From chemistry-request@server.ccl.net Tue Aug 15 01:42:35 2000 Received: from mail.sun.ac.za (mail.sun.ac.za [146.232.128.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id BAA15722 for ; Tue, 15 Aug 2000 01:42:26 -0400 Received: from akad.sun.ac.za ([146.232.80.254]) by mail.sun.ac.za with esmtp (Exim 2.10 #1) id 13OZST-0002uk-00 for chemistry@ccl.net; Tue, 15 Aug 2000 07:40:17 +0200 Received: from SUN_AKAD/SpoolDir by AKAD.SUN.AC.ZA (Mercury 1.48); 15 Aug 00 07:40:17 +0200 Received: from SpoolDir by SUN_AKAD (Mercury 1.48); 15 Aug 00 07:40:05 +0200 Received: from maties (146.232.209.204) by AKAD.SUN.AC.ZA (Mercury 1.48); 15 Aug 00 07:40:02 +0200 Reply-To: From: "Jan Dillen" To: Subject: What is wrong with J.Comp.Chem.? Date: Tue, 15 Aug 2000 07:40:01 +0200 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Dear all, My copy of issue 7 of this year's J.Comput.Chem. does not contain one single minus sign. Both the formulae in ALL the articles and the tables with numerical data are affected. Originally, I though that this was a fluke and that I just happened to be unlucky, but I recently received issues 10 & 11, and both suffer from the same disease. Right parentheses also seem to be missing in some, but not all mathematical formulae. Has anyone else noticed this problem? Here are a few pages for a quick test of some clearly missing minus signs: p 521 eq 14 & 15; p 548 eq 12 p 849 eq 2; p 894 eq 1 & 2 p 976 Table II (all values >0); p 990 eq 2 I will summarise and if a trend emerges, contact the editors and/or publisher. Jan Dillen From chemistry-request@server.ccl.net Tue Aug 15 01:48:21 2000 Received: from arbornet.org (m-net.arbornet.org [209.142.209.161]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id BAA15792 for ; Tue, 15 Aug 2000 01:48:20 -0400 Received: from localhost (mrdonkey@localhost) by arbornet.org (8.10.2/8.10.2) with ESMTP id e7F5P6j99366 for ; Tue, 15 Aug 2000 01:25:06 -0400 (EDT) Date: Tue, 15 Aug 2000 01:25:06 -0400 (EDT) From: Mr Donkey To: chemistry@ccl.net Subject: DelPhi2UHBD Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII CCLers, has anyone written a delphi2uhbd (or grasp2uhbd) potential file converter. I saw a uhbd2grasp at Mcmahonn's UCSD ftp site, and I just changed all the reads to writes and vice versa, and it is semi-working. But sometimes it doesnt' work right. (The Fortran program from the ftp site is dated 1996, maybe the uhbd format has changed since then?) Thanks for any help - Don Don Key mrdonkey@m-net.arbornet.org From chemistry-request@server.ccl.net Tue Aug 15 07:35:30 2000 Received: from yogi.pc1.uni-duesseldorf.de (yogi.pc1.uni-duesseldorf.de [134.99.152.44]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA18245 for ; Tue, 15 Aug 2000 07:35:30 -0400 Received: (from jochen@localhost) by yogi.pc1.uni-duesseldorf.de (8.9.3/8.9.3) id NAA00807; Tue, 15 Aug 2000 13:35:05 +0200 MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Message-ID: <14745.10984.295915.376306@yogi.pc1.uni-duesseldorf.de> Date: Tue, 15 Aug 2000 13:35:04 +0200 (CEST) From: Jochen Kuepper To: Theoretical Chemistry Group Cc: chemistry@ccl.net Subject: CCL:Fortran 90 compiler on Linux In-Reply-To: <3.0.3.32.20000814131807.007bd670@silver.ch.unito.it> References: <3.0.3.32.20000814131807.007bd670@silver.ch.unito.it> X-Mailer: VM 6.72 under 21.1 (patch 12) "Channel Islands" XEmacs Lucid Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id HAA18246 Theoretical Chemistry Group writes: > We installed 15 PC (Linux RedHat) for students exercises. > They should use Frotran90. We need suggestions on possible > solutions. http://www.fortran.com/compilers.html Jochen -- Heinrich-Heine-Universität, Institut für Physikalische Chemie I Universitätsstr. 