From chemistry-request@server.ccl.net Tue May 25 12:24:41 1999 Received: from postoffice.npac.syr.edu (postoffice.npac.syr.edu [128.230.7.230]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA22932 for ; Tue, 25 May 1999 12:24:33 -0400 Received: from snake.npac.syr.edu (snake.npac.syr.edu [128.230.162.60]) by postoffice.npac.syr.edu (8.9.3/8.9.3) with ESMTP id MAA25852; Tue, 25 May 1999 12:18:22 -0400 (EDT) Received: from localhost (bernhold@localhost) by snake.npac.syr.edu (8.9.3/8.9.3) with SMTP id MAA18150; Tue, 25 May 1999 12:18:21 -0400 (EDT) Message-Id: <199905251618.MAA18150@snake.npac.syr.edu> X-Authentication-Warning: snake.npac.syr.edu: bernhold@localhost didn't use HELO protocol Reply-to: bernhold@npac.syr.edu To: Gary Kedziora cc: chemistry@ccl.net cc: bernhold@npac.syr.edu Subject: Re: CCL:databases, archives, and perhaps XML repositories In-reply-to: <199905250003.TAA04063@mercury.chem.nwu.edu> MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-ID: <18146.927649100.1@snake.npac.syr.edu> Date: Tue, 25 May 1999 12:18:20 -0400 From: "David E. Bernholdt" On Mon, 24 May 1999 19:03:27 -0500 (CDT) Gary Kedziora wrote: > I know that the Ecce program is an interesting and useful interface > to a database of quantum chemistry information. Minor correction: Ecce (extensible computational chemistry environment) is really a "problem solving environment" for chemistry which happens to be designed to store results in a database system. IMHO databasing here is useful, but secondary. For more information about Ecce see http://www.emsl.pnl.gov:2080/docs/ecce/ Dave Feller at PNNL has also been working on a database of QC results. I seem to recall him announcing an online prototype here some time back. Carl Mellius (sp?) at Sandia-Livermore used to have an online database of his calculations. > Here is a proposal. We could create our own repositories of > program output in XML (or some other suitable format) under > the control of our HTML server. Then robot programs could be > developed to go out and look for that information, retrieve it, > and put it into a form suitable for a database. I suspect that this will happen naturally to some extent if/when programs start producing suitably marked-up output. My biggest concern about any such database is validation of the contents. Simply crawling the web for new results is practically an invitation for people to maliciously or otherwise inject erroneous data. What if someone has tweaked the code and does not document it properly in the file that's put out for public consumption? >From my discussions with Dave Feller, he works very hard at validating information before archiving it (even including basis sets for the EMSL Basis Set Library). Otherwise, I think you need to know a fair amount about the provenance of a calculation before you can decide how trustworthy it is, and different people may have different ideas about that. There seems to be a big difference between producing a database and producing a database you can trust. Now one interesting scheme would be some kind of automatic validation. To be useful, this published information is going to have to completely describe the calculation if it is going to be useful. So in principle, the web crawler that picks it up as a candidate for the database could first put it into a queue for validation. This would require repeating the calculation independently to verify the result. The "distributed.net" model, which has been used to solve a number of cryptographic problems in a robust, distributed, "background" fashion is very interesting, though there are obvious problems trying to port this model to the chemistry community. David -- David E. Bernholdt | Email: bernhold@npac.syr.edu Northeast Parallel Architectures Center | Phone: +1 315 443 3857 111 College Place, Syracuse University | Fax: +1 315 443 1973 Syracuse, NY 13244-4100 | URL: http://www.npac.syr.edu From chemistry-request@server.ccl.net Tue May 25 14:28:22 1999 Received: from dfw-ix3.ix.netcom.com (dfw-ix3.ix.netcom.com [206.214.98.