From chemistry-request@server.ccl.net Tue Nov 9 22:17:46 1999 Received: from relay2.scripps.edu (relay2.scripps.edu [137.131.200.30]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id WAA20788 for ; Tue, 9 Nov 1999 22:17:46 -0500 Received: from job.scripps.edu (job.scripps.edu [137.131.108.78]) by relay2.scripps.edu (8.9.3/TSRI-3.1.0r) with ESMTP id TAA07524; Tue, 9 Nov 1999 19:07:24 -0800 (PST) Received: from localhost (garrett@localhost) by job.scripps.edu (8.9.1a/TSRI-2.8) with SMTP id TAA02800; Tue, 9 Nov 1999 19:07:24 -0800 (PST) Date: Tue, 9 Nov 1999 19:07:24 -0800 (PST) From: "Garrett M. Morris" X-Sender: garrett@job To: CHEMISTRY@ccl.net cc: tzvika_a@md2.huji.ac.il Subject: New AutoDock FAQ up on the web... In-Reply-To: <38283C4B.6C65E17@oxmol.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi Everyone, Recently, Tvzika Aviv (tzvika_a@md2.huji.ac.il) asked a question about a shell script that called a nawk program, but which gave an "arg list too long" error. I have answered this question in the new FAQ which I am going to build on >from now on, as more questions come in. You can all take a look at this on the web, at: http://www.scripps.edu/pub/olson-web/doc/autodock/index.html and click on the "FAQ" link at the top or bottom of the page, or on the "Frequently Asked Questions (FAQ)" link under the AutoDock Links section. The direct URL is: http://www.scripps.edu/pub/olson-web/doc/autodock/faq.html Check this page often, and let me know if you have any AutoDock-related FAQs you have, so I can keep it up-to-date. More information about the latest version of AutoDock can be found in the Journal of Computational Chemistry, in the article: Morris, G. M., Goodsell, D. S., Halliday, R.S., Huey, R., Hart, W. E., Belew, R. K. and Olson, A. J. (1998), "Automated Docking Using a Lamarckian Genetic Algorithm and an Empirical Binding Free Energy Function", J.Comput.Chem., 19:1639-1662, Happy Docking, 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 Wed Nov 10 06:28:27 1999 Received: from main.amu.edu.pl (root@main.amu.edu.pl [150.254.65.7]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA22435 for ; Wed, 10 Nov 1999 06:28:26 -0500 From: jolanala@main.amu.edu.pl Received: from k2r0p7 (pb154.poznan.ppp.tpnet.pl [212.160.11.154]) by main.amu.edu.pl (8.9.1a/8.9.1) with SMTP id MAA07756 for ; Wed, 10 Nov 1999 12:20:23 +0100 (MET) Message-Id: <199911101120.MAA07756@main.amu.edu.pl> To: CHEMISTRY@ccl.net Date: Wed, 10 Nov 1999 12:19:50 +0100 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: request X-Confirm-Reading-To: jolanala@main.amu.edu.pl X-pmrqc: 1 Priority: normal X-mailer: Pegasus Mail for Win32 (v3.01d) Content-Transfer-Encoding: 7BIT Hi Netters, Does anybody know how can I convert word file from PC to Mac. Jolanta From chemistry-request@server.ccl.net Wed Nov 10 09:22:55 1999 Received: from nucleus.harvard.edu (nucleus.harvard.edu [140.247.90.196]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA24070 for ; Wed, 10 Nov 1999 09:22:55 -0500 Received: from localhost (daizadeh@localhost) by nucleus.harvard.edu (8.9.3/8.9.3) with ESMTP id JAA09777 for ; Wed, 10 Nov 1999 09:17:52 -0500 (EST) Date: Wed, 10 Nov 1999 09:17:52 -0500 (EST) From: Iraj Daizadeh To: chemistry@ccl.net Subject: MultipleAlignmentParse. Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL, Anyone have source for a program that can read-in a clustal-formatted multiple alignment and return the number of occurrances of a particular amino acid in a particular column. Any suggestions would be appreciated. Thanks, Iraj Iraj Daizadeh, Ph.D. Harvard University Department of Cellular and Molecular Biology The Biological Laboratories 16 Divinity Avenue Cambridge, MA 02138 Phone: (617) 495-0783 (617) 495-0560 Fax: (617) 496-4313 Email: daizadeh@nucleus.harvard.edu WebPage: http://mcb.harvard.edu/gilbert/daizadeh From chemistry-request@server.ccl.net Wed Nov 10 16:43:30 1999 Received: from neon.chem.ucla.edu (neon.chem.ucla.edu [128.97.35.251]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA26012 for ; Wed, 10 Nov 1999 16:43:30 -0500 Received: from localhost (yunfeng@localhost) by neon.chem.ucla.edu (8.8.0/8.8.0) with SMTP id NAA23019 for ; Wed, 10 Nov 1999 13:44:19 -0800 (PST) X-Authentication-Warning: neon.chem.ucla.edu: yunfeng owned process doing -bs Date: Wed, 10 Nov 1999 13:44:19 -0800 (PST) From: Yunfeng Hu To: chemistry@ccl.net Subject: about precomplex Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi,everyone Recently I'm doing some ion reaction and dipolar cycloaddition calculation. I found in both cases that the energy of reactants(simple energy sum of each reactant faraway) is larger than that of TS in gas phase. Can someone tell me how to find the precomplex in an unexpensive way? Thanks in advance. Yunfeng From chemistry-request@server.ccl.net Wed Nov 10 18:28:56 1999 Received: from mtiwmhc02.worldnet.att.net (mtiwmhc02.worldnet.att.net [204.127.131.37]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA26403 for ; Wed, 10 Nov 1999 18:28:56 -0500 Received: from dell ([12.73.131.179]) by mtiwmhc02.worldnet.att.net (InterMail v03.02.07.07 118-134) with SMTP id <19991110231931.GHAC11011@dell>; Wed, 10 Nov 1999 23:19:31 +0000 Message-Id: <3.0.6.32.19991110151835.00920100@postoffice.worldnet.att.net> X-Sender: davidgallagher@postoffice.worldnet.att.net X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.6 (32) Date: Wed, 10 Nov 1999 15:18:35 -0800 To: Yunfeng Hu From: David Gallagher Subject: Re: about precomplex Cc: chemistry@ccl.net In-Reply-To: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" If you are using MOPAC, first check you have a true transition state by running a FORCE calculation which should show one and only one negative vibration. Then run the IRC=1 and IRC=-1 calculations to find the reactants and products (minima) on either side of the transition state. One of these may lead to the precomplex or intermediate that you suspect. Regards, David Gallagher, Fujitsu CCS. At 01:44 PM 11/10/99 -0800, Yunfeng Hu wrote: >Hi,everyone >Recently I'm doing some ion reaction and dipolar cycloaddition >calculation. I found in both cases that the energy of reactants(simple >energy sum of each reactant faraway) is larger than that of TS in gas >phase. Can someone tell me how to find the precomplex in an unexpensive >way? >Thanks in advance. > >Yunfeng > > >