From chemistry-request@ccl.net Mon Jan 26 13:02:02 2004 Received: from web13602.mail.yahoo.com (web13602.mail.yahoo.com [216.136.175.113]) by server.ccl.net (8.12.8/8.12.8) with SMTP id i0QI20SX025097 for ; Mon, 26 Jan 2004 13:02:00 -0500 Message-ID: <20040126180348.40846.qmail|at|web13602.mail.yahoo.com> Received: from [130.127.206.27] by web13602.mail.yahoo.com via HTTP; Mon, 26 Jan 2004 10:03:48 PST Date: Mon, 26 Jan 2004 10:03:48 -0800 (PST) From: Yu Sun Subject: Re: ADL: Syntax error using autodock 3.0 To: "Pandey, Jaya" , "'autodock|at|scripps.edu '" Cc: "'chemistry|at|ccl.net'" In-Reply-To: <73564B8DE398D61180500008C75D7E49033E5E26@NTMAIL03> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Spam-Status: No, hits=0.9 required=7.0 tests=FROM_ENDS_IN_NUMS autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi, Jaya I frequently use get-docked command on the dlg files. Never encounter any problems. Is your dlg file correct ? If you want, send me your dlg file(tarred and zipped, to: yus|at|clemson.edu). I can test it to see if there is a problem in your dlg file. Yu --- "Pandey, Jaya" wrote: > Hi All, > > I have just started using Autodock 3.0. I was trying to do the > examples. > When I give the "get docked" command it returns with saying "synatx > error in > line 7" and gets aborted. Can somebody give me the clues why that > would > happen. I will be thankful. > > Jaya Pandey > > - __________________________________ Do you Yahoo!? Yahoo! SiteBuilder - Free web site building tool. Try it! http://webhosting.yahoo.com/ps/sb/ From chemistry-request@ccl.net Mon Jan 26 09:15:49 2004 Received: from fikus.jh-inst.cas.cz (fikus.jh-inst.cas.cz [147.231.28.135]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i0QEFkSX016029 for ; Mon, 26 Jan 2004 09:15:47 -0500 Received: from fikus.jh-inst.cas.cz (root@localhost) by fikus.jh-inst.cas.cz (8.9.3/8.9.3/Debian/GNU) with local id PAA04253 for chemistry{at}ccl.net; Mon, 26 Jan 2004 15:17:33 +0100 Received: from tracy.jh-inst.cas.cz (tracy.jh-inst.cas.cz [147.231.28.129]) by fikus.jh-inst.cas.cz (8.9.3/8.9.3/Debian/GNU) with ESMTP id PAA04143 for ; Mon, 26 Jan 2004 15:17:29 +0100 Received: from TRACY/SpoolDir by tracy.jh-inst.cas.cz (Mercury 1.48); 26 Jan 04 15:17:32 +0200 Received: from SpoolDir by TRACY (Mercury 1.48); 26 Jan 04 15:17:06 +0200 Received: from uochb.cas.cz (147.231.29.220) by tracy.jh-inst.cas.cz (Mercury 1.48) with ESMTP; 26 Jan 04 15:16:58 +0200 Message-ID: <40152155.1090407{at}uochb.cas.cz> Date: Mon, 26 Jan 2004 15:16:53 +0100 From: "Mgr. Lubos Vrbka" Reply-To: lubos.vrbka{at}uochb.cas.cz Organization: IOCB User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.6) Gecko/20040113 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry{at}ccl.net Subject: CCL: summary - water diffusion constants Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Masca-Timestamp: Mon, 26 Jan 2004 15:17:33 +0100 [fikus.jh-inst.cas.cz] 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 CCL'ers, many thanks to all who replied. i briefly summarize the output: Krynicki K. et al. Disc. Faraday Soc. 66 (1978), 199-208 Weingartner H. Zeit. Phys. Chem. Neue Folge 132 (1982) 129-149 Price W.S. et al. J. Phys. Chem. A 103 (1999) 448-450 Smith P.E. et al. J. Chem. Phys. 100 (1994) 3169-3174 Wensink E.J. et al. J. Chem. Phys. 119 (2003) 7308-7317 Blumhagen K. et al. Int. J. Quantum Chemistry 59 (1996) 271-279 Watanabe et al. Chem. Phys. 131, 157, 1989 Berendsen et