From chemistry-request@server.ccl.net Fri Feb 18 04:47:41 2000 Received: from gerwazy.chem.uni.wroc.pl (gerwazy.chem.uni.wroc.pl [156.17.103.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA09296; Fri, 18 Feb 2000 04:47:38 -0500 Received: from wchuwr.chem.uni.wroc.pl ([156.17.103.1]) by gerwazy.chem.uni.wroc.pl (8.8.8+Sun/8.8.8) with ESMTP id JAA13965; Fri, 18 Feb 2000 09:44:48 +0100 (MET) Received: from WCHUWR/SpoolDir by wchuwr.chem.uni.wroc.pl (Mercury 1.44); 18 Feb 00 09:42:37 MET Received: from SpoolDir by WCHUWR (Mercury 1.44); 18 Feb 00 09:42:31 MET From: "Andrzej Szymoszek" Organization: University of Wroclaw (Chemistry) To: chemistry@ccl.net, chemistry-request@ccl.net Date: Fri, 18 Feb 2000 09:42:26 MET Subject: RE: A question on molecular volume calculation Priority: normal X-mailer: Pegasus Mail v3.40 Message-ID: <4B5280D40@wchuwr.chem.uni.wroc.pl> Dear All, A couple of weeks ago I posted to the ccl a question concerning programs that compute "molecular volume". Here is the summary of answers: Tom Hawkins (thawkins@osmetech.plc.uk) and Olivier Maresca (olivier@piimsdm9.univ-mrs.fr) suggested WebLabViewer Lite for Windows or Mac. Andre Mauricio de Olivieira (amolive@dedalus.lcc.umfg.br) added Molekel: http://igc.ethz.ch/molekel/menu.html (as they write there, only for SGI) E. Hiramatsu (ehiramatsu@ma3.justnet.ne.jp) noticed Tinker: http://dasher.wustl.edu/tinker/ And finally, Mark Mackey (mark_mackey@merck.com): On 1 Feb 00 at 7:16, Mackey, Mark wrote: > It's easy to compute a good approximation to molecular volume. > 1) Calculate a bounding box for your molecule. > 2) Generate 10,000 random points in the box > 3) For each point, see whether it is inside the molecule (just a simple van > der Waals distance check against each atom) > 4) The molecular volume = (no. of points inside molecule)/10000 * volume of > box > > This method, although somewhat random, is easily good enough, especially > when you consider that 'molecular volume' is an inherently fuzzy concept. If > you need higher accuracy, just use a larger number of points! You need to be > reasonably confident about the random number generator you are using, > however. > I must say, I more or less followed the last suggestion. Thanks to all for their contribution, Andrzej Szymoszek From chemistry-request@server.ccl.net Fri Feb 18 04:56:50 2000 Received: from mf006.infoweb.ne.jp (mf006.infoweb.ne.jp [210.131.99.16]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA09357 for ; Fri, 18 Feb 2000 04:56:49 -0500 Received: from [192.168.1.55] by mf006.infoweb.ne.jp (8.9.3+3.2W/3.7W-10/13/99) with ESMTP id RAA24823 for ; Fri, 18 Feb 2000 17:50:55 +0900 Mime-Version: 1.0 X-Mailer: Macintosh Eudora Pro Version 4.2.1-J Reply-To: fwip5390@mb.infoweb.ne.jp Message-Id: Date: Fri, 18 Feb 2000 17:51:47 +0900 To: chemistry@ccl.net From: Narushi Goto Subject: Compile options on LinuxPPC Content-Type: text/plain; charset="us-ascii" ; format="flowed" Hi all, Has anyone successfully compiled QM codes (like GAMESS, CADPAC, Gaussian) with g77 under LinuxPPC on PowerBook G3 or Power Macintosh G3/G4? If someone knows the compile options and/or tips, please advice me. Best regards, Narushi From chemistry-request@server.ccl.net Thu Feb 17 15:47:00 2000 Received: from mjco-s2.ice.mpg.de (mjco-s2.ice.mpg.de [195.37.47.3]) by server.ccl.net (8.8.7/8.8.7) with SMTP id PAA06128 for ; Thu, 17 Feb 2000 15:46:59 -0500 Received: from ice.mpg.de (unverified [195.37.47.130]) by mjco-s2.ice.mpg.de (EMWAC SMTPRS 0.83) with SMTP id ; Thu, 17 Feb 2000 20:43:54 +0100 Message-ID: <38AC4F73.3FCE99A3@ice.mpg.de> Date: Thu, 17 Feb 2000 20:43:47 +0100 From: Christoph Steinbeck Reply-To: steinbeck@ice.mpg.de Organization: Max-Planck-Institute of Chemical Ecology X-Mailer: Mozilla 4.7 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Re: CCL Digest of 2000/02/16 References: <200002170735.CAA01158@server.ccl.net> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit > Dear ccl'ers, > > I want to run g98 using Linda on a couple of one-processor pentium/linux > boxes. I wasn't able to find out about HOW to launch the program. I guess > that ntsnet is involved but I'm not sure at all. > I'd appreciate any hints. > Regards, > > Reinaldo > Once you've compiled the stuff you can use the g98l script in the $g98root/g98/bsd subdir. This just adds the $g98root/g98/linda-exe subdir to the front of your path so that the linda-linked substitutes for the regular g98 exes are found instead of the original ones. You will also have to prepare a .tsnet.config in your home dir with a line like Tsnet.Appl.nodelist: mynode1 mynode2 mynode3 which is listing the cluster nodes. Please let me know if it helps. Despite of a lot of support from Doug Fox I wasn't able to get the system up and running. In my case a worker process gets started on the second node but it dies immediately with the master process on the first node waiting for minutes for it to complete and the die. Cheers, Chris -- Dr. Christoph Steinbeck (http://www.ice.mpg.de/~stein) MPI of Chemical Ecology, Tatzendpromenade 1a, 07745 Jena, Germany Tel: +49(0)3641 643644 - Fax: +49(0)3641 643665 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. From chemistry-request@server.ccl.net Thu Feb 17 18:01:14 2000 Received: from hermes.iupui.edu (hermes.iupui.edu [134.68.220.31]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA06713 for ; Thu, 17 Feb 2000 18:01:14 -0500 Received: from macgw.chem.iupui.edu (macgw.chem.iupui.edu [134.68.137.71]) by hermes.iupui.edu (8.9.3/8.9.3/1.2IUPUIPO) with SMTP id QAA09304 for ; Thu, 17 Feb 2000 16:55:41 -0500 (EST) Message-ID: Date: 17 Feb 2000 17:07:35 -0500 From: "Boyd" Subject: Call for papers / Washington To: "OSC CCL" X-Mailer: Mail*Link SMTP for Quarterdeck Mail; Version 4.1.0 Hi, The American Chemical Society's Computers in Chemistry Division (COMP) is organizing a new type of symposium at the Washington, DC, national meeting, August 20-24, 2000. A $1000 will be awarded to the best oral paper presented at the Emerging Technologies Symposium. The papers will be evaluated based on the impact the research will have on the future of computational chemistry and allied sciences. To participate, e-mail a 1000-word abstract to me as soon as possible, but no later than April 1, 2000. The abstract must be in text-only or MS Word. These long abstracts will be reviewed by a panel of experts. The best contributions will be selected for oral presentations at the meeting in Washington. The remaining contributions will be presented at a special evening poster session. It is essential that you ALSO submit a short regular ACS abstract to the web-based system at http://www.acs.org/meetings/ by April 12. At the meeting, the oral presentations will be judged by the panel of experts, and the winner of the $1000 prize will be selected and awarded following the talks. Sincerely, 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 Editor, Reviews in Computational Chemistry http://chem.iupui.edu/rcc/rcc.html Department of Chemistry Indiana University-Purdue University at Indianapolis 402 North Blackford Street Indianapolis, Indiana 46202-3274, U.S.A. Telephone 317-274-6891, FAX 317-274-4701 E-mail boyd@chem.iupui.edu From chemistry-request@server.ccl.net Fri Feb 18 03:04:28 2000 Received: from web3404.mail.yahoo.com (web3404.mail.yahoo.com [204.71.203.58]) by server.ccl.net (8.8.7/8.8.7) with SMTP id DAA08821 for ; Fri, 18 Feb 2000 03:04:28 -0500 Message-ID: <20000218065645.28097.qmail@web3404.mail.yahoo.com> Received: from [202.141.2.3] by web3404.mail.yahoo.com; Thu, 17 Feb 2000 22:56:45 PST Date: Thu, 17 Feb 2000 22:56:45 -0800 (PST) From: Rachita Sharma Subject: selenamides To: chemistry@CCL.