From chemistry-request@server.ccl.net Mon Dec 4 14:28:47 2000 Received: from stillwater.cs.umt.edu (stillwater.cs.umt.edu [150.131.15.39]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA21227 for ; Mon, 4 Dec 2000 14:28:46 -0500 Received: from [150.131.15.54] (dakota.cs.umt.edu [150.131.15.54]) by stillwater.cs.umt.edu (8.9.3+Sun/8.9.3) with ESMTP id MAA12093 for ; Mon, 4 Dec 2000 12:28:47 -0700 (MST) User-Agent: Microsoft Outlook Express Macintosh Edition - 5.01 (1630) Date: Mon, 04 Dec 2000 12:44:32 -0700 Subject: RE: Looking for BABEL and DRAGON users From: "Clair W. Cabal" To: Message-ID: Mime-version: 1.0 Content-type: text/plain; charset="US-ASCII" Content-transfer-encoding: 7bit I am very grateful to everyone who sent me information. A copy of part of my original message is followed by a few of the responses. ============================================================= I am using Babel to convert a chemical data set from SMILES notation to MOL file notation so that I can use Prof. Todeschini's DRAGON program to generate theoretical descriptors. I think the conversion is OK (based on comparing my generated files to the sample files in DRAGON. However, I always get an error in trying to calculate the descriptors with Dragon. I was in hopes that someone with a real understanding of these two formats might point out my error. Here is the output from Babel for one molecule. This SMILES data does not even list the molecule name, so on line two Babel puts the SMILES representation of the molecule. I have added the .mol2 which is necessary for DRAGON to recognize this file. @MOLECULE O=C(Cn1ccnc1)c2ccc3ccccc3c2.mol2 18 20 0 0 0 SMALL NO_CHARGES @ATOM 1 O1 0.0000 0.0000 0.0000 O.2 1 <1> 0.0000 2 C1 0.0000 0.0000 0.0000 C.2 1 <1> 0.0000 3 C2 0.0000 0.0000 0.0000 C.3 1 <1> 0.0000 4 N1 0.0000 0.0000 0.0000 N.pl3 1 <1> 0.0000 5 C3 0.0000 0.0000 0.0000 C.2 1 <1> 0.0000 6 C4 0.0000 0.0000 0.0000 C.2 1 <1> 0.0000 7 N2 0.0000 0.0000 0.0000 N.pl3 1 <1> 0.0000 8 C5 0.0000 0.0000 0.0000 C.2 1 <1> 0.0000 9 C6 0.0000 0.0000 0.0000 C.2 1 <1> 0.0000 10 C7 0.0000 0.0000 0.0000 C.2 1 <1> 0.0000 11 C8 0.0000 0.0000 0.0000 C.2 1 <1> 0.0000 12 C9 0.0000 0.0000 0.0000 C.2 1 <1> 0.0000 13 C10 0.0000 0.0000 0.0000 C.2 1 <1> 0.0000 14 C11 0.0000 0.0000 0.0000 C.2 1 <1> 0.0000 15 C12 0.0000 0.0000 0.0000 C.2 1 <1> 0.0000 16 C13 0.0000 0.0000 0.0000 C.2 1 <1> 0.0000 17 C14 0.0000 0.0000 0.0000 C.2 1 <1> 0.0000 18 C15 0.0000 0.0000 0.0000 C.2 1 <1> 0.0000 @BOND 1 1 2 2 2 2 3 1 3 2 9 1 4 3 4 1 5 4 5 ar 6 4 8 ar 7 5 6 ar 8 6 7 ar 9 7 8 ar 10 9 10 ar 11 9 18 ar 12 10 11 ar 13 11 12 ar 14 12 13 ar 15 12 17 ar 16 13 14 ar 17 14 15 ar 18 15 16 ar 19 16 17 ar 20 17 18 ar With this exact input, the error I get in DRAGON when I attempt to calculate descriptors is: Errors reading molecules ..... 1 Mol. 1 d:\user\cabal\chemdata\out15-~2.mol Input past end of file. (62) RESPONSES: ============================================================= Date: Fri, 01 Dec 2000 10:51:12 +1000 From: Frank Burden Subject: Babel and Dragon To: cabal@cs.umt.edu Hi Clair I received your message through my collaborator David Winkler just when I was working on exactly the same problem. I have found that the converted file works in Dragon if you add just @ to the end of the Babel generated file. Its a difficult life! or as a former prime minister of Australia (Malcolm Fraser) put it 'Life is not meant to be easy'. This has now become part of the Australian vernacular and it certainly fits anything to do with molecule files and their conversions. Cheers Frank ========================== Associate Professor Frank Burden School of Chemistry Monash University VIC 3800 Australia Voice:+613 9905 4559 Fax:+613 9905 4597 http://web.chem.monash.edu.au/Staff/Burden/ ========================== ============================================================= MY