From chemistry-request@server.ccl.net Mon May 6 04:14:50 2002 Received: from rrzd1.rz.uni-regensburg.de (root@[132.199.1.6]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g468Env05905 for ; Mon, 6 May 2002 04:14:50 -0400 Received: from listserv.ngate.uni-regensburg.de (kroesus2.rz.uni-regensburg.de [132.199.2.208]) by rrzd1.rz.uni-regensburg.de (8.9.3/8.9.3-KLW-Linux-0.1) with ESMTP id KAA21118 for ; Mon, 6 May 2002 10:14:45 +0200 Received: from KROESUS2/SpoolDir by listserv.ngate.uni-regensburg.de (Mercury 1.48); 6 May 02 10:14:48 +0200 Received: from SpoolDir by KROESUS2 (Mercury 1.48); 6 May 02 10:14:27 +0200 From: "Georg Schmeer" Organization: Universitaet Regensburg To: chemistry@ccl.net Date: Mon, 6 May 2002 10:14:21 +0200 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: Compiling g98 A11 with ATLAS, Addendum Message-ID: <3CD6577C.20806.66765F@localhost> Priority: normal X-mailer: Pegasus Mail for Win32 (v3.12c) Dear All, on Friday evening, May 3, I must be too tired to do correct calculations and therefore I have to apologize for the faulty information about the acceleration of gaussian98 using the ATLAS library. After performing correct calculations of the test-file test429.com I can say that the gain in cpu-time is about 5 to 20% - and not 400% as I wrote. Nevertheless I mean that the use of ATLAS as linear algebra package for Gaussian98 is recommended. Sincerely yours Georg Schmeer Prof. Dr. Georg Schmeer Institut fuer Physikalische und Theoretische Chemie Universitaet Regensburg D-93040 Regensburg Georg.Schmeer@chemie.uni-regensburg.de Tel: 0941-943-4745 Fax: 0941-943-1690 From chemistry-request@server.ccl.net Mon May 6 05:29:44 2002 Received: from mailer.gwdg.de ([134.76.10.26]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g469Tiv07216 for ; Mon, 6 May 2002 05:29:44 -0400 Received: from vrlab03.mpibpc.gwdg.de ([134.76.211.99] helo=mpi-bpc.mpg.de) by mailer.gwdg.de with esmtp (Exim 3.33 #11) id 174eoS-0006tZ-00 for chemistry@ccl.net; Mon, 06 May 2002 11:29:44 +0200 Message-ID: <3CD64CF5.5000808@mpi-bpc.mpg.de> Date: Mon, 06 May 2002 11:29:25 +0200 From: Vlad Cojocaru User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:0.9.4) Gecko/20011126 Netscape6/6.2.1 X-Accept-Language: en-us MIME-Version: 1.0 To: CCL list Subject: Computational Chemistry conferences Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Hi Does anyone know some Computational Chemistry workshops or courses in Europe in the near future? Thanks, vlad -- Vlad Cojocaru Max Planck Institut for Biophysical Chemistry Deparment: 060 Am Fassberg 11, 37077 Goettingen, Germany tel: ++49-551-201.1389 e-mail: Vlad.Cojocaru@mpi-bpc.mpg.de From chemistry-request@server.ccl.net Mon May 6 09:39:50 2002 Received: from f2node23.rhrz.uni-bonn.de ([131.220.14.223]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g46Ddnv12082 for ; Mon, 6 May 2002 09:39:50 -0400 Received: from mcpc1051 (mcpc1051.pharma.uni-bonn.de [131.220.136.15]) by f2node23.rhrz.uni-bonn.de (AIX4.3/8.9.3/8.9.3) with ESMTP id PAA29852 for ; Mon, 6 May 2002 15:39:45 +0200 Content-Type: text/plain; charset="iso-8859-1" From: Mathias Weigt Reply-To: m.weigt@uni-bonn.de To: chemistry@ccl.net Subject: Re: CCL:Compiling g98 A11 with ATLAS, Addendum Date: Mon, 6 May 2002 15:40:03 +0200 X-Mailer: KMail [version 1.4] References: <3CD6577C.20806.66765F@localhost> In-Reply-To: <3CD6577C.20806.66765F@localhost> MIME-Version: 1.0 Message-Id: <200205061540.03238.weigt@uni.de> Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g46Ddov12083 On Monday 06 May 2002 10:14, Georg Schmeer wrote: > Dear All, > on Friday evening, May 3, I must be too tired to do correct > calculations and therefore I have to apologize for the faulty > information about the acceleration of gaussian98 