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA24028 for ; Tue, 25 May 1999 14:28:22 -0400 Received: (from smap@localhost) by dfw-ix3.ix.netcom.com (8.8.4/8.8.4) id NAA09511 for ; Tue, 25 May 1999 13:20:05 -0500 (CDT) Received: from tfx-us3-04.ix.netcom.com(204.30.67.100) by dfw-ix3.ix.netcom.com via smap (V1.3) id rma009466; Tue May 25 13:19:45 1999 Message-Id: <4.1.19990525141507.00982a00@192.168.0.10> X-Sender: kmtakita@192.168.0.10 X-Mailer: QUALCOMM Windows Eudora Pro Version 4.1 Date: Tue, 25 May 1999 14:16:13 -0400 To: chemistry@server.ccl.net From: Kim Takita Subject: Re: Data Management for Materials Sciences Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" A new initiative is emerging within the materials industry to answer the questions that are arising with increasing frequency: How can we fully take advantage of new materials design opportunities now available with advances in computational methods and power? Can we computational chemistry program developers to agree on a standard for disseminating information suitable for a database? How can we enlist the aid of developers toprovide useful interfaces for interoperatability among vendor supplied software components? If you are struggling with these questions, this international forum will begin to provide the answers: Materials Informatics: Effective Data Management for New Materials Discovery , June 28-29, 1999, at The Omni Parker House, in Boston, MA., USA. Conference website: http://www.knowledgefoundation.com/informatics.html The Knowledge Foundation has organized the first meeting of its kind to bring together end-users, vendors, government and leading academics to begin to address these questions in a practical way. An initial meeting for defining a purpose and action plan for an Industry Consortium for Materials Informatics will be held in conjunction with the program. The fact that IT systems are not designed for the chemical & materials sciences contrasts dramatically with the high level of innovation that is required in materials design/engineering for this cost-conscious and competitive industry. This is just one of the reasons why this conference is so timely. This program will provide you with the basis for enhanced data management strategies WITHIN your own organization, as well as suggest groundwork for taking advantage of external resources. Visit our website, call 617-367-7979 or fax us at 617-367-7912 for a flyer. If you have specific questions regarding the program please contact Kim Takita, Vice President at ext. 202. The Knowledge Foundation, Inc., is a conference and publishing firm dedicated to identifying emerging technologies and providing a forum wherein key players >from industry, academia, and government work together to spur these technologies toward widespread commercialization. Thank you for your attention and time. Kim Takita Vice President The Knowledge Foundation 101 Merrimac Street Boston, MA 02114 617-367-7979 ext. 202 617-367-7912 (fax) Email: kmtakita@knowledgefoundation.com http://www.knowledgefoundation.com From chemistry-request@server.ccl.net Tue May 25 21:07:16 1999 Received: from toucan.prod.itd.earthlink.net (toucan.prod.itd.earthlink.net [207.217.120.98]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id VAA26923 for ; Tue, 25 May 1999 21:07:14 -0400 Received: from lrz.de (1Cust162.tnt1.rancho-cucamonga.ca.da.uu.net [208.251.225.162]) by toucan.prod.itd.earthlink.net (8.9.3/8.9.3) with ESMTP id SAA28168; Tue, 25 May 1999 18:00:51 -0700 (PDT) Received: (from eugene.leitl@localhost) by lrz.de (8.8.8/8.8.8) id RAA18956; Tue, 25 May 1999 17:58:33 -0700 From: Eugene Leitl MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Date: Tue, 25 May 1999 17:58:33 -0700 (PDT) To: CHEMICAL INFORMATION SOURCES DISCUSSION LIST Cc: chemistry@ccl.net Subject: SMILES (was IUPAC rules online and ACD/Name Version 4) In-Reply-To: <3.0.6.32.19990525203036.00836d10@mail.acdlabs.com> References: <3.0.6.32.19990525203036.00836d10@mail.acdlabs.com> X-Mailer: VM 6.43 under 20.4 "Emerald" XEmacs Lucid Message-ID: <14155.17456.175322.637303@lrz.de> I'm curious: does anybody use (unique) SMILES for nomenclature _and_ as a search key? http://www.daylight.com/dayhtml/smiles/smiles-relatives.html http://www.daylight.com/dayhtml/doc/theory/theory.toc.html I'm interested in any pointers to sources devoted to parsing, creation and other manipulation of SMILES strings. So far, I'm only aware of Babel http://www.chem.ohiou.edu/~dolata/babel.html TIA, Eugene Leitl Tony Williams writes: > There have been a number of discussions of late regarding chemical > nomenclature and some pointers to IUPAC nomenclature. For