From cdac.ernet.in!gadre@parcom.ernet.in Mon Feb 16 09:12:16 1998 Received: from naveen.ncst.ernet.in for cdac.ernet.in!gadre@parcom.ernet.in by www.ccl.net (8.8.3/950822.1) id IAA21742; Mon, 16 Feb 1998 08:31:25 -0500 (EST) Received: from iucaa (iucaa.ernet.in [202.141.155.1]) by naveen.ncst.ernet.in (8.6.12/8.6.6) with SMTP id TAA22853 for ; Mon, 16 Feb 1998 19:09:42 +0530 Received: from iucaa by iucaa (5.65v3.2/SMI-4.1) id AA31294; Mon, 16 Feb 1998 18:58:20 +0500 Received: by parcom.cdac.ernet.in (4.1/SMI-4.1) id AA18695; Mon Feb 16 18:45:46 1998 (GMT + 0530) Date: Mon Feb 16 18:45:46 1998 (GMT + 0530) From: gadre@cdac.ernet.in Subject: Urea dimer/oligomers ab initio/semiempirical ? Message-Id: <9802161315.AA18695@parcom.cdac.ernet.in> To: CHEMISTRY@www.ccl.net Dear Sirs and Madams : Are you aware of any ab initio/semi-empirical RECENT study on urea dimer, trimer and higher aggregate formation? We are interested in understanding the how and why of this process. Any information on energetics, geometries etc. will be welcome. Thanking you in advance...............Shridhar Gadre From bryanv@chemweb.com Mon Feb 16 10:12:16 1998 Received: from mhexchange.epress.co.uk for bryanv@chemweb.com by www.ccl.net (8.8.3/950822.1) id JAA22097; Mon, 16 Feb 1998 09:19:37 -0500 (EST) Received: by mhexchange.epress.co.uk with Internet Mail Service (5.5.1960.3) id ; Mon, 16 Feb 1998 14:19:08 -0000 Message-ID: From: Bryan Vickery Subject: "Should the Medicinal Chemist have Access to Modeling Tools? Does the Web have the Answer" Date: Mon, 16 Feb 1998 14:19:05 -0000 Monday February 16, 1998, London "Should the Medicinal Chemist have Access to Modeling Tools? Does the Web have the Answer" ChemWeb announce their third in a series of Virtual Lectures. The live event will take place in ChemWeb's Chemistry Auditorium on Wednesday February 25, 1998 from 16:00 GMT. The presentation, given by Dr. Osman Guner of MSI, will showcase Web-based client server software, WebLab (TM) MedChem Explorer (TM), allowing participants real-time hands-on experience through the Internet. Conference participants will then be able to schedule several hours of hands-on access, through a URL announced during the lecture, to MedChem Explorer (TM). You can register for the event at http://chemweb.vei.co.uk/ Registration and participation is FREE. Abstract follows: ___________________________________________________________ Abstract As medicinal chemists use computers, networks and the Internet in their daily lives, they are expected to be more productive. In addition, there has been an increasing motivation to have medicinal chemists more involved in computational chemistry tasks. Computational tools hold the promise of directing medicinal chemists towards compounds with a higher probability of success. This is because computational tools facilitate the rational decision making involved in designing drugs with a desired activity. Generally, medicinal chemists have been collaborating with molecular modelers who use complicated computational tools; however, as the medicinal chemists' computational demands increase, they welcome the opportunity to use these computational tools in their own environment. The Internet provides this opportunity. Practically all pharmaceutical companies are now effectively using their corporate intranet to communicate and retrieve information. Web browsers connected to corporate networks have become one of the most important productivity tools in the hands of chemists. A modeling and analysis environment that is built on top of this infrastructure can benefit from the familiar interface and paradigm in which medicinal chemists are comfortable. It is believed at MSI that successful deployment of modeling and analysis tools to the non-computational chemist is possible by: Utilizing existing intranet infrastructure within corporations Using Web browsers as the primary tool for accessing information and performing modeling and analysis tasks Establishing a client-server Web environment as well as a native desktop application Integrating into the existing corporate informatics environment Making tools more user-friendly and easy-to-use, providing an intuitive