using the ATLAS > library. After performing correct calculations of the test-file > test429.com I can say that the gain in cpu-time is about 5 to 20% > - and not 400% as I wrote. > Nevertheless I mean that the use of ATLAS as linear algebra package > for Gaussian98 is recommended. > Sincerely yours Here is a good site for compiling instruction with ATLAS: http://quanta.synchem.kyoto-u.ac.jp/~maho/Computer/quantum_chemistry/Gaussian98_linux_ifc_e.html It is not for the Portland Group Compiler but for Intel ifc. -- Mathias Weigt From chemistry-request@server.ccl.net Mon May 6 00:04:39 2002 Received: from mail.shcnc.AC.CN ([202.127.16.28]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4644cv28820 for ; Mon, 6 May 2002 00:04:38 -0400 Received: from PC18 ([202.127.19.225]) by mail.shcnc.AC.CN (8.12.1/8.12.1) with SMTP id g46J5I5A007101 for ; Mon, 6 May 2002 12:05:18 -0700 (PDT) Message-Id: <200205061905.g46J5I5A007101@mail.shcnc.AC.CN> Date: Mon, 6 May 2002 12:1:50 +0800 From: bxiong To: "chemistry@ccl.net" Subject: summary:SYBYL background color change methods X-mailer: FoxMail 3.0 beta 2 [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: 7bit Here is the summary of SYBYL background color change methods: my question is: I want to export a graph from a SYBYL, but the background is black. How can I change the color of background from black to white? the answers are: 1, Dr. Song says: I think maybe there is not a proper way for you to change the color of backgroud to white. In fact,in SYBYL,it did supply three backgroud color,ie,solid,fade and split.You can though click VIEW from the main menu,and then click Backprop. Maybe the fade backgroud can meet your need. An alternative way is to use InsightII. It supply utilities for you to change the backgroud to white. You can have a try! 2,Dr. Ibrahim says: In sybyl windows go to Font ( the left side of your windows) and there you can change the background colour to what you want. 3,Dr. Ramy says: Create a file called '.color.def' that includes the following lines: #---------------------------------------------------------------------- # SYBYL background colors # # 0 - solid backdrop color # 1 - split backdrop top color # 2 - split backdrop middle color # 3 - split backdrop bottom color # 4 - fade backdrop top color # 5 - fade backdrop bottom color # background 0 0.0 0.0 0.0 /this makes the main background black background 1 1.0 1.0 1.0 background 2 1.0 1.0 1.0 background 3 1.0 1.0 1.0 background 4 0.0 0.65 0.65 background 5 0.0 0.15 0.15 #---------------------------------------------------------------------- Then place the following line in your .login file: setenv TA_COLORMAP $HOME/.color.def To make your background white, from within Sybyl, select Split as your background color. I am very glad to receive their reply. thanks ver ymuch! and hope this is helpful to others. best wishes to you, Dr. Song, Dr. Ibrahim Dr. Ramy! Best regards! bxiong@mail.shcnc.ac.cn Xiong Bin Shanghai Institute of Materia Medica, C.A.S. phone:021-64311833-222(office) From chemistry-request@server.ccl.net Mon May 6 00:19:19 2002 Received: from zcsn04.astrazeneca.com ([193.128.1.35]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g464JIv29285 for ; Mon, 6 May 2002 00:19:18 -0400 Received: from zcsn14.ukhx.astrazeneca.net (zcsn14.ukhx.astrazeneca.net [192.168.199.14]) by zcsn04.astrazeneca.com (8.9.3/8.9.3.DEF) with ESMTP id FAA27016; Mon, 6 May 2002 05:19:03 +0100 (BST) Received: from zcsn24.ukhx.astrazeneca.net (zcsn24.ukhx.astrazeneca.net [156.71.11.98]) by zcsn14.ukhx.astrazeneca.net (8.9.3/8.9.3) with ESMTP id FAA26799; Mon, 6 May 2002 05:17:58 +0100 (BST) Received: from ukapzcmsxhub01.ukap.astrazeneca.net (ukapzcmsxhub01.ukap.astrazeneca.net [156.71.158.135]) by zcsn24.ukhx.astrazeneca.net (8.10.1/8.10.1) with ESMTP id g464Hvk04462; Mon, 6 May 2002 05:17:57 +0100 (BST) Received: by ukapzcmsxhub01.ukap.astrazeneca.net with Internet Mail Service (5.5.2650.21) id ; Mon, 6 May 2002 05:17:57 +0100 Message-ID: <9FE9B85A29CDD511883D0002A53FF21A0B77FE@INBGCASMSX01> From: "Parthiban, Srinivasan" To: "'bxiong'" , chemistry@ccl.net Subject: RE: how to change background color of SYBYl? Date: Mon, 6 May 2002 05:13:48 +0100 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-Type: text/plain; charset="GB2312" Hi Bin 1. Click FONT icon from the Icon-bar (at the left) 2. Click Colors & Backdrop 3. you would see 13 horizontal bars with the last bar in Black color with a label backdrop, CLICK this 4. Now adjust the RGB (move the scroll bars from left to right end) 5. Click Apply Now you have it. -Parthiban S -----Original Message----- From: bxiong [mailto:bxiong@mail.shcnc.ac.cn] Sent: Saturday, May 04, 2002 3:43 PM To: chemistry@ccl.net Subject: CCL:how to change background color of SYBYl? Dear CCL: I want to export a graph from a SYBYL, but the background is black. How can I change the color of background from black to white? Best regards! bxiong@mail.shcnc.ac.cn Xiong Bin Shanghai Institute of Materia Medica, C.A.S. phone:021-64311833-222(office) -= 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 Mon May 6 02:29:12 2002 Received: from thor.chem.sdu.dk ([130.225.142.15]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g466TBv00637 for ; Mon, 6 May 2002 02:29:11 -0400 Received: from localhost (tetz@localhost) by thor.chem.sdu.dk (SGI-8.9.3/8.9.3) with ESMTP id IAA49757; Mon, 6 May 2002 08:31:49 +0200 (MDT) Date: Mon, 6 May 2002 08:31:49 +0200 From: Per Tetzschner Olsen To: George Hall cc: chemistry@ccl.net Subject: Re: CCL:Hessian In-Reply-To: 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 g466TCv00638 Dear George I would recommend TINKER or BatchMin. TINKER is free, but Batchmin is a part of Macromodel and Maestro, which belongs to schrodinger.com Per On Sun, 5 May 2002, George Hall wrote: > > Dear CCL: > > I am looking for a program to calculate the Hessian. > > Alternatively if someone can point me some literature and input. > > Thanks. > > George Hall. > > > _________________________________________________________________ > Join the world’s largest e-mail service with MSN Hotmail. > 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 > > > > > > From chemistry-request@server.ccl.net Mon May 6 07:43:59 2002 Received: from ns.ice.mpg.de ([195.37.47.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g46Bhwv09293 for ; Mon, 6 May 2002 07:43:58 -0400 Received: from relax.ice.mpg.de ([10.10.11.61] helo=ice.mpg.de) by ns.ice.mpg.de with esmtp (Exim 3.14 #17) id 174guM-00014D-00; Mon, 06 May 2002 13:43:58 +0200 Message-ID: <3CD66C7A.4050905@ice.mpg.de> Date: Mon, 06 May 2002 13:43:54 +0200 From: Christoph Steinbeck User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.0; en-US; rv:1.0rc1) Gecko/20020417 X-Accept-Language: en-us, en MIME-Version: 1.0 To: Vlad Cojocaru CC: CCL list Subject: Re: CCL:Computational Chemistry conferences References: <3CD64CF5.5000808@mpi-bpc.mpg.de> Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Vlad Cojocaru wrote: > Hi > Does anyone know some Computational Chemistry workshops or courses in > Europe in the near future? > Thanks, > vlad > The "Computers-Information-Chemistry (CIC)" division of the German Chemical Society (http://www2.chemie.uni-erlangen.de/external/cic/) has its 16. annual workshop in Kleinmachnow (very close to Berlin) on 10. - 12. November 2002. The workshop will be in german. However, english talks and posters are of course welcome. The program covers - Chemoinformatics, struktura bioinformatics - Spectroscopy and Computer Assisted Structure Elucidation - Visualisation - Modelling and Quantumchemistry. Currently, we have an open call for papers. Please see the CIC pages for details. Regards, Christoph Steinbeck -- Dr. Christoph Steinbeck (http://www.ice.mpg.de/departments/ChemInf) MPI of Chemical Ecology, Winzerlaer Str. 10, Beutenberg Campus, 07745 Jena, Germany Tel: +49(0)3641 571263 - Fax: +49(0)3641 571202 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. From chemistry-request@server.ccl.net Mon May 6 10:47:52 2002 Received: from gordon.chem.wayne.edu (mer@[141.217.26.