those of you > interested the IUPAC rules have been available online for a while now [...] From chemistry-request@server.ccl.net Wed May 26 09:49:33 1999 Received: from arnold.chem.uoa.gr (arnold.chem.uoa.gr [195.134.76.50]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA00704 for ; Wed, 26 May 1999 09:49:32 -0400 Received: from localhost (jkerk@localhost) by arnold.chem.uoa.gr (8.8.8/8.8.8) with SMTP id QAA18308 for ; Wed, 26 May 1999 16:41:02 +0300 (EET DST) Date: Wed, 26 May 1999 16:41:02 +0300 (EET DST) From: John Kerkines To: chemistry@ccl.net Subject: Atomic RHF Wavefunctions Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL, Often, most RHF wavefunctions for atoms have to be written as linear combinations of a few Slater determinants for the RHF wavefunction to maintain the correct spatial and spin symmetry, especially in excited states of atoms. Since the coefficients of these Slater determinants are determined by the momentum coupling schemes (Clebsch-Gordan, etc.), I was wondering if there exists a computer program or a written compilation (in paper or electronic form) of these wavefunctions for let's say the low-lying electronic states of each atom (but not only for the ground ones). I'll summarize the replies for the list. Regards, ************************************************************ * Ioannis S. Kerkines * * M.Sc. Student in Physical Chemistry * * Department of Chemistry / University of Athens * * Panepistimiopolis Tel: ++30 1 727-4569, 727-4551 * * Zografou, 157 10 FAX: ++30 1 723-3219 (attn:) * * HELLAS (Greece) Email: jkerk@arnold.chem.uoa.gr * ************************************************************ From chemistry-request@server.ccl.net Wed May 26 06:56:43 1999 Received: from mail.rwth-aachen.de (mail.RWTH-Aachen.DE [137.226.144.9]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA31296 for ; Wed, 26 May 1999 06:56:34 -0400 Received: from ac.rwth-aachen.de (pae102.ac.RWTH-Aachen.DE) by mail.rwth-aachen.de (PMDF V5.1-12 #30440) with ESMTP id <01JBNJOEUU2G00019U@mail.rwth-aachen.de> for CHEMISTRY@ccl.net; Wed, 26 May 1999 12:50:32 +0200 Date: Wed, 26 May 1999 12:47:28 +0200 From: Krzysztof Radacki Subject: GaussView 1.0 and Gaussian98 Sender: root@mail.rwth-aachen.de To: CCL Message-id: <374BD140.59227E6F@ac.rwth-aachen.de> Organization: Inst. Inorg. Chem., RWTH Aachen, Germany MIME-version: 1.0 X-Mailer: Mozilla 4.08 [en] (X11; I; Linux 2.0.36 i586) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit Dear CCL'ers, all who has new Gaussian98 and has old GaussView 1.0 can use the small program below to convert Gaussian98 log-files to form that is 'comaptible' with old and good :) Gaussian94. It took me some time to find what realy reads GaussView. The difference is in table "Standard Orientation". There is an additional column "atom type" which should be removed. That what makes the program. It's surely very bad code 'cause it first my program in C (that's only one compilator we have on all computers in Computation Centrum) but it works. Regards Krzys Radacki _________________________-------------------------------------------------- ------------------------- e-mail: Krys.Radacki@ac.RWTH-Aachen.DE --- --------------------------------------------------------------------------- ============================================== save code below as g98do94.c compile it with gcc -o 98do94 98do94.c ================ CUT HERE ================== /* Program -- 98do94 converts Gaussian98 log-files to format that can be read in by GaussView 1.0. Last mod 19:45 May 16, 1999. Copyright (C) 1999 by Krzys Radacki. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA */ #include #include #include #include void syntax() { fprintf(stderr, "\n" "+--------------------------------------------------------+\n" "+ Program 98do94 converts Gaussian98 log-files to format +\n" "+ that can be read in by GaussView 1.0. +\n" "+ by Krzys Radacki, 1999 +\n" "+--------------------------------------------------------+\n\n" " Syntax: g98do94 [infile] [outfile] \n\n"); exit(1); } void main(argc,argv) int argc; char *argv[]; { void syntax(); char line[85]; char test1[30]=" Center Atomic Atomic "; char test2[30]=" Number Number Type "; FILE *infile, *outfile; fpos_t pozycja, pozycja2; int ola,ala; if(argc!=3) syntax(); if(argc==3) { if(!(infile=fopen(argv[1],"r"))) { fprintf(stderr,"Can't open input file %s.