C=S bonds with up to 12 atoms in the backbone. Which ab initio method should I use ? Which basis sets ? Thank you for your time. Phuong-Cac Thi Phuong-Cac Nguyen Ian Wark Research Institute University of South Australia Australia phuong-cac.nguyen@unisa.edu.au From chemistry-request@server.ccl.net Fri Aug 18 10:39:04 2000 Received: from goshen.rutgers.edu (0@goshen.rutgers.edu [165.230.180.150]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA07898 for ; Fri, 18 Aug 2000 10:39:03 -0400 Received: from eden.rutgers.edu (molly.envsci.rutgers.edu [165.230.5.148]) by goshen.rutgers.edu (8.8.8/8.8.8) with ESMTP id KAA28638 for ; Fri, 18 Aug 2000 10:38:51 -0400 (EDT) Message-ID: <399D4DF7.9041A77F@eden.rutgers.edu> Date: Fri, 18 Aug 2000 10:53:43 -0400 From: "Mary O'Connor" X-Mailer: Mozilla 4.08 [en] (Win98; I) MIME-Version: 1.0 To: chemistry@ccl.net Subject: (no subject) Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL folks: Are there any comprehensive reviews (no older than 1994) on the "evolution" of Gaussian basis sets? I would like one that derives (shows the math) of the Gaussian functions in detail, with a thorough explanation of how the primitives are formed and contracted, as well as a critique of the accuracy and uses of the most common basis sets. I have the article by Davidson and Feller from 1986 (Chemical Reviews), but would like something newer, if available. Thanks to all. Mary O'Connor Doctoral Candidate Rutgers University New Brunswick, NJ From chemistry-request@server.ccl.net Fri Aug 18 03:08:25 2000 Received: from draco.netpower.no (draco.netpower.no [212.33.133.34]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA05006 for ; Fri, 18 Aug 2000 03:08:23 -0400 From: acctcard2@hotmail.com Received: from basse.org ([212.33.133.63]) by draco.netpower.no (8.10.2/8.9.3) with SMTP id e7I77kN05407; Fri, 18 Aug 2000 09:07:50 +0200 Received: from 209.179.248.145 ([209.179.248.145]) by basse.org with Microsoft SMTPSVC(5.0.2195.1600); Fri, 18 Aug 2000 08:53:09 +0200 Message-ID: <00004f0f13a0$0000706a$00001a80@> To: Subject: Merchant Account - Limited Time - No Setup Fee 6784 Date: Thu, 17 Aug 2000 23:58:59 -0700 X-Priority: 3 X-MSMail-Priority: Normal X-OriginalArrivalTime: 18 Aug 2000 06:53:10.0779 (UTC) FILETIME=[F8E46CB0:01C008E0] HOW TO SUBSTANTIALLY INCREASE SALES: Easily accept major credit cards right away! 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Act now and all Setup & App. fees waived From chemistry-request@server.ccl.net Fri Aug 18 09:44:26 2000 Received: from pallas_ex003.pallas_uk ([195.167.133.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA07633 for ; Fri, 18 Aug 2000 09:44:25 -0400 Received: by pallas_ex003.pallas_uk with Internet Mail Service (5.5.2650.21) id ; Fri, 18 Aug 2000 14:41:30 +0100 Message-ID: <6972C0DE6B5DD41189F60000F81A10F7C851@pallas_ex003.pallas_uk> From: David Clark To: "'chemistry@ccl.net'" Subject: New Book Date: Fri, 18 Aug 2000 14:41:29 +0100 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-Type: text/plain; charset="iso-8859-1" Hello all As the editor, I am pleased to announce the publication of "Evolutionary Algorithms in Molecular Design" by Wiley-VCH. The book comprises 12 chapters >from experts in the application of EAs to molecular design problems 1 Introduction to Evolutionary Algorithms - Dr. Abby L. Parrill 2 Small-molecule Geometry Optimization and Conformational Search - Dr. Ron Wehrens 3 Protein-Ligand Docking - Dr. Garrett M. Morris, Prof. Arthur J. Olson and Dr. David S. Goodsell 4 De Novo Molecular Design - Dr. Valerie J. Gillet 5 Quantitative Structure-Activity Relationships - Dr. Sung-Sau So 6 Chemometrics - Dr. Ron Wehrens and Prof. Lutgarde M. C. Buydens 7 Chemical Structure Handling - Prof. Peter Willett 8 Molecular Diversity Analysis and Combinatorial Library Design - Dr. Lutz Weber 9 Evolutionary Algorithms in Crystallographic Applications - Prof. Kenneth D.M. Harris 10 Structure Determination by NMR Spectroscopy - Dr. Bryan C. Sanctuary 11 Protein Folding - Dr. Jan T. Pedersen 12 New Techniques and Future Directions - Dr. Andrew Tuson and Dr. David E. Clark For more information, please visit the Wiley-VCH web site: http://www.wiley-vch.de/books/tis/eng/3-527-30155-0.html Best wishes David David E. Clark, PhD ChemMedICa Pharmaceuticals Ltd. Rainham Road South Dagenham Essex RM10 7XS Tel. +44-(0)20-8919-3353/3820 Fax. +44-(0)20-8919-3859 Registered in England No. 3671653 Registered Office: Rolls House, 7 Rolls Building, Fetter Lane, London EC4A 1NH From chemistry-request@server.ccl.net Fri Aug 18 09:25:17 2000 Received: from world.std.com (root@world-f.std.com [199.172.62.