1, Geb. 26.43 Raum 02.29 40225 Düsseldorf, Germany phone ++49-211-8113681 http://www.Jochen-Kuepper.de fax ++49-211-8115195 From chemistry-request@server.ccl.net Tue Aug 15 11:05:03 2000 Received: from ccshst09.cs.uoguelph.ca (ccshst09.cs.uoguelph.ca [131.104.96.18]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA19101 for ; Tue, 15 Aug 2000 11:05:03 -0400 Received: from msnet.mathstat.uoguelph.ca (msnet.mathstat.uoguelph.ca [131.104.32.59]) by ccshst09.cs.uoguelph.ca (8.9.3/8.9.3) with ESMTP id LAA18987 for ; Tue, 15 Aug 2000 11:04:49 -0400 (EDT) Message-Id: <200008151504.LAA18987@ccshst09.cs.uoguelph.ca> Received: from MSNET/SpoolDir by msnet.mathstat.uoguelph.ca (Mercury 1.48); 15 Aug 00 11:02:34 -0500 Received: from SpoolDir by MSNET (Mercury 1.48); 15 Aug 00 11:02:17 -0500 From: "Bill Smith" Organization: Math & Stats, University of Guelph To: Date: Tue, 15 Aug 2000 11:02:09 -0400 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: Re: CCL:What is wrong with J.Comp.Chem.? Priority: normal In-reply-to: X-mailer: Pegasus Mail for Win32 (v3.12b) Hi,I suspect the problem may relate to the printing of an Adobe acrobat file - probably on an HP Laserjet type of printer. We've had such problems in the past, unrelated to the journal you mention. Try upgrading your copy of Adobe Reader, or else try a different printer. Changing the printer settings may also solve the problem. On 15 Aug 00, at 7:40, Jan Dillen wrote: > Dear all, > > My copy of issue 7 of this year's J.Comput.Chem. > does not contain one single minus sign. Both the > formulae in ALL the articles and the tables with > numerical data are affected. > > Originally, I though that this was a fluke > and that I just happened to be unlucky, but I > recently received issues 10 & 11, and both suffer > >from the same disease. Right parentheses also > seem to be missing in some, but not all > mathematical formulae. > > Has anyone else noticed this problem? > > Here are a few pages for a quick test of some > clearly missing minus signs: > > p 521 eq 14 & 15; p 548 eq 12 > p 849 eq 2; p 894 eq 1 & 2 > p 976 Table II (all values >0); p 990 eq 2 > > I will summarise and if a trend emerges, contact > the editors and/or publisher. > > Jan Dillen > > -= 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 > > > > > Best Regards, W. R. Smith, Professor Dept. of Mathematics and Statistics and School of Engineering Room 546 MacNaughton Building University of Guelph Stone Road and Gordon Streets Guelph, Ontario, CANADA N1G 2W1 Tel: 519-824-4120, ext. 3038; FAX: 519-837-0221; http://www.mathstat.uoguelph.ca/faculty/smith/ From chemistry-request@server.ccl.net Tue Aug 15 12:29:31 2000 Received: from cranc02.cra.canon.com (gatekeeper.cis.canon.com [205.227.186.66]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA19543 for ; Tue, 15 Aug 2000 12:29:30 -0400 Received: by cranc02.cra.canon.com with Internet Mail Service (5.5.2650.21) id ; Tue, 15 Aug 2000 09:28:11 -0700 Message-ID: <3FD2BCBD9153D41192B100C04F1FD832067D1C@cranc02.cra.canon.com> From: "Thoms, Travis" To: "'CHEMISTRY@ccl.net'" Subject: A novice and HOMO-LUMO band gap calculations Date: Tue, 15 Aug 2000 09:28:06 -0700 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-Type: text/plain; charset="iso-8859-1" Greetings: Being rather new to this list and to molecular modeling in general, I hope that you will suffer a naive question from me. I am currently trying to use Hyperchem Pro 6 (PM3 method) to calculate band gap energies of conjugated small molecules, as well as calculated UV-Vis absorptions. The numbers that I am getting are a little unrealistic. HOMO-LUMO bandgaps of 7 eV for systems known to be about 2.5 eV. The UV absorption peak of, say, styrene is calculate to be at 211 nm (241 nm, literature). Are my expectations the unrealistic piece of this puzzle? Are there better forcefields or software packages for the task at hand? Thank you, Travis Thoms From chemistry-request@server.ccl.net Tue Aug 15 11:04:12 2000 Received: from schrodinger.com (root@thermidore.schrodinger.com [199.245.177.