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g46Elqv13604 for ; Mon, 6 May 2002 10:47:52 -0400 Received: from localhost (mer@localhost) by gordon.chem.wayne.edu (8.10.2+Sun/8.10.2) with ESMTP id g46EllF02160 for ; Mon, 6 May 2002 10:47:47 -0400 (EDT) Date: Mon, 6 May 2002 10:47:46 -0400 (EDT) From: "mer@chem.wayne.edu" To: chemistry@ccl.net Subject: computational chemistry and drugs Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi all: I am looking for studies/cases where computer-aided drug design/molecular modeling/computational chemistry have played a major role in the discovery of compounds that are now in clinical use. Thanks. From chemistry-request@server.ccl.net Mon May 6 15:22:51 2002 Received: from ultra.chem.ucsb.edu ([128.111.114.119]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g46JMpa19885 for ; Mon, 6 May 2002 15:22:51 -0400 Received: from localhost (bushnell@localhost) by ultra.chem.ucsb.edu (8.9.3+Sun/8.9.1) with ESMTP id MAA18391; Mon, 6 May 2002 12:22:43 -0700 (PDT) Date: Mon, 6 May 2002 12:22:42 -0700 (PDT) From: John Bushnell To: Bin Shan cc: chemistry@ccl.net Subject: Re: CCL:Where can I get a guide to the use of IOP of Gaussian98? In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII There is a list of IOp's in the Gaussian 98 Programmer's Reference, or alternatively online at Gaussian: http://www.gaussian.com/iops.htm Or, you can try digging through the source. :-) - John On Sat, 4 May 2002, Bin Shan wrote: > As I just learned, > > adding IOP(5/13=1) which allows the SCF to print > out the MO's even in the event that convergence was not reached. > > there are also some other IOP functionality I know,like Fock Matrix : > iop(5/33=3) > Overlap Matrix : iop(3/33=1) > > But how are these lines interpreted and where how do I know what kind of > combination generates what kind of functionality.Is there any guide or > tutorial on this?I would be very interested. > From chemistry-request@server.ccl.net Mon May 6 15:27:35 2002 Received: from freyr.chem.washington.edu ([128.95.128.138]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g46JRZa19978 for ; Mon, 6 May 2002 15:27:35 -0400 Received: from localhost (fer@localhost) by freyr.chem.washington.edu (8.11.6/8.11.6) with ESMTP id g46JQYc04794 for ; Mon, 6 May 2002 12:26:34 -0700 Date: Mon, 6 May 2002 12:26:33 -0700 (PDT) From: "Fernando D. Vila" To: Computational Chemistry List Subject: Looking for some properties of water and ice Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi everybody.. I have been trying to find references to some properties of water and ice without much success. I need references to theoretical calculations of the bulk modulus of ice and to the dipole-quadrupole (A) and quadrupole-quadrupole (C) polarizabilities of the water monomer (either theoretical or experimental). Best regards and thanks in advance, Fer. ******************************************************************************* Fernando D. Vila Voice (206)616-3207 Department of Chemistry Fax (206)685-8665 University of Washington E-mail fdv@u.washington.edu Seattle, WA 98195, USA WWW http://faculty.washington.edu/fdv *******************************************************************************