al. J. Phys. Chem. 91, 6269, 1987 Mahoney et al. J. Chem. Phys. 114, 363, 2001) Netz P.A. et al. J. Chem. Phys. 115 (2001) 344-348 Netz P.A. et al. J. Mol. Liquids 101 (2002) 159-168 Netz P.A. et al. Physica A - Statistical Mechanics and its applications 314 (2002) 470-476 Stanley H.E. et al. Physica A - Statistical Mechanics and its applications 315 (2002) 281-289 Clancy P. et al. J. Chem. Phys. 116 (2002) 5090-5098 for following link provided by anirban i wasn't sure about the appropriate citation: Eugene Stanley's papers (specially one in Physical Review E 1999) might be Starr F.W. et al. Phys. Rev. E 60 (1999) 6757-6768 Starr F.W. et al. Phys. Rev. E 60 (1999) 1084-1087 once more - thank you very much, your help is very appreciated. kind regards, lubos -- ..................................................... Mgr. Lubos Vrbka Center for Complex Molecular Systems and Biomolecules Institute of Organic Chemistry and Biochemistry Academy of Sciences of the Czech Republic Prague, Czech Republic ..................................................... From chemistry-request@ccl.net Mon Jan 26 10:41:14 2004 Received: from med-gwia-02a.med.umich.edu (med-gwia-02a.med.umich.edu [141.214.93.150]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i0QFfDSX019410 for ; Mon, 26 Jan 2004 10:41:13 -0500 Received: from gwia-02-MTA by med-gwia-02a.med.umich.edu with Novell_GroupWise; Mon, 26 Jan 2004 10:43:01 -0500 Message-Id: X-Mailer: Novell GroupWise Internet Agent 6.5.2 Beta Date: Mon, 26 Jan 2004 10:42:40 -0500 From: "Renxiao Wang" To: Subject: Summary: references of marketed drugs by structure-based design Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Disposition: inline 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 Hi, CCLers! Last week I posted a question asking for references of marketed drugs whose invention were largely aided by structure-based design methods. Most of the replies point to the following review article: Larry Hardy & Antony Malikayil, The impact of structure-guided drug design on clinical agents, Current Drug Discovery, 2003, December, 15-20. http://www.currentdrugdiscovery.com/2003/december.html This paper discussed ~40 compounds developed with SBDD, seven of them are marketed drugs. Here are some addtional examples: Crixivan (1,2), Viracept (3), Trusopt (4), Zanamivir (5,6) 1. BD Dorsey, RB Levin, SL McDaniel, JP Vacca, JP Guare, PL Darke, JA Zugay, EA Emini, WA Schleif, JC. Quintero, JH Lin, I-W Chen, MK Holloway, PMD Fitzgerald, MG. Axel, D Ostovic, PS Anderson, JR Huff. L-735,524: The Design of a Potent and Orally Bioavailable HIV Protease Inhibitor. J Med Chem 37:3443-3451, 1994. 2. Holloway, M. K. et al. In Computer-Aided Molecular Design, Reynolds, C. H. et al., Eds. ACS Symp. Series 589:36-50, 1995. 3. SW Kaldor, VJ Kalish, JF Davies, II, BV Shetty, JE Fritz, K Appelt, JA Burgess, KM Campanale, NY Chirgadze, DK Clawson, BA Dressman, SD Hatch, DA Khalil, MB Kosa, PP Lubbehusen, MA Muesing, AK Patick, SH Reich, KS Su, JH Tatlock. Viracept (Nelfinavir Mesylate, AG1343): A Potent, Orally Bioavailable Inhibitor of HIV-1 Protease. J Med Chem 40:3979-3985, 1997. 4. J Greer, JW Erickson, JJ Baldwin, MD Varney. Application of the Three-Dimensional Structures of Protein Target Molecules in Structure-Based Drug Design J Med Chem 37:1035-1054; 1994. 