From chemistry-request@ccl.net Thu Feb 26 11:21:51 2004 Received: from Post-Office.UH.EDU (NS3.UH.EDU [129.7.1.20]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i1QGLocS006958 for ; Thu, 26 Feb 2004 11:21:50 -0500 Received: from 129-7-239-220.dhcp.uh.edu (129-7-239-220.dhcp.uh.edu [129.7.239.220]) by Post-Office.UH.EDU (PMDF V6.0-025 #30599) with ESMTP id <0HTP0AU869F0D1..at..Post-Office.UH.EDU> for chemistry..at..ccl.net; Thu, 26 Feb 2004 10:21:00 -0600 (CST) Date: Thu, 26 Feb 2004 10:19:33 -0600 From: Jerry Ebalunode Subject: Re: CCL:Question on using AutoDock 3.0 In-reply-to: <20040226072530.16911.qmail..at..web9702.mail.yahoo.com> To: Bruno Sopko , chishotr..at..whitman.edu, chemistry..at..ccl.net Reply-to: jebalunode..at..UH.EDU Message-id: <200402261019.33509.jebalunode..at..uh.edu> Organization: University of Houston MIME-version: 1.0 Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: 7bit Content-disposition: inline User-Agent: KMail/1.5.4 References: <20040226072530.16911.qmail..at..web9702.mail.yahoo.com> X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net What is your default unix shell? Is it bash , csh or tcsh? On Thursday 26 February 2004 01:25 am, Bruno Sopko wrote: > I am afraid you will have to recompile the source code. It should work. > > Bruno Sopko > > chishotr..at..whitman.edu wrote: > > I am attempting to use AutoDock 3.0 free of charge from Scripps in order to > do molecular docking and modeling and am having a bit of trouble. I am > using a MacOS X platform, and have downloaded and located the appropriate > executables, but am unable to get them to run. When I click on the > "AutoDock" executable, it brings up a Unix terminal with the following > message: > > Last login: Mon Feb 23 11:39:35 on ttyp1 > /Users/biology/Desktop/autodock3; exit > Welcome to Darwin! > SCI-317-03:~ biology$ /Users/biology/Desktop/autodock3; exit > Segmentation fault > logout > [Process completed] > > > Does anyone have any information that could help me with this problem? My > Unix knowledge is fairly limited, so any relevant information would be much > appreciated. Thank you very much for your help. > > Tyler Chisholm > Whitman College > Walla Walla, WA 99362 > > -------------------------------------------------- > This mail sent through Whitman College Webmail 3.1 > > > and send your message to: CHEMISTRY..at..ccl.net > > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > Jan Labanowski, jlabanow..at..nd.edu (read about it on CCL Home Page) > > > > > > > --------------------------------- > Do you Yahoo!? > Get better spam protection with Yahoo! Mail -- Cheers, Jerry Ebalunode Graduate Research Assistant RM 402F Houston Science Center Phone: 713-743-8367 Dept. of Biology and Biochemistry University of Houston 4800 Calhoun Road Houston, TX 77204 From chemistry-request@ccl.net Thu Feb 26 12:07:11 2004 Received: from mailgate.tripos.com (mailgate.tripos.com [192.160.145.7]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i1QH79cS008236 for ; Thu, 26 Feb 2004 12:07:09 -0500 Message-ID: From: "Paul Hawkins" To: "Szilveszter Juhos" , Date: Thu, 26 Feb 2004 12:09:42 -0500 Subject: RE: Docking software vithout validation MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4925.2800 In-Reply-To: <20040226073653.GB845$at$computer.org> Importance: Normal X-eShield-AntiVirus: Passed X-eShield-AntiVirus-Message: Scanned by http://www.bluecoat.com/eShield X-Spam-Status: No, hits=0.8 required=7.0 tests=PRIORITY_NO_NAME autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Szilva, How would you judge success in such a comparison? Several criteria come to mind; Reproduction of rmsd of a ligand from a crystal structure? Ranking the "native" ligand highest in a cross-docking experiment? Scoring high affinity compounds well, and low affinity compounds poorly? Or perhaps a good correlation between score and binding affinity? Enriching known active compounds from a large pool of known inactive compounds? I look forward to your response. Paul. Paul Hawkins Applications Scientist Tripos Inc 1699 South Hanley Road St. Louis MO 63144 Ph: 617-899-4151 E-mail: phawkins$at$tripos.com www.tripos.com -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request$at$ccl.net]On Behalf Of Szilveszter Juhos Sent: Thursday, February 26, 2004 2:37 AM To: chemistry$at$ccl.net Subject: CCL:Docking software vithout validation Dear All, As flexible docking getting to be an accepted tool in virtual screening, it is nice to see the growing number of such software available on the market. My only problem is that most of them in the last months comes without any validation data stating simply that "we are the champions". It is just like walking in from the street and trying to sell something without scientific background. Probably it works for double glazing but I am pretty sure companies spent months with validation so I would encourage them to publish their comparison data. It is true not only for docking of course. The so called "GOLD set" is more or less the "golden standard" of such docking studies and easily available, it is even pre-processed for docking. So please, please use it and random library sets (as used ie with Glide) if possible. Thanks: Szilva -= This is automatically added to each message by the mailing script =- To send e-mail to subscribers of CCL put the string CCL: on your Subject: line and send your message to: CHEMISTRY$at$ccl.net Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST$at$ccl.net HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs If your mail is bouncing from CCL.NET domain send it to the maintainer: Jan Labanowski, jlabanow$at$nd.edu (read about it on CCL Home Page) -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@ccl.net Thu Feb 26 13:11:15 2004 Received: from user-12l23ps.cable.mindspring.com (user-12l23ps.cable.mindspring.com [69.81.15.60]) by server.ccl.net (8.12.8/8.12.8) with SMTP id i1QIB7cS010003 for ; Thu, 26 Feb 2004 13:11:12 -0500 Received: from 182.222.80.234 by 69.81.15.60; Thu, 26 Feb 2004 13:12:18 -0500 Message-ID: From: "Angie Rios" Reply-To: "Angie Rios" To: chemistry)at(ccl.net Subject: SPEED UP Your DSL, Cable, Satellite or T1 Connection, polysaccharide abo petition borroughs Date: Thu, 26 Feb 2004 13:12:18 -0500 X-Mailer: MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="--4665121740470017238" X-Spam-Status: No, hits=0.8 required=7.0 tests=BIZ_TLD autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net ----4665121740470017238 Content-Type: text/plain; Content-Transfer-Encoding: 7Bit Are you getting the most out of your Internet Connection? 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