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear CCLers I am the student of MSc Chemistry.I am doing research on Selenamides& Selenilimines. If you have any information regarding these compounds,kindly please sent on the following address: Rachita.v.sharma __________________________________________________ Do You Yahoo!? Talk to your friends online with Yahoo! Messenger. http://im.yahoo.com From chemistry-request@server.ccl.net Thu Feb 17 19:51:12 2000 Received: from ozone.umsl.edu (ozone.umsl.edu [134.124.105.185]) by server.ccl.net (8.8.7/8.8.7) with SMTP id TAA07244 for ; Thu, 17 Feb 2000 19:51:12 -0500 Received: from ozone.umsl.edu (ozone.umsl.edu [134.124.105.185]) by ozone.umsl.edu (950413.SGI.8.6.12/950213.SGI.AUTOCF) via ESMTP id RAA21018 for ; Thu, 17 Feb 2000 17:45:09 -0800 Sender: wang@ozone.umsl.edu Message-ID: <38ACA425.63705EA1@ozone.umsl.edu> Date: Thu, 17 Feb 2000 17:45:09 -0800 From: XIA WANG Organization: UMSL X-Mailer: Mozilla 4.5 [en] (X11; I; IRIX64 6.4 IP27) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Ask information about database Dea All, There are two default database in UNITY or SYBYL/UNITY software, NCI and Maybridge database. I wonder whether the number of compounds in these database are CAS registry number, and where I can find or buy these compounds. Thanks. Wang, Xia Wang;Xia tel;fax:(314)516-5342 tel;home:(314)524-1178 tel;work:(314)516-6882 org:Center for Molecular Electronics &;Department of Chemistry, UM-St.Louis adr:;;8001 Natural Bridge Road;St. Louis;MO;63121;USA email;internet:wang@ozone.umsl.edu title:Ph.D fn:Xia Wang From chemistry-request@server.ccl.net Fri Feb 18 09:07:03 2000 Received: from dalton.quimica.unlp.edu.ar (root@dalton.quimica.unlp.edu.ar [163.10.18.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA11542 for ; Fri, 18 Feb 2000 09:06:58 -0500 Received: from bilbo (jubert4.quimica.unlp.edu.ar [163.10.18.18]) by dalton.quimica.unlp.edu.ar (8.9.0/8.9.0) with SMTP id JAA15307 for ; Fri, 18 Feb 2000 09:42:06 -0300 Message-Id: <3.0.1.32.20000218095822.00695dac@dalton.quimica.unlp.edu.ar> X-Sender: pis_diez@dalton.quimica.unlp.edu.ar X-Mailer: Windows Eudora Light Version 3.0.1 (32) Date: Fri, 18 Feb 2000 09:58:22 -0300 To: chemistry@ccl.net From: Reinaldo Pis Diez Subject: Summary -> G98 + Linda under Linux Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear ccl'ers, Some days ago I sent a mail to the list asking about how to run g98 under the linda environment on pentium/linux platforms. I wish to thank Doug Fox from Gaussian who sent the correct answer which is appended below. Now I have g98 running under Linda on a couple of pentium/linux boxes. Regards to all, Reinaldo ************************Doug's mail*********************************** The G98 binary distribution for Linux has G98 compiled with Linda but as you noted you need to get Linda from either Gaussian or SCA. There is a demo version which SCA makes available which you can use to test this and they have gotten it on the RedHat 6.1 distribution. I presume this is what you have been playing with. The best plan is to have Linda and G98 on one machine and mount it on the other nodes via NFS and either make it look the same, i.e. /usr/local/g98 on all machines, or at least put in links so that it can be addressed the same way. Set up