5. von Itzstein, M.; Wu, W. Y.; Kok, G. B.; Pegg, M. S.; Dyason, J. C.; Jin, B.; Van Phan, T.; Smythe, M.; White, H. F.; Oliver, S. W.; Colman, P. M.; Varghese, J. N.; Ryan, D. M.; Woods, J. M.; Bethell, R. C.; Hotham, V. J.; Cameron, J. M.; Penn, C. R. Rational Design of Potent Sialidase-based Inhibitors of Influenza Virus Replication. Nature, 363, 418-423 (1993). 6. M. von Itzstein, Jeffrey C. Dyason, Stuart W. Oliver, Hume F. White, Wen-Yang Wu, Gaik B. Kok and Michael S. Pegg, A Study of the Active Site of Influenza Sialidase: An Approach to the Rational Design of Novel Anti-Influenza Drugs. J. Med. Chem., 39, 388-391, (1995). Again, thanks for all of the responses! With best regards, Renxiao -------------------------------------------------------------------------------------------------- Renxiao Wang, Ph.D. Research Investigator Department of Internal Medicine, Hematology/Oncology Division University of Michigan Medical School Ann Arbor, MI 48109, U.S.A. Tel: (734) 764-2449; Fax: (734) 764-2532 E-mail: renxiao_at_med.umich.edu Web: http://sw8.im.med.umich.edu/~arthur/ -------------------------------------------------------------------------------------------------- From chemistry-request@ccl.net Mon Jan 26 01:32:01 2004 Received: from ntmms01.chla.usc.edu (chl179129.usc.edu [128.125.179.129]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i0Q6W0SX022846 for ; Mon, 26 Jan 2004 01:32:00 -0500 Received: from 10.3.1.165 by ntmms01.chla.usc.edu with ESMTP (CHLA SMTP Relay (MMS v5.6.0)); Sun, 25 Jan 2004 22:33:07 -0800 X-Server-Uuid: 3F66CE27-8E7A-45D4-9872-50BC1A7F95DE Received: by NTSMTP01 with Internet Mail Service (5.5.2653.19) id ; Sun, 25 Jan 2004 22:33:07 -0800 Message-ID: <73564B8DE398D61180500008C75D7E49033E5E26@NTMAIL03> From: "Pandey, Jaya" To: "'autodock/at/scripps.edu '" cc: "'chemistry/at/ccl.net'" Subject: Syntax error using autodock 3.0 Date: Sun, 25 Jan 2004 22:33:04 -0800 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) X-WSS-ID: 6C0A6B291XS981609-01-01 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 7bit 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 Hi All, I have just started using Autodock 3.0. I was trying to do the examples. When I give the "get docked" command it returns with saying "synatx error in line 7" and gets aborted. Can somebody give me the clues why that would happen. I will be thankful. Jaya Pandey -----Original Message----- From: Yu Sun To: Sameer P. Kawatkar; autodock/at/scripps.edu Sent: 1/23/04 8:57 AM Subject: Re: ADL: Parameters for aliphatic and aromatic carbons Dear Sameer, --- "Sameer P. Kawatkar" wrote: > Hi, > I have a question about the parameters for the aliphatic and > aromatic > carbons. Are the parameters for both of these are same except for > the atom > types? (i.e. do we only have to change the atom type for aromatic > carbon > to 'A' and for aliphatic 'C' and use the same parameters for both > these > types in the gpf file?) > Check gpf3gen.awk, they are different: C 12.77 4.0 A 10.80 0.6 But the program will assigne the correct parameters after you change "C" to "A" I think. Yu > thanks > > > -- > Sameer P. Kawatkar, > Prof. Geert-Jan Boons's Group, > Complex Carbohydrates Research Center, > University of Georgia, > 220 Riverbend Road, > Athens, Georgia 30602 > > > > -- ADL: AutoDock List --- > http://www.scripps.edu/pub/olson-web/doc/autodock/ --- > __________________________________ Do you Yahoo!? Yahoo! SiteBuilder - Free web site building tool. Try it! http://webhosting.yahoo.com/ps/sb/ -- ADL: AutoDock List --- http://www.scripps.edu/pub/olson-web/doc/autodock/ ---