From chemistry-request@server.ccl.net Wed Aug 16 12:22:34 2000 Received: from p2.fhp.bsunet (natpool1-1.bsu.unibel.by [195.50.4.44]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA26775 for ; Wed, 16 Aug 2000 12:15:03 -0400 Received: from localhost (sa@localhost) by p2.fhp.bsunet (8.9.3/8.9.3/my hands 8.9.3-0.1) with ESMTP id SAA10982; Wed, 16 Aug 2000 18:30:28 +0300 Date: Wed, 16 Aug 2000 18:30:28 +0300 (EEST) From: Alexander Kulak To: Theoretical Chemistry Group cc: chemistry@ccl.net Subject: Re: CCL:Fortran 90 compiler on Linux In-Reply-To: <3.0.3.32.20000814131807.007bd670@silver.ch.unito.it> Message-ID: Organization: Inst. Phys. Chem. problems of BSU X-Mailer: a pretty tearline MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, On Mon, 14 Aug 2000, Theoretical Chemistry Group wrote: TCG> We installed 15 PC (Linux RedHat) for students exercises. TCG> They should use Frotran90. TCG> We need suggestions on possible solutions. Welcome to my short page about F90 and 77 for Linux: http://www.geocities.com/CapeCanaveral/Launchpad/5820/fortran/ Some people prefer Absoft, other - Portland, Lahey, Fujitsu. Besides, a sequential CRYSTAL code compiled by Absoft compiler gives some errorneous test results, while Portland ones are reasonable good. b.w., Alexander Kulak [ http://i.am/kulak ] From chemistry-request@server.ccl.net Wed Aug 16 14:40:21 2000 Received: from iris.iupui.edu (iris.iupui.edu [134.68.220.32]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA27317 for ; Wed, 16 Aug 2000 14:40:21 -0400 Received: from macgw.chem.iupui.edu (macgw.chem.iupui.edu [134.68.137.71]) by iris.iupui.edu (8.9.3/8.9.3/1.2IUPUIPO) with SMTP id NAA19998 for ; Wed, 16 Aug 2000 13:40:23 -0500 (EST) Message-ID: Date: 16 Aug 2000 13:55:55 -0500 From: "Boyd" Subject: history To: "OSC CCL" X-Mailer: Mail*Link SMTP for Quarterdeck Mail; Version 4.1.0 Hi, In the last 10 years, several prominent computational chemists have died sadly. These include Michael Dewar, Michael Zerner, Jeremy Burdett, and Jan Almlof. What other prominent computational chemists who have passed away in the last 10 years? Thanks, Don Donald B. Boyd, Ph.D. Editor, Journal of Molecular Graphics and Modelling (publication of the ACS COMP division and MGMS) http://chem.iupui.edu/~boyd/jmgm.html Research Professor of Chemistry Indiana University-Purdue University at Indianapolis E-mail boyd@chem.iupui.edu From chemistry-request@server.ccl.net Wed Aug 16 05:31:05 2000 Received: from server.biokemi.su.se (server.biokemi.su.se [130.237.179.5]) by server.ccl.net (8.8.7/8.8.7) with SMTP id FAA24287 for ; Wed, 16 Aug 2000 05:31:05 -0400 Received: from mail.biokemi.su.se (unverified [130.237.179.175]) by server.biokemi.su.se (EMWAC SMTPRS 0.83) with SMTP id ; Wed, 16 Aug 2000 11:31:15 +0200 Sender: zhang@ccl.net Message-ID: <399A5E91.97979EDE@mail.biokemi.su.se> Date: Wed, 16 Aug 2000 11:27:45 +0200 From: Xiao-Ping Zhang Reply-To: zhang@biokemi.su.se X-Mailer: Mozilla 4.72 [en] (X11; U; Linux 2.2.14-12 i686) X-Accept-Language: en MIME-Version: 1.0 To: narisara tanvirat , chemistry@ccl.net Subject: Re: CCL:Running Autodock References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear narisara, As autodock authors pointed out, these scripts are awk programs. Check your system to see what awk program (awk, gawk, oawk or nawk) is installed and make sure that the script call the correct awk. Good luck! Xiao-Ping narisara tanvirat wrote: > > To all subscribers esp. AutoDOck 3.0 users > I just started using AutoDock 3.0 and also UNIX. I have problems with using > all the UNIX scripts that mention in the UserGuide. Now I have my ligand and > macromolecule in PDB format, but I dont know how to convert them to PDBQ > format. How can I make all the scripts work? Do I need to change in the > computer in order to do so? Bear with me. I'm very beginner. > > Have a good one > > Narisara Tanvirat > Chemistry Department > California State University, Sacramento > > ________________________________________________________________________ > Get Your Private, Free E-mail from MSN Hotmail at http://www.hotmail.com > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net -- ****************************** Xiao-Ping Zhang Department of Biochemistry Arrhenius Laboratories of Natural Sciences Stockholm Universities 106 91 Stockholm Sweden Phone: 046-08-162472 /162582 Fax: 046-08-153679 e-mail: zhang@biokemi.su.se From chemistry-request@server.ccl.net Wed Aug 16 06:15:03 2000 Received: from sina.com ([202.106.187.167]) by server.ccl.net (8.8.7/8.8.7) with SMTP id GAA24508 for ; Wed, 16 Aug 2000 06:14:59 -0400 Received: (qmail 11059 invoked by uid 99); 16 Aug 2000 10:14:56 -0000 Message-ID: <20000816101456.11058.qmail@sina.com> From: cgliu To: chemistry@ccl.net Cc: chem-education@mailbase.ac.uk, PChem-L@grove.iup.edu, ccp5world@dl.ac.uk Subject: Stories of molecular modelling wanted. Date: Wed Aug 16 10:14:56 2000 X-Mailer: SinaMail 3.0Beta (FireToad) X-Priority: 3 Disposition-Notification-To: cgliu Dear all I don't know if it is appropriate to post this message here. If it is not appropriate, I am sorry for it. But I do hope you can help me. Does anyone know any stories about the successful application of molecular modelling in the invent of new materials, such as the superconductor, catalysts, medicine, nonlinear optical materials, magnetic materials and anything else? I will teach a course on the molecular modelling, and I would have some examples at hand to interest my students. Chungen =================================================================== 新浪免费电子邮箱 http://mail.sina.com.cn 参加新浪奥运情侣特使评选活动，亲临悉尼千禧奥运盛会。快来参加。 http://ad2.sina.com.cn/ads/olympics/ From chemistry-request@server.ccl.net Wed Aug 16 19:16:07 2000 Received: from galileu.dqfex.ufpe.br (root@galileu.dqfex.ufpe.br [150.161.40.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id TAA28543 for ; Wed, 16 Aug 2000 19:16:04 -0400 Received: from dqfex.ufpe.br (danon.dqf.ufpe.br [150.161.5.125]) by galileu.dqfex.ufpe.br (8.9.3/8.8.7) with ESMTP id UAA16880 for ; Wed, 16 Aug 2000 20:16:28 -0300 Message-ID: <399B20F6.879B1EC6@dqfex.ufpe.br> Date: Wed, 16 Aug 2000 20:17:10 -0300 From: Wagner Faustino X-Mailer: Mozilla 4.7 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: lanthanides basis set Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers, Does anybody know where can I find a complete (No ECPs!) gaussian basis set for lanthanides (Eu and Tb)? Best Regards, Wagner Faustino DQF - LQTC - UFPE From chemistry-request@server.ccl.net Wed Aug 16 19:26:38 2000 Received: from t1.chem.umn.edu (t1.chem.umn.edu [160.94.96.132]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id TAA28609 for ; Wed, 16 Aug 2000 19:26:37 -0400 Received: from t232c (t224a.chem.umn.edu [160.94.96.170]) by t1.chem.umn.edu (8.9.3/8.9.3) with SMTP id RAA12427 for ; Wed, 16 Aug 2000 17:23:58 -0500 Message-ID: <001401c007d9$b2c4e640$aa605ea0@chem.umn.edu> From: "Piotr Paneth" To: Subject: mndo/d Co parameters Date: Wed, 16 Aug 2000 18:28:35 -0500 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 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 Hi all: could someone give me a pointer to MNDO/d parameters for Co if available. Thanx in advace, Piotr From chemistry-request@server.ccl.net Wed Aug 16 21:04:13 2000 Received: from mailhost.gu.edu.au (kraken.itc.gu.edu.au [132.234.250.31]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id VAA29242 for ; Wed, 16 Aug 2000 21:03:49 -0400 Received: from redback.ins.gu.edu.au (redback.ins.gu.edu.au [132.234.11.201]) by mailhost.gu.edu.au (8.10.1/8.10.1) with ESMTP id e7H16GR10198 for ; Thu, 17 Aug 2000 11:06:16 +1000 (EST) Received: from REDBACK/SpoolDir by redback.ins.gu.edu.au (Mercury 1.47); 17 Aug 00 11:03:35 +1000 Received: from SpoolDir by REDBACK (Mercury 1.47); 17 Aug 00 11:03:17 +1000 Received: from mailbox.gu.edu.au (132.234.117.15) by redback.ins.gu.edu.au (Mercury 1.47) with ESMTP; 17 Aug 00 11:03:14 +1000 Sender: thomas@kraken.itc.gu.edu.au Message-ID: <399B39BF.205DFC26@mailbox.gu.edu.au> Date: Thu, 17 Aug 2000 11:02:56 +1000 From: Thomas Haselhorst X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX64 6.5 IP30) X-Accept-Language: de-DE, en MIME-Version: 1.0 To: chemistry@ccl.net Subject: AUTODOCK 3.0.5 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit dear all, i have some problems running AUTODOCK 3.0.5. i worked with the example files, without any problems! but setting up my own protein-ligand complex i found my ligand not within the binding site ...rather somewhere in the protein. I increased the grid space (0.5A) but unfortenuately without success. in any case the ligand is moving out of the grid. here are my questions: 1. what can i do to overcome bumbs of the ligand with the receptor ?? 2. furthermore, i am interested in docking a carbohydrate into the binding site of an enzyme. it is known from x-ray structure that the ring conformation of the bound sugar is not any longer a chair conformation. in which way i can setup AUTOTORS to modify the ring conformation ??? thank you very much in advance. I appreciate any help !!! sincerely yours Thomas Haselhorst --------------------------------------------------------- Dr Thomas Haselhorst Centre for Biomolecular Science and Drug Discovery Griffith University (Gold Coast Campus) PMB 50 Gold Coast Mail Centre Queensland 9726 Australia email: t.haselhorst@mailbox.gu.edu.au http://www.gu.edu.au/centre/cbsdd Ph: +61 7 5594 8060 Fax: +61 7 5594 8098 --------------------------------------------------------