From chemistry-request@ccl.net Thu Feb 26 02:33:31 2004 Received: from mail2.uklinux.net (s4.uklinux.net [80.84.72.14]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i1Q7XTcS024835 for ; Thu, 26 Feb 2004 02:33:30 -0500 Received: from Moon (unknown [212.97.0.169]) by mail2.uklinux.net (Postfix) with ESMTP id 8CCEE409FAF for ; Thu, 26 Feb 2004 07:34:37 +0000 (UTC) Received: from szilva by Moon with local (Exim 3.35 #1 (Debian)) id 1AwG4j-0000EB-00 for ; Thu, 26 Feb 2004 08:36:53 +0100 Date: Thu, 26 Feb 2004 08:36:53 +0100 From: Szilveszter Juhos To: chemistry!at!ccl.net Subject: CCL: Docking software vithout validation Message-ID: <20040226073653.GB845!at!computer.org> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.3.28i 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 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 From chemistry-request@ccl.net Thu Feb 26 09:01:29 2004 Received: from ns01.ul.pt (ns01.ul.pt [194.117.1.42]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i1QE1RcS002540 for ; Thu, 26 Feb 2004 09:01:27 -0500 Received: from exchange01.ul.pt ([10.101.251.101]) by ns01.ul.pt (8.11.6/8.11.6) with ESMTP id i1QE1Tp30999 for ; Thu, 26 Feb 2004 14:01:35 GMT content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="Windows-1252" X-MimeOLE: Produced By Microsoft Exchange V6.0.6249.0 Subject: Geometry Optimization Rookie question Date: Thu, 26 Feb 2004 14:02:24 -0000 Message-ID: <20EEEB6FC0FA60418ADFD585FAD645211E9305!at!exchange01.ul.pt> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: Geometry Optimization Rookie question Thread-Index: AcP8cSjSqaTdD0fZTZ+Oj9tBXwqVlg== From: =?Windows-1252?Q?Jos=E9_Gon=E7alo_Deira_Duarte_Justino?= To: 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 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i1QE1TcS002544 Hi u all! Just a simple question: what method would u use to calculate bond angles and lenghts and similar of compounds like 1-phenyl-antracene? Any sugestions welcome are - I've tried semi-empirical (AM1 and PM3) but I'm somewhat disastified with the results! Cheers, Tino From chemistry-request@ccl.net Thu Feb 26 10:59:59 2004 Received: from ccc018.chemie.uni-erlangen.de (ccc018.chemie.uni-erlangen.de [131.188.128.18]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i1QFxvcS005513 for ; Thu, 26 Feb 2004 10:59:58 -0500 Received: from localhost (localhost [127.0.0.1]) by ccc018.chemie.uni-erlangen.de (Postfix) with ESMTP id 2F4E311A75; Thu, 26 Feb 2004 17:01:05 +0100 (CET) Received: from ccc018.chemie.uni-erlangen.de ([127.0.0.1]) by localhost (ccc018 [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 23355-09; Thu, 26 Feb 2004 17:00:58 +0100 (CET) Received: from chemie.uni-erlangen.de (equinox.chemie.uni-erlangen.de [131.188.128.90]) by ccc018.chemie.uni-erlangen.de (Postfix) with ESMTP id 523D411A6C for ; Thu, 26 Feb 2004 17:00:58 +0100 (CET) Sender: Harald.Lanig!at!chemie.uni-erlangen.de Message-ID: <403E183A.E22BBCFA!at!chemie.uni-erlangen.de> Date: Thu, 26 Feb 2004 17:00:58 +0100 From: Harald Lanig Organization: Computer-Chemie-Centrum X-Mailer: Mozilla 4.79 [en] (X11; U; Linux 2.4.18-4GB i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry!at!ccl.net Subject: 1st Circular: 18th Molecular Modelling Workshop - May 18-19, 2004 in Erlangen, Germany Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Virus-Scanned: by amavisd-new at chemie.uni-erlangen.de 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 Dear list members, the first Circular giving additional details concerning the 18th Darmstaedter Molecular Modelling Workshop in Erlangen, Germany (May 18-19, 2004) is now available via the URL http://www.chemie.uni-erlangen.de/ccc/conference/mmws04/circular1.html Thank you very much for your consideration! Regards, -Harald Lanig -- ------------------------------------------------------------------------ Dr. Harald Lanig Universitaet Erlangen/Nuernberg Computer-Chemie-Centrum Naegelsbachstr. 25, D-91052 Erlangen Phone +49(0)9131-85 26525 Mailto:lanig..at..chemie.uni-erlangen.de Fax +49(0)9131-85 26565 http://www.ccc.uni-erlangen.de/lanig ------------------------------------------------------------------------ From chemistry-request@ccl.net Thu Feb 26 02:24:24 2004 Received: from web9702.mail.yahoo.com (web9702.mail.yahoo.com [216.136.129.138]) by server.ccl.net (8.12.8/8.12.8) with SMTP id i1Q7OKcS024581 for ; Thu, 26 Feb 2004 02:24:20 -0500 Message-ID: <20040226072530.16911.qmail=at=web9702.mail.yahoo.com> Received: from [193.179.225.19] by web9702.mail.yahoo.com via HTTP; Wed, 25 Feb 2004 23:25:30 PST Date: Wed, 25 Feb 2004 23:25:30 -0800 (PST) From: Bruno Sopko Subject: Re: CCL:Question on using AutoDock 3.0 To: chishotr=at=whitman.edu, chemistry=at=ccl.net In-Reply-To: <1077565653.403a58d57a2ee=at=www.whitman.edu> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="0-68384484-1077780330=:15892" X-Spam-Status: No, hits=0.0 required=7.0 tests=HTML_MESSAGE autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net --0-68384484-1077780330=:15892 Content-Type: text/plain; charset=us-ascii 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 -= 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) -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ --------------------------------- Do you Yahoo!? Get better spam protection with Yahoo! Mail --0-68384484-1077780330=:15892 Content-Type: text/html; charset=us-ascii
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

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