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA07549 for ; Fri, 18 Aug 2000 09:25:16 -0400 Received: (from jle@localhost) by world.std.com (8.9.3/8.9.3) id IAA14676 for chemistry@ccl.net; Fri, 18 Aug 2000 08:53:26 -0400 (EDT) Date: Fri, 18 Aug 2000 08:53:26 -0400 (EDT) From: Joe M Leonard Message-Id: <200008181253.IAA14676@world.std.com> To: chemistry@ccl.net Subject: Spelunking question Folks, Does anybody have a clean copy of Mopac 6 source which I can get? The copy on CCL seems to have modifications for an Ultrix Decstation - I'd like as clean a copy as possible. Thanks in advance! Joe Leonard jle@world.std.com From chemistry-request@server.ccl.net Fri Aug 18 09:30:00 2000 Received: from theory.tc.cornell.edu (tc.cornell.edu [128.84.30.174]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA07559 for ; Fri, 18 Aug 2000 09:29:59 -0400 Received: from tc.cornell.edu (norbert.tc.cornell.edu [128.84.20.68]) by theory.tc.cornell.edu (8.8.4/8.8.3/CTC-1.0) with ESMTP id JAA15384; Fri, 18 Aug 2000 09:29:46 -0400 Message-ID: <399D3996.A16D546A@tc.cornell.edu> Date: Fri, 18 Aug 2000 09:26:46 -0400 From: Richard Gillilan X-Mailer: Mozilla 4.7 [en] (WinNT; I) X-Accept-Language: en MIME-Version: 1.0 To: Douglas_Stack/CAS/UNO/UNEBR@unomail.unomaha.edu CC: chemistry@ccl.net, Richard_Lomneth/CAS/UNO/UNEBR@unomail.unomaha.edu Subject: Re: CCL:Imagining Software References: <8625693E.006B21C2.00@unomail.unomaha.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Douglas_Stack/CAS/UNO/UNEBR@unomail.unomaha.edu wrote: > Does anyone know of a software package (Windows based preferably) that can that > a graphic file that represents 3-D on a 2-D image (color coded contour for > example) and generate a 2-D, graph of that data a certain point. This would > involve drawing a line across the picture and the program generating an x vs. y > graph for the data points on that line. If I could find a program that could > convert a color-coded .tiff into x,y,z coordinates, I could import the data to > Excel and accomplish the same thing. What is desired is to generate x vs. y. > graphs from a "3-D" picture (represented as a color coded .tiff image) by > selecting different segments of the .tiff image. > OpenDX (www.opendx.org) can do this kind of thing. If you read the tiff in with ReadImage, it will actaully reside within the data model as a regular grid with a colors component. If you Mark colors as data, you can then interpolate the data onto any arbitrary line via Map, or select out a row or column of pixels and send it to the Plot module. Plot is not as fancy or full-featured as some other 2D plot programs, but it will do the trick. You could also simple use OpenDX to convert your data and write it out. As always, OpenDX takes some time to learn (just like learning a scripting language) ... it is free. Richard Gillilan Cornell Theory Center From chemistry-request@server.ccl.net Fri Aug 18 14:14:54 2000 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 OAA09355 for ; Fri, 18 Aug 2000 14:14:51 -0400 Received: from localhost (amolive@localhost) by dedalus.lcc.ufmg.br (8.9.3/8.9.3) with SMTP id PAA31219; Fri, 18 Aug 2000 15:14:08 -0300 Date: Fri, 18 Aug 2000 15:14:08 -0300 (BSC) From: andre mauricio de oliveira To: Douglas_Stack/CAS/UNO/UNEBR@unomail.unomaha.edu cc: chemistry@ccl.net, Richard_Lomneth/CAS/UNO/UNEBR@unomail.unomaha.edu Subject: Re: CCL:Imagining Software In-Reply-To: <8625693E.006B21C2.00@unomail.unomaha.