single task focus for each application. An example for implementation of the above criteria will be showcased with Web-based client server software, WebLab(tm) MedChem Explorer(tm). The provision of access to UNIX-based modeling software (including Cerius2 and Catalyst), as well as corporate databases (such as ISIS, Catalyst, and Daylight) will be discussed. The discussion will also highlight how the intuitive browser-based interface accesses exactly the same tools used by computational chemists, directly from laptops or PCs, within the same environment used for writing reports and spreadsheets as well as accessing the Internet and Email. Osman F. Guner _____________________________________________________________ The lecture will take the form of a one hour slide show with real-time chat and discussion. We look forward to welcoming you to the ChemWeb Chemistry Auditorium at VEI. ** Please post this announcement wherever applicable ** ____________________________________________________________ ChemWeb is the World Wide Club for the Chemical Community - Membership is FREE. Join us today at http://ChemWeb.com/ ________________________________ Bryan A. Vickery Development Executive - ChemWeb Inc. Middlesex House 34 - 42 Cleveland Street London W1P 6LB http://ChemWeb.com/ T: + 44 171 323 0323 F: + 44 171 436 9293 From karl.irikura@nist.gov Tue Feb 17 08:12:29 1998 Received: from email.nist.gov for karl.irikura@nist.gov by www.ccl.net (8.8.3/950822.1) id HAA01278; Tue, 17 Feb 1998 07:51:53 -0500 (EST) Received: from bratsche (bratsche.nist.gov [129.6.194.154]) by email.nist.gov (8.8.5/8.8.5) with SMTP id HAA06025 for ; Tue, 17 Feb 1998 07:50:33 -0500 (EST) Message-Id: <3.0.5.32.19980217072719.00a313a0@mailserver3.nist.gov> X-Sender: irikura@mailserver3.nist.gov X-Mailer: QUALCOMM Windows Eudora Pro Version 3.0.5 (32) Date: Tue, 17 Feb 1998 07:27:19 -0800 To: chemistry@www.ccl.net From: Karl Irikura Subject: recommendations for MM software? Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" CCL: What MM software would you recommend for a brief (< 5 contact hours) laboratory course? The students will mostly be senior-level experimentalists. Ideally, something with a nice GUI and a short learning curve. The emphasis will be thermochemistry, so the FF should be something that reports heats of formation (e.g. MM2, MM3). Thanks for any help! Karl I. ---------------------------------------------- Dr. Karl K. Irikura Physical and Chemical Properties Division National Institute of Standards and Technology NIST 221/A111 Gaithersburg, MD 20899 voice: 301-975-2510 fax: 301-869-4020 e-mail: karl.irikura@nist.gov http://www.nist.gov/compchem/ ---------------------------------------------- From alex.klinsky@scientist.com Tue Feb 17 10:12:30 1998 Received: from unet.univie.ac.at for alex.klinsky@scientist.com by www.ccl.net (8.8.3/950822.1) id KAA02458; Tue, 17 Feb 1998 10:05:56 -0500 (EST) Received: from cardenolid (l222t5p44.netway.at [195.96.18.44]) by unet.univie.ac.at (8.7.1/8.7.1) with SMTP id QAA51762 for ; Tue, 17 Feb 1998 16:05:45 +0100 Message-ID: <000901bd3bb5$35f4d8c0$2c1260c3@cardenolid> From: "Alex" To: Subject: Autodock 2.4 for Windows NT ? Date: Tue, 17 Feb 1998 16:02:58 +0100 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 4.72.2106.1 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.1 Dear Colleaques ! Does anybody know of a working port of autodock 2.4 to the Windows NT platform or at least a working version for Intel Linux. Thanks in advance, Alexander Klinsky Institute of pharmaceutical chemistry Department of odour research University of Vienna Austria Europe From David.DeVito@chiphy.unige.ch Tue Feb 17 10:21:41 1998 Received: from sc2a.unige.ch for David.DeVito@chiphy.unige.ch by www.ccl.net (8.8.3/950822.1) id JAA01670; Tue, 17 Feb 1998 09:13:46 -0500 (EST) Received: from PCC2340E.unige.ch ([129.194.52.14]) by sc2a.unige.ch (PMDF V5.1-10 #10385) with SMTP id <01ITOVQTKM10001H1R@sc2a.unige.ch> for chemistry@www.ccl.net; Tue, 17 Feb 1998 15:13:33 MET Date: Tue, 17 Feb 1998 15:13:53 +0100 From: David De Vito Subject: Gamess basis set for Rhodium To: chemistry@www.ccl.net Message-id: <006f01bd3bae$47281780$0e34c281@PCC2340E.unige.ch> MIME-version: 1.0 X-Mailer: Microsoft Outlook Express 4.72.2106.4 Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: 7bit X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 X-Priority: 3 Hello ! I'd like make some calculations on a [Rh(H2O)6]2+ system and the problem is: what kind of basis set can I use ? For ECP basis set, the Gamess user's manual says that one can use the Stevens/Basch/Krauss/Jasien/Cundari valence basis set. But, I would like use a full electron basis set. Can someone advise me about this ? Thank you very much for the help ! Best regards, D. De Vito. **************************************************************** D. De Vito Department of Physical Chemistry Group of Prof. Weber (Computational Chemistry) University of Geneva Office 106 - Sciences II 30, Quai Ernest-Ansermet 1211 Geneva 4 / Switzerland +4122 / 702.65.35 (Office) +4179 / 310.05.76 (Mobile) +4122 / 733.38.35 (Home) http://lcta/~devito (Personal Page) http://www.unige.ch/sciences/chimie (Web Master) **************************************************************** From daizadeh@kappa.ucdavis.edu Tue Feb 17 14:12:32 1998 Received: from kappa.ucdavis.edu for daizadeh@kappa.ucdavis.edu by www.ccl.net (8.8.3/950822.1) id NAA03891; Tue, 17 Feb 1998 13:22:05 -0500 (EST) Received: (from daizadeh@localhost) by kappa.ucdavis.edu (950413.SGI.8.6.12/950213.SGI.AUTOCF) id KAA08496; Tue, 17 Feb 1998 10:27:03 -0800 From: "Iraj Daizadeh" Message-Id: <9802171027.ZM8494@kappa.ucdavis.edu> Date: Tue, 17 Feb 1998 10:27:03 -0800 X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: chemistry@www.ccl.net Subject: Fock matrix and Gaussian. Cc: Doug Fox Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hello. I used the following to print out the FOCK (alpha, beta) matrix from Gaussian 94: NTT = Nbasis*(NBasis+1)/2 Call FileIO(2,-IRwFA,NTT,V,0) do 212 i=1,NTT 212 write (IUnitFA,2010) V(i) C Call FileIO(2,-IRwFB,NTT,V,0) do 213 i=1,NTT 213 write (IUnitFB,2010) V(i) Interestingly, when I compared the values generated from this method to the standard Gaussian output; viz., IOp(5/33=5); I found that my numbers were slightly different from theirs. Input Deck: ------------------------------------------------------------------------------- # HF/sto-2g 6d 10f field=z+1000000 geom=coord pop=regular IOp(5/33=5) currents: H2 1+ ion , uhf 1 2 H 0.0 0.0 -4.0 He 0.0 0.0 0.0 H 0.0 0.0 4.0 ------------------------------------------------------------------------------- My output: Gaussian output: -0.528103473677385300000000000000E+00 -0.528103D+00 -0.207077182228009010000000000000E-03 -0.207077D-03 -0.957752692231662150000000000000E+00 -0.957753D+00 0.312943635332713380000000000000E-06 0.000000D+00 -0.257198121834262120000000000000E-03 -0.257198D-03 -0.446838441550770900000000000000E+00 -0.446838D+00 ------------------------------------------------------------------------------ The problem lies in the (1,3) (transposed) element. The number 10^-6 should have been printed out in the standard Gaussian output file; it wasn't. Any information would be greatly appreciated. Since our calculations rely almost completely on these small numbers, this may cause severe problems in our calculations. Thank you in advance for any aid into this matter. Iraj. -- Iraj Daizadeh Department of Chemistry University of California One Shields Ave. Davis, CA 95616-5295 Phone: 530.754.8695 Fax: 530.752.8995 email: daizadeh@kappa.ucdavis.edu From mao@csb0.IPC.PKU.EDU.CN Tue Feb 17 19:12:33 1998 Received: from csb0.IPC.PKU.EDU.CN for mao@csb0.IPC.PKU.EDU.CN by www.ccl.net (8.8.3/950822.1) id TAA05440; Tue, 17 Feb 1998 19:06:18 -0500 (EST) Received: by csb0.IPC.PKU.EDU.CN (920330.SGI/940406.SGI.AUTO) for CHEMISTRY@www.ccl.net id AA16208; Wed, 18 Feb 98 08:05:51 -0800 Date: Wed, 18 Feb 1998 08:05:50 -0800 (PST) From: Fenglou Mao To: "CHEMISTRY@www.ccl.net" Subject: Add Water to Proteins Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, cclers, Will anyone introduce any programs or papers about adding water to proteins? Thanks! Sincerely Yours, FengLou Mao ******************************* ADD:Mr. FengLou Mao Peking University BeiJing P.R.China Tel:86-10-62751490 Fax:86-10-62751725 