your .cshrc file so that the G98 and Linda runtime environments are defined when links are started via rsh. You should also define GAUSS_SCRDIR so that it points to a local disk on each machine to avoid making NFS disk traffic the limiting resource. The checkpoint and RWF will only be accessed on the master node but each worker will create a Gau_xxx.scr file on its local scratch directory. Finally, you need to start g98 with the script g98/bsd/g98l which amends the GAUSS_EXEDIR environment variable so find the Linda version of links. This approach is best suited to HF and DFT where disk I/O is minimal. MP2 energy and gradient also works well but higher order methods are generally bound by disk I/O to the RWF file for the MO integrals. ******************************end of mail******************************** From chemistry-request@server.ccl.net Fri Feb 18 17:17:25 2000 Received: from sos1.chem.iupui.edu ([134.68.137.53]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA14006 for ; Fri, 18 Feb 2000 17:17:25 -0500 Received: from localhost (dgao@localhost) by sos1.chem.iupui.edu (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id QAA39715 for ; Fri, 18 Feb 2000 16:09:48 -0500 (EST) Date: Fri, 18 Feb 2000 16:09:48 -0500 From: Daquan Gao To: chemistry@ccl.net Subject: Surface and volume calculations Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, I would like pointers to fast algorithms(preferentially analytical) of computing the surface areas of molecules? Any idea is also appreciated. Yours Truly, Daquan Gao From chemistry-request@server.ccl.net Fri Feb 18 21:21:16 2000 Received: from amon.reed.edu (amon.reed.edu [134.10.2.10]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id VAA14950 for ; Fri, 18 Feb 2000 21:21:15 -0500 Received: from isis.reed.edu (isis.reed.edu [134.10.2.1]) by amon.reed.edu (8.8.8/8.8.8) with ESMTP id RAA11285 for ; Fri, 18 Feb 2000 17:15:23 -0800 (PST) Message-id: <11101792@isis.reed.edu> Date: 18 Feb 2000 17:15:23 PST From: Alan.Shusterman@directory.reed.edu (Alan Shusterman) Subject: diatomic MOs To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Disposition: inline Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id VAA14951 (I apologize in advance if you get this email twice, but the campus computer sent me a message saying that this email bounced back unsent.) A basic MO question. I'm teaching inorganic chemistry this semester and I've reached the MO theory of homonuclear diatomics (Li2, Be2, etc.). The book makes the traditional convincing, but qualitative, argument regarding the sequence of sigma and pi levels. Namely, pz-pz sigma bonding level is below the pi bonding levels for N2, O2, F2, but above for B2 and C2. I thought it would be nice for my students to verify this for themselves computationally (and see the actual s-pz mixing), but I find that when I try UHF and HF calculations on these molecules I can't reproduce all of the textbook predictions. For example, the pi bonding levels come BELOW the pz-pz = bonding combination in F2 and triplet O2 (HF & UHF/6-311+G*), and the pz-pz bonding MO comes BELOW the pi bonding levels in triplet C2 (UHF). Can anyone point me to the original calculations and/or experiments = that the textbook discussion is based on? Or, if not that, to calculations that I could do that are capable of reproducing the textbook's claims. (This argument re: B2, C2, N2, etc., is duplicated in nearly every book that I can find, but I can't find any relevant research-grade literature on the topic.) The next class is on Monday... :-< Thanks, Alan ----------------- Alan Shusterman Department of Chemistry Reed College Portland, OR www.reed.edu/~alan