\n",argv[1]); } else { infile=fopen(argv[1],"r"); outfile=fopen(argv[2],"w"); for(;;) { if(NULL==fgets(line,85,infile)) break; ala=strncmp(test1,line,30); if(0==strncmp(test1,line,30)) { fputs(line,outfile); fgets(line,85,infile); if(0==strncmp(test2,line,30)) { fputs(line,outfile); fgets(line,85,infile); fputs(line,outfile); fgets(line,85,infile); if(line[29]=='0') ola=1; while (ola==1) { line[29]=' '; fputs(line,outfile); fgets(line,85,infile); if(line[29]=='0') ola=1; else ola=0; } fputs(line,outfile); } else fputs(line,outfile); } else fputs(line,outfile); } } fclose(infile); fclose(outfile); } exit(0); } From chemistry-request@server.ccl.net Wed May 26 11:13:56 1999 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA01829; Wed, 26 May 1999 11:13:56 -0400 Received: from krakow.ccl.net (krakow.ccl.net [192.148.249.195]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id LAA12282; Wed, 26 May 1999 11:10:46 -0400 (EDT) Date: Wed, 26 May 1999 11:10:45 -0400 (EDT) From: Jan Labanowski To: chemistry@ccl.net cc: Jan Labanowski , team@ccl.net Subject: I am sorry for the spam on CCL... Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I am sorry for the spam which appeared on the CCL. (About delicious and healthy snacks, and how you will get rich in a day). Please junk it... Do not respond to them, do not ask to be removed from their list (since you will be placed on their list if you do!!!). In the future... If it does not belong to CCL and you got it from CCL, just junk it, do not take any actions, etc. While I try to filter this stuff, there is no way to do it 100% fail proof with my resources. Sorry, and thank you for your patience (only few people wanted to beat me up... {:-)}. The sad thing is that the message was actually stopped by the CCL scripts. A new student was processing the mail stopped for review, and mixed up messages to be resent. This was a human error... This really made me uncomfortable, and we had the orientation again... I hope, it will improve... Jan jkl@ccl.net Jan K. Labanowski | phone: 614-292-9279, FAX: 614-292-7168 Ohio Supercomputer Center | Internet: jkl@ccl.net 1224 Kinnear Rd, | http://www.ccl.net/chemistry.html Columbus, OH 43212-1163 | http://www.ccl.net/ From chemistry-request@server.ccl.net Wed May 26 12:01:54 1999 Received: from hugh.chem.uic.edu (HUGH.CHEM.UIC.EDU [131.193.195.93]) by server.ccl.net (8.8.7/8.8.7) with SMTP id MAA02434 for ; Wed, 26 May 1999 12:01:54 -0400 Received: by hugh.chem.uic.edu (940816.SGI.8.6.9/940406.SGI.AUTO) id KAA14038; Wed, 26 May 1999 10:04:34 -0500 Date: Wed, 26 May 1999 10:04:26 +36000 From: Richard Wood To: computational chemistry list Subject: A question Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi all on the CCL I have a question for you. I have run 16 molecular dynamics simulations of the same molecule, each one using a different set of initial velocities. From these MD simulations, I have calculated various properties and obtained their averages. I have found the lowest PE for each MD sim and the corresponding conformation. My question is this: is there any way that I can generate an "average" conformation that would give me these "average" properties? I will post all replies. Richard From chemistry-request@server.ccl.net Wed May 26 13:48:59 1999 Received: from rs5.thch.uni-bonn.de (rs5.thch.uni-bonn.de [131.220.44.15]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA03588 for ; Wed, 26 May 1999 13:48:58 -0400 Received: (from bernd@localhost) by rs5.thch.uni-bonn.de (8.8.8/8.8.5) id TAA16812 for chemistry@www.ccl.net; Wed, 26 May 1999 19:45:21 +0200 From: Bernd Engels Message-Id: <199905261745.TAA16812@rs5.thch.uni-bonn.de> Subject: errors in methods of compchem To: chemistry@server.ccl.net (Computational Chemistry List) Date: Wed, 26 May 1999 19:45:21 +0200 (MES) X-Mailer: ELM [version 2.4 PL23] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit dear all, I am looking for systems which are theoretically difficult. I am interested in all kind of systems, i.e. in systems which makes problems for DFT and/or Coupled Clusters and/or Moller-Plesset etc. there should be a lot of systems which are really problematic and (what a pity) where the problems where never published. I will summarize Bernd Engels Prof. fuer Theor. Org. Chemie Universitaet Wuerzburg From