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA19081 for ; Tue, 15 Aug 2000 11:04:11 -0400 Received: from sally.schrodinger.com (shenkin@sally.schrodinger.com [166.84.149.25]) by schrodinger.com (8.8.5/8.8.5) with ESMTP id IAA29430 for ; Tue, 15 Aug 2000 08:03:58 -0700 Received: from localhost (shenkin@localhost) by sally.schrodinger.com (8.8.8/8.8.5) with ESMTP id LAA23600 for ; Tue, 15 Aug 2000 11:03:56 -0400 X-Authentication-Warning: sally.schrodinger.com: shenkin owned process doing -bs Date: Tue, 15 Aug 2000 11:03:56 -0400 (EDT) From: Peter Shenkin To: chemistry@ccl.net Subject: Re: CCL:Fortran 90 compiler on Linux In-Reply-To: <14745.10984.295915.376306@yogi.pc1.uni-duesseldorf.de> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=X-UNKNOWN Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id LAA19082 Hi, Also www.polyhedron.com for benchmarks, though their LINUX listings aren't comprehensive. We've had good experiences with Absoft Pro F77/F90. One of our apps on LINUX increased in speed by 50% when going to Absoft F77 from g77. -P. On Tue, 15 Aug 2000, Jochen Kuepper wrote: > Theoretical Chemistry Group writes: > > We installed 15 PC (Linux RedHat) for students exercises. > > They should use Frotran90. We need suggestions on possible > > solutions. > > http://www.fortran.com/compilers.html > > Jochen > -- > Heinrich-Heine-Universität, Institut für Physikalische Chemie I > Universitätsstr. 1, Geb. 26.43 Raum 02.29 > 40225 Düsseldorf, Germany phone ++49-211-8113681 > http://www.Jochen-Kuepper.de fax ++49-211-8115195 > > > -= 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 > > > > > From chemistry-request@server.ccl.net Tue Aug 15 14:40:30 2000 Received: from rzumail2.unizh.ch (rzumail2.unizh.ch [130.60.128.10]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA20222 for ; Tue, 15 Aug 2000 14:40:30 -0400 Received: from zisgi.unizh.ch (zisgi.unizh.ch [130.60.19.17]) by rzumail2.unizh.ch (8.9.3/8.9.3/07) with ESMTP id UAA08869 for ; Tue, 15 Aug 2000 20:40:30 +0200 (MET DST) Date: Tue, 15 Aug 2000 20:40:30 +0200 From: "Dr. Peter Burger" To: chemistry@ccl.net Subject: CCL: F90 & Linux Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Just worth my 0.01 cents: My favourite is the Portland group compiler (commercial) excellent & fast & robust! http://www.pgroup.com You may as well check www.lahey.com (Fujitsu Linux) Info and F90 & Linux can be found at. http://studbolt.physast.uga.edu/templon/fortran.html There is also info on the free Pacific-Sierra f90tog77 translator. Peter --------------------------------------------------- Peter Burger Anorg.-chem. Institut Universitaet Zuerich From chemistry-request@server.ccl.net Tue Aug 15 16:59:38 2000 Received: from hotmail.com (f145.law3.hotmail.com [209.185.241.145]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA20780 for ; Tue, 15 Aug 2000 16:59:38 -0400 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Tue, 15 Aug 2000 13:57:37 -0700 Received: from 130.86.22.85 by lw3fd.law3.hotmail.msn.com with HTTP; Tue, 15 Aug 2000 GMT X-Originating-IP: [130.86.22.85] From: "narisara tanvirat" To: chemistry@ccl.net Subject: Running Autodock Date: Tue, 15 Aug 2000 20:57:37 GMT Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 15 Aug 2000 20:57:37.0738 (UTC) FILETIME=[718392A0:01C006FB] 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