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Dr Stack, Maybe MatLab and Origin 5.0 are able to pursue this task. Greets. On Thu, 17 Aug 2000 Douglas_Stack/CAS/UNO/UNEBR@unomail.unomaha.edu wrote: > Does anyone know of a software package (Windows based preferably) that can that > a graphic file that represents 3-D on a 2-D image (color coded contour for > example) and generate a 2-D, graph of that data a certain point. This would > involve drawing a line across the picture and the program generating an x vs. y > graph for the data points on that line. If I could find a program that could > convert a color-coded .tiff into x,y,z coordinates, I could import the data to > Excel and accomplish the same thing. What is desired is to generate x vs. y. > graphs from a "3-D" picture (represented as a color coded .tiff image) by > selecting different segments of the .tiff image. > > Thanks in advance, > > Douglas E. Stack > Assistant Professor > Department of Chemistry > University of Nebraska at Omaha > Omaha, NE 68182-0109 > (402) 554-3647 > (402) 554-3888 (fax) > destack@unomaha.edu > > > > -= 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 Fri Aug 18 10:49:03 2000 Received: from scup.pdc.kth.se (root@isdn81.modempool.kth.se [130.237.10.81]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA08182 for ; Fri, 18 Aug 2000 10:49:01 -0400 Received: (from vahtras@localhost) by scup.pdc.kth.se (8.9.3/8.9.3) id OAA04308; Fri, 18 Aug 2000 14:35:22 +0200 Date: Fri, 18 Aug 2000 14:35:22 +0200 From: Olav Vahtras To: chemistry@ccl.net Subject: NWChem/ECCE workshop in Stockholm Message-ID: <20000818143522.R1209@ghiaurov.pdc.kth.se> Mail-Followup-To: chemistry@ccl.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Mailer: Mutt 1.0.1i Announcement: A workshop on the quantum chemistry code NWChem and the graphical interface ECCE will be held in Stockholm at the Royal Institute of Technology, October 19-20. All lectures and tutorials will be held by staff from Pacific Northwest National Laboratories (PNNL). Topics will include Hartree-Fock, MCSCF, coupled cluster, DFT, molecular mechanics, mixed QM/MM methods. For more information and registration, please see http://www.pdc.kth.se/training/2000/NWChem -- Olav Vahtras vahtras@pdc.kth.se Center for Parallel Computers Phone +46 8 790 62 70 Royal Institute of Technology Mobile +46 70 644 44 55 SE-100 44 Stockholm Fax +46 8 24 77 84 Sweden From chemistry-request@server.ccl.net Fri Aug 18 15:12:05 2000 Received: from facepe.dqf.ufpe.br (root@facepe.dqf.ufpe.br [150.161.5.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA09641 for ; Fri, 18 Aug 2000 15:12:01 -0400 Received: from npd.ufpe.br (danon.dqf.ufpe.br [150.161.5.125]) by facepe.dqf.ufpe.br (8.9.3/8.8.7) with ESMTP id QAA09893 for ; Fri, 18 Aug 2000 16:15:29 -0300 Message-ID: <399D8AB1.E5071AB5@npd.ufpe.br> Date: Fri, 18 Aug 2000 16:12:49 -0300 From: Patricia Farias X-Mailer: Mozilla 4.7 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: vibrational Schrodinger equation Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hi CCL´s ! I need an algorithm that solves the vibrational Schrödinger equation (Numerov-Cooley method or others). I would be grateful if some of you could help me with some information related to this topic. Thanks in advance Patricia Farias Depto. de Quimica Fundamental - UFPE Recife - PE - Brasil From chemistry-request@server.ccl.net Fri Aug 18 15:44:40 2000 Received: from ucb-ap.ucb-group.com (mail.ucb-group.com [195.90.79.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA09769 for ; Fri, 18 Aug 2000 15:44:39 -0400 Received: from ntexch1.hq.ucb (localhost [127.0.0.1]) by ucb-ap.ucb-group.com (8.9.3/8.9.3) with ESMTP id VAA29226 for ; Fri, 18 Aug 2000 21:27:59 +0200 (MET DST) Message-ID: <9FAD6F6FBD8ED21192D50008C7B1629403AD10F0@camrsv1.cambridge.ucb> From: Rao Sreedhara To: "'chemistry@ccl.net'" Date: Fri, 18 Aug 2000 21:33:32 +0200 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-Type: text/plain; charset="iso-8859-1" Dear CCLers, Can anyone share their experiences with MOPAC 2000 for protein optimzations? I would like to know the kind of structural differences between a simple homology models vs. "optimized" structures using Mozyme in MOPAC 2000. -Sree Rao voleti@hotmail.com