NOTE: It turns out that Frank Burden was actually doing MDL to MOL file conversion, however he correctly identifies a problem - see below. ============================================================= From: "R.Todeschini" To: Subject: Dragon Date: Fri, 1 Dec 2000 11:53:05 +0100 Dear Clair, I know you have some troubles in converting SMILES notation to MOL file by Babel in order to use the software DRAGON. The difference between standard MOL file and those converted by Babel is the lacking of a final row with a string: @..... The reaidng routine that I programmed try to check a final row for the final searching for @. Today I will try to solve this problem and put in my Website the new version (without change the version number) which will be simply updated at December 1. Best regards, Roberto Todeschini ---------------------------------------------------------------------------- -- Milano Chemometrics and QSAR Research Group Dept. of Environmental Sciences P.za della Scienza, 1 - 20126 Milano (italy) WebSite: http://www.disat.unimib.it/chm/ ============================================================= From: Doug Henry To: "'Clair W Cabal'" Cc: Doug Henry Subject: RE: Looking for BABEL and DRAGON users Date: Thu, 30 Nov 2000 17:51:46 -0800 I found Dragon to be sensitive to spaces within lines and at the ends of lines. I have been able to make it run on .hin and mdl SDFiles. For .hin files, I have to remove some blanks - I use sed.exe for Windows: http://ftp.yars.free.net/pub/software/windows/programming/cygwin/latest/sed/ with the following bat file: -------------------------- @ECHO OFF REM runs babel on input smiles convert to sdfile REM runs sed to squeeze blanks(say this bat file is "convert.bat") REM convert test.smi test.hin setlocal set ARG1=%1 if exist %ARG1%.smi goto file_exists echo File not found: %ARG1%.smi goto exit :file_exists ..\babel -ismiles %ARG1%.smi -ohin temp1.tmp type temp1.tmp | sed -e "s/ / /g" | sed -e "s/ / /g" > temp2.tmp copy temp2.tmp %ARG1%.hin erase *.tmp :exit ------------------------ For MDL sdfiles, it seems Dragon chokes on 0.0000 coordinates which Babel puts out, so I use a Perl script to replace 0.0000 with some arbitrary value: # Perl script to read a molfile, convert 0.0000 to n.0000 where n is mod line no, 10 # Usage: # babel -ismiles -osdf # perl # Then run Dragon on sdfile2 open (IFILE, "<$ARGV[0]") or die("Unable to open input file: ",$ARGV[0]); open (OFILE, ">$ARGV[1]") or die("Unable to open output file: ",$ARGV[1]); $lineno = 0; while () { $lineno += 1; $linemod = $lineno % 10; s/ 0.0000/ $linemod.0000/; print OFILE; } You can get perl for windows at: www.activestate.com/Products/ActivePerl/Download.html Good luck... DH ============================================================= From: "Elena Fioravanzo" To: "Clair W Cabal" Subject: R: Looking for BABEL and DRAGON users Date: Fri, 1 Dec 2000 11:35:52 +0100 Dear Clair, unfortunately DRAGON, as it is not the ultimate version, works only with a well defined format of MOL files. I had the same problem and I solved it just deleting the blank spaces at the end of lines. I do not know if it is your case, just check everything. ... and, please, let Prof. Todeschini know your problem, maybe he will fix it in the next version of the program. Sincerely Elena --------------------------------------------------------- dott. Elena Fioravanzo - Consultant S.IN - Soluzioni Informatiche S.a.s. Via Salvemini 9 I-36100 Vicenza Italy - Europe Voice ++39 0444 240341 Mobile ++39 0347 4054991 Fax ++39 0444 533954 E-mail s.in-support@mclink.it Web http://www.goldnet.it/sin/ ============================================================= I hope this information will be helpful. Clair ----------------------------------------------------- Clair Cabal Research Assistant Machine Learning