chemistry-request@server.ccl.net Wed May 26 14:23:16 1999 Received: from schrodinger.com (root@thermidore.schrodinger.com [192.156.98.99]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA04876 for ; Wed, 26 May 1999 14:23:16 -0400 Received: from sandra.schrodinger.com (sandra.schrodinger.com [206.231.140.250]) by schrodinger.com (8.8.5/8.8.5) with ESMTP id LAA32220 for ; Wed, 26 May 1999 11:24:50 -0700 Received: from localhost (shenkin@localhost) by sandra.schrodinger.com (8.8.5/8.8.5) with ESMTP id OAA06992 for ; Wed, 26 May 1999 14:24:21 -0400 X-Authentication-Warning: sandra.schrodinger.com: shenkin owned process doing -bs Date: Wed, 26 May 1999 14:24:21 -0400 (EDT) From: Peter Shenkin To: computational chemistry list Subject: Average conformation; was, Re: CCL:A question In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, You could get the "average" conformation by doing an rms superposition of all conformations on the first and averaging coordinates, or by doing a more sophisticated multiconformer superposition and then averaging coordinates. Simon Kearsley has published a multiple conformation superposition method. So have we, in our XCluster paper (J. Comp. Chem., v15, pp899-916, 1994). Ours involves looking at all pairwise superpositions. However you do the superposition, the "average" conformation, defined as above, might not be terribly useful. For instance, if half the conformations have a +60-degree torsion and the other half have a -60-degree torsion, the average might have a 0-degree torsion, and thus would not resemble any conformation in the ensemble. OTOH, this might be what you want for some applications. It is sometimes more useful to use the "most representative" structure; this is the actual structure from the data set that has the smallest rms interatomic displacement from the average structure. It's like using the number from a list of numbers which is closest to the average, rather than using the average itself. In XCluster, we first try to find meaningful clusters (maybe there would be two, one with the +60 and one with the -60 torsion). Then we write out the the most representative structure from each cluster. Or we can write out the average structure, if that's what you really want. Hope this helps, -P. On Wed, 26 May 1999, Richard Wood wrote: > Hi all on the CCL > I have a question for you. I have run 16 molecular dynamics > simulations of the same molecule, each one using a different set of > initial velocities. From these MD simulations, I have calculated various > properties and obtained their averages. I have found the lowest PE for > each MD sim and the corresponding conformation. My question is this: is > there any way that I can generate an "average" conformation that would > give me these "average" properties? > > I will post all replies. > > Richard > > -= 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 > > > > > -- ********* Peter S. Shenkin; Schrodinger, Inc.; (201)433-2014 x111 ********* *********** shenkin@schrodinger.com; http://www.schrodinger.com *********** From chemistry-request@server.ccl.net Wed May 26 16:24:52 1999 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA05955 for ; Wed, 26 May 1999 16:24:52 -0400 Received: from herald.cc.purdue.edu (herald.cc.purdue.edu [128.210.11.29]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id QAA21786 for ; Wed, 26 May 1999 16:21:37 -0400 (EDT) Received: from [129.105.14.120] by herald.cc.purdue.edu; Wed, 26 May 1999 15:21:38 -0500 Reply-To: From: "Fredrick C. Hagemeister" To: "Hiris" , "CHEME" , "Ccl" Subject: Looking for a doubling crystal unit for Lambda FL3002 Date: Wed, 26 May 1999 15:20:50 -0500 Message-Id: <000501bea7b5$3fc2c200$780e6981@flood.chem.nwu.edu> 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 8.5, Build 4.71.2173.0 Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Please excuse thi sidetrack. Does anyone have or can help me find a doubling crystal unit (mount and everything) for a Lambda Physik FL3002 dye laser? Alternatively, do you know of any laser resalers like http://www.laserresale.com/ that might have such a thing? Thanks. * Fredrick (Fred) C. Hagemeister * Dept. of Chemistry * Northwestern University * Technological Institute * 2145 Sheridan Road * Evanston, IL 60208-3113 * phone: (847)467-2340 * FAX: (847)491-7713 * home: (847)509-7895 * email: fredhag@nwu.edu