From lzj@csb0.IPC.PKU.EDU.CN Tue Feb 17 21:12:35 1998 Received: from csb0.IPC.PKU.EDU.CN for lzj@csb0.IPC.PKU.EDU.CN by www.ccl.net (8.8.3/950822.1) id UAA05772; Tue, 17 Feb 1998 20:32:39 -0500 (EST) Received: by csb0.IPC.PKU.EDU.CN (920330.SGI/940406.SGI.AUTO) for chemistry@www.ccl.net id AA16928; Wed, 18 Feb 98 09:32:33 -0800 Date: Wed, 18 Feb 1998 09:32:30 -0800 (PST) From: Liu Zhijie To: Computational Chemistry List Subject: Processes in Genetic Algorithm Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL members, I would like to know some new information of Genetic Algorithm(GA).In particular,I am interested in the concrete methods in the reproduction,mutation and cross-over processes of GA. Any recommends and helpful references will be appreciated. Sincerely yours, Elmer ********************************************************************** Chinese Name: Zhijie Liu * English Name : Elmer ********************************************************************** MOLECULAR DESIGN LABORATORY *** TEL : 8610-62751490 (LAB ) INSTITUTE OF PHYSICAL CHEMISTRY *** 8610-62752096-1082 (DORM) PEKING UNIVERSITY *** FAX : 8610-62751725 BEIJING 100871 , P.R.CHINA *** EMAIL : lzj@ipc.pku.edu.cn ********************************************************************** ADDRESS: BUILDING 46* ROOM 1082* PEKING UNIVERSITY* 100871* P.R.CHINA ********************************************************************** From herrmann@hermes.informatik.uni-stuttgart.de Tue Feb 17 22:12:36 1998 Received: from ifi.informatik.uni-stuttgart.de for herrmann@hermes.informatik.uni-stuttgart.de by www.ccl.net (8.8.3/950822.1) id WAA06135; Tue, 17 Feb 1998 22:07:21 -0500 (EST) Received: by agamemnon.informatik.uni-stuttgart.de with ESMTP; Wed, 18 Feb 1998 04:06:44 +0100 (MET) Received: (from herrmann@localhost) by odysseus.informatik.uni-stuttgart.de (8.8.5/8.8.5) id EAA21494; Wed, 18 Feb 1998 04:06:42 +0100 (MET) Date: Wed, 18 Feb 1998 04:06:42 +0100 (MET) Message-Id: <199802180306.EAA21494@odysseus.informatik.uni-stuttgart.de> From: Frank Herrmann To: lzj@csb0.IPC.PKU.EDU.CN CC: chemistry@www.ccl.net In-reply-to: (message from Liu Zhijie on Wed, 18 Feb 1998 09:32:30 -0800 (PST)) Subject: Re: CCL:Processes in Genetic Algorithm Dear Elmer, The basic book about genetic algorithms is Goldbergs book. See below the references to this and some other books. Look at my web-page for some GA links and a bibliography of GAs applied to molecular structure prediction. hope this helps, --------------------------------------------------------------------- Frank Herrmann, Computer Scientist, PhD Student Institute of Parallel and Distributed High-Performance Systems (IPVR) University of Stuttgart Breitwiesenstrasse 20-22 D-70565 Stuttgart (Germany) email: Frank.Herrmann@informatik.uni-stuttgart.de http://www.informatik.uni-stuttgart.de/ipvr/bv/personen/herrmann.html --------------------------------------------------------------------- How often we forget all time, when lone Admiring Nature's universal throne; Her woods- her wilds- her mountains- the intense Reply of HERS to OUR intelligence! Stanzas . Edgar Allan Poe --------------------------------------------------------------------- @book{holland, author={John H. Holland}, title={Adaptation in Natural and Artificial Systems}, publisher={The University of Michigan Press}, address={Ann Arbor, MI}, year=1975} @book{goldberg, author={David E. Goldberg}, title={Genetic algorithms in search, optimization, and machine learning}, publisher={Addison-Wesley Publishing Company, Inc.}, year=1989} @book{davis, editor={Lawrance Davis}, title={Genetic Algorithms and Simulated Annealing}, publisher={Morgan Kaufmann Publishers}, year=1987} @book{handbook, editor={Lawrence Davis}, title={Handbook of Genetic Algorithms}, publisher={Van Nostrand Reinhold}, year=1991} @book{foundations, editor={Gregory J. E. Rawlins}, title={Foundations of Genetic Algorithms}, publisher={Morgan Kaufmann Publishers}, year=1991} @book{rechenberg, author={Ingo Rechenberg}, title={Evolutionsstrategie}, publisher={Friedrich Frommann Verlag}, year=1973} @book{smith, author={John Maynard Smith}, title={Evolutionary Genetics}, publisher={Oxford University Press}, year=1989}