Research Lab Department of Computer Science University of Montana Missoula, Montana 59812 cabal@cs.umt.edu fax: (406) 243-5139 ----------------------------------------------------- From chemistry-request@server.ccl.net Tue Dec 5 01:39:47 2000 Received: from snipe.prod.itd.earthlink.net (snipe.prod.itd.earthlink.net [207.217.120.62]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id BAA24109 for ; Tue, 5 Dec 2000 01:39:47 -0500 Received: from piglet (dialup-209.244.67.254.Chicago1.Level3.net [209.244.67.254]) by snipe.prod.itd.earthlink.net (EL-8_9_3_3/8.9.3) with SMTP id WAA23093 for ; Mon, 4 Dec 2000 22:39:34 -0800 (PST) From: "Slawomir Z. Janicki" To: "CCL" Subject: Coulomb and exchange integrals Date: Tue, 5 Dec 2000 00:36:37 -0600 Message-ID: <000001c05e85$b7c1b300$fe43f4d1@piglet> 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 V5.50.4522.1200 Are Coulomb and exchange integrals defined in MCSCF? If yes, how can I get them from GAMESS? Slawomir Janicki janicki1@earthlink.net From chemistry-request@server.ccl.net Tue Dec 5 12:28:37 2000 Received: from galaxy.pnl.gov (galaxy.pnl.gov [130.20.64.136]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA27548 for ; Tue, 5 Dec 2000 12:28:37 -0500 Received: from CONVERSION-DAEMON by pnl.gov (PMDF V5.2-33 #42505) id <01JXC9FMY47U8WW205@pnl.gov> for chemistry@ccl.net; Tue, 5 Dec 2000 09:25:48 PST Received: from vscan2.pnl.gov ([130.20.64.141]) by pnl.gov (PMDF V5.2-33 #42505) with SMTP id <01JXC9F8HFE88WW27W@pnl.gov> for chemistry@ccl.net; Tue, 05 Dec 2000 09:25:28 -0800 (PST) Received: from 130.20.128.21 by vscan2.pnl.gov (InterScan E-Mail VirusWall NT) ; Tue, 05 Dec 2000 09:25:26 -0800 (Pacific Standard Time) Received: by PNLMSE1.pnl.gov with Internet Mail Service (5.5.2448.0) id ; Tue, 05 Dec 2000 09:23:19 -0800 Date: Tue, 05 Dec 2000 09:22:00 -0800 From: "Windus, Theresa L" Subject: NWChem 4.0 To: "'nwchem-users@emsl.pnl.gov'" , "'hpcs1-users@emsl.pnl.gov'" , "'chemistry@ccl.net'" Message-id: <6DBB005AF9DDD31193030008C7A49DC831F58C@pnlmse8.pnl.gov> MIME-version: 1.0 X-Mailer: Internet Mail Service (5.5.2448.0) Content-type: text/plain; charset="iso-8859-1" The latest version of NWChem, version 4.0, is now available to the public. Please point your browser to http://www.emsl.pnl.gov/pub/docs/nwchem for complete information about this latest release and for download information. New capabilities in NWChem include: o ONIOM - ONIOM hybrid method of Morokuma and co-workers o COSMO - the continuum solvation 'Conductor-Like Screening' Model of A. Klamt and G. Schuurmann to describe dielectric screening effects in solvents. o NBO - Natural Bond Orbital analysis is now available inside NWChem (not just the interface which was in the previous versions). o SODFT - Spin-orbit density functional theory. o MD - While this is not a new capability, the MD module has been rewritten to allow for new force fields to be incorporated in a modular fashion. Additional major additions to the capabilities include: o The Douglas-Kroll(-Hess) approach is implemented. It can be used at all levels of theory. Gradients have been implemented allowing geometry optimizations and frequency calculations using the Douglas-Kroll Hamiltonian. o Inclusion of code to evaluate relativistic integrals based on Dyall's modified Dirac (DmD) equation. A one-electron approximation very similar to the Douglas-Kroll-Hess approach has been implemented with gradients. Two-electron scalar relativistic corrections have been implemented for energies only. o Vibrational analysis now allows different masses to be used for a previously calculated hessian - see VIB description. o Input files to standard graphics packages such as RasMol or XMol can be generated to animate vibrational modes - see VIB description. o Several new DFT functionals have been added: o Exchange-Correlation PBE0, HCTH402 and Becke1997GGA-1 functionals From chemistry-request@server.ccl.net Tue Dec 5 13:55:28 2000 Received: from hamiltonian.chem.cornell.edu (root@hamiltonian.chem.cornell.edu [128.253.229.83]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA27888 for ; Tue, 5 Dec 2000 13:55:28 -0500 From: marketa@hamiltonian.chem.cornell.edu Received: from localhost (marketa@localhost) by hamiltonian.chem.cornell.edu (8.11.0/8.11.0) with ESMTP id eB5JvB123445 for ; Tue, 5 Dec 2000 13:57:11 -0600 Date: Tue, 5 Dec 2000 13:57:11 -0600 (CST) To: chemistry@ccl.net Subject: Z-matrix input for C60 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I wonder if someone could provide me with a Z-matrix input for buckminster-fullerene C60. I need my program to recognize as much of the icosahedral symmetry as possible. Thank you, Marketa Munzarova From chemistry-request@server.ccl.net Tue Dec 5 16:15:54 2000 Received: from coyote.iupui.edu (coyote.iupui.edu [134.68.220.82]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA28364 for ; Tue, 5 Dec 2000 16:15:54 -0500 Received: from macgw.chem.iupui.edu (macgw.chem.iupui.edu [134.68.137.71]) by coyote.iupui.edu (8.9.3/8.9.3/IUPUIPO.1.3) with SMTP id QAA30406 for ; Tue, 5 Dec 2000 16:15:54 -0500 (EST) Message-ID: Date: 5 Dec 2000 16:34:58 -0500 From: "Boyd" Subject: Gordon Conference To: "OSC CCL" X-Mailer: Mail*Link SMTP for Quarterdeck Mail; Version 4.1.0 Dear CCLers: With the end of the year approaching and some taxpayers thinking about making charitable donations, we would like to bring the following to your attention. This past summer Dr. Terry R. Stouch, Chair of the 8th biennial Gordon Research Conference (GRC) on computational chemistry, made arrangements for an interest-bearing account managed by the GRC office. The account will help support future GRCs on Computational Chemistry. In honor of the late Prof. Zerner, the account is called the Mike Zerner Lecture Fund of the GRC on Computational Chemistry. Contributions are welcome, not only from former participants of the Gordon Conferences on Computational Chemistry but also all who want to help perpetuate these useful conferences. The GRC is a 501c3 nonprofit organization, and donations are tax deductible. The GRC office will send a letter acknowledging a contribution for your tax records. Donations (payable to Gordon Research Conferences) should be sent to the Gordon Research Center, University of Rhode Island, P.O. Box 984, West Kingston, RI 02892-0984, USA. The contributions should be indicated for the Mike Zerner Lecture Fund of the GRC on Computational Chemistry. Thank you and best wishes for the new year. Bernard R. Brooks (Chair, 2002) William C. Swope (Chair-Elect, 2004) Terry R. Stouch (Chair, 2000) Jeffry D. Madura (Chair, 1998 Kendall N. Houk (Chair, 1994) John McKelvey (Chair, 1992) William L. Jorgensen (Chair, 1990) Peter A. Kollman (Chair, 1988) Kenny B. Lipkowitz (Chair, 1986) Donald B. Boyd (Chair, 1986 & 1988) From chemistry-request@server.ccl.net Tue Dec 5 21:25:47 2000 Received: from hamiltonian.chem.cornell.edu (root@hamiltonian.chem.cornell.edu [128.253.229.83]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id VAA29634 for ; Tue, 5 Dec 2000 21:25:47 -0500 From: marketa@hamiltonian.chem.cornell.edu Received: from localhost (marketa@localhost) by hamiltonian.chem.cornell.edu (8.11.0/8.11.0) with ESMTP id eB63RjY25050 for ; Tue, 5 Dec 2000 21:27:45 -0600 Date: Tue, 5 Dec 2000 21:27:45 -0600 (CST) To: chemistry@ccl.net Subject: summary: C60 input coordinates Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I would like to thank to Gert von Helden, N. Dragoe and Roy Jensen who sent me promptly several different types of C60 coordinates. If anybody else is interested in getting their replies, please contact me at mm335@cornell.edu Marketa