From chemistry-request@server.ccl.net Mon May 8 05:36:19 2000 Received: from alpha.luc.ac.be (alpha.luc.ac.be [193.190.2.30]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA29116 for ; Mon, 8 May 2000 05:36:18 -0400 Received: from sbg-ts (sbg-ts.luc.ac.be [193.190.1.15]) by alpha.luc.ac.be (8.9.3/8.9.3) with SMTP id LAA24593 for ; Mon, 8 May 2000 11:36:05 +0200 (MET DST) Date: Mon, 8 May 2000 11:36:05 +0200 (MET DST) Message-Id: <200005080936.LAA24593@alpha.luc.ac.be> X-Sender: skwasnie@mail.luc.ac.be X-Mailer: Windows Eudora Pro Version 2.1.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@ccl.net From: sergiusz kwasniewski Subject: basisset retrieval in g98 Hi, I've ran into a problem which I don't believe I've had with the previous version of g98 .. since I've installed A.7 on the alpha UNIX server, I can't seem to retrieve the final basisset from the checkpoint file .. did someone else encounter this problem ? g98 removes all temporary files from scratch except the name.chk file that you've stated in the input. you insert the same checkpoint file in a new input file to retrieve both the geometry and basisset using : >>>> $rungauss chk=/scratch/name.chk mem=12000000 #n MP2 guess=read geom=checkpoint GFINPUT ChkBasis name 0 1 <<<< seems that it does not find the original checkpoint file or the data in it. >>>> No Z-matrix found on checkpoint file. Cartesian coordinates read from the checkpoint file: /scratch/skwasnie/Gau-21150.chk FileIO operation on non-existent file. FileIO: IOper= 2 IFilNo(1)=-20997 Len= 140008 IPos= 0 Q= 43980 02523400 <<<<< the checkpoint file mentioned (21150) is a new one started from current input file rather than the one from the previous job. is there something I've missed ? I would appreciate any kind of help .. Serge ___________________________________________________ Sergiusz Kwasniewski LUC SBG/TS Universitaire Campus Gebouw D 3590 Diepenbeek BELGIUM tel(direct): 032 (0)11/268315 fax : 032 (0)11/268301 email : sergiusz.kwasniewski@luc.ac.be http://www.luc.ac.be/Research/TheoChem ___________________________________________________ From chemistry-request@server.ccl.net Mon May 8 06:29:47 2000 Received: from alpha.luc.ac.be (alpha.luc.ac.be [193.190.2.30]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA29341 for ; Mon, 8 May 2000 06:29:46 -0400 Received: from sbg-ts (sbg-ts.luc.ac.be [193.190.1.15]) by alpha.luc.ac.be (8.9.3/8.9.3) with SMTP id MAA03148 for ; Mon, 8 May 2000 12:29:36 +0200 (MET DST) Date: Mon, 8 May 2000 12:29:36 +0200 (MET DST) Message-Id: <200005081029.MAA03148@alpha.luc.ac.be> X-Sender: skwasnie@mail.luc.ac.be X-Mailer: Windows Eudora Pro Version 2.1.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@ccl.net From: sergiusz kwasniewski Subject: Re: CCL:basisset retrieval in g98 Hi, the % are correct in the input files. I've forgotten them in my email. the $GAUSS_EXEDIR and $GAUSS_SCRDIR is the same in my profile as I didn't change it .. so I expect it to be something else .. Serge >Hi Sergiusz, > >I can imagine two mistakes: > >First: The missing % (but I don't know, if they are still necessary) >Second: Have you set the environment variable $GAUSS_EXEDIR and > $GAUSS_SCRDIR correctly (esp. the last one)? > >Hope this helps > >Alex > > >--- > >Dr. Alexander Hofmann >Institut fuer Angewandte Chemie Berlin-Adlershof e.V. >Richard-Willstaetter-Str. 12 > >D-12489 Berlin > >hofmann@aca-berlin.de > >Tel.: 030/6392-4408 >Fax.: 030/6392-4350 > >PGP-Private key: >http://www.uni-leipzig.de/~quant/hofmann/alexander.hofmann.pubkey.asc > > > ___________________________________________________ Sergiusz Kwasniewski LUC SBG/TS Universitaire Campus Gebouw D 3590 Diepenbeek BELGIUM tel(direct): 032 (0)11/268315 fax : 032 (0)11/268301 email : sergiusz.kwasniewski@luc.ac.be http://www.luc.ac.be/Research/TheoChem ___________________________________________________ From chemistry-request@server.ccl.net Mon May 8 09:32:18 2000 Received: from elsnycs18518.elsevier.com ([206.137.72.15]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA31108 for ; Mon, 8 May 2000 09:32:17 -0400 Received: from elsnycs18517.elsevier.com (unverified) by elsnycs18518.elsevier.com (Content Technologies SMTPRS 4.1.2) with ESMTP id for ; Mon, 8 May 2000 09:25:05 +0100 Received: from elsnycs18678.elsevier.com (elsnycs18678.elsevier.com [206.137.75.31]) by elsnycs18517.elsevier.com (2.6 Build 1 (Berkeley 8.8.6)/8.8.4) with ESMTP id JAA00835 for ; Mon, 08 May 2000 09:27:57 -0400 Received: by elsnycs18678.elsevier.com with Internet Mail Service (5.5.2448.0) id ; Mon, 8 May 2000 09:30:35 -0400 Message-ID: <7B2BD12DCFD0D211A3B70008C707D73B01432FA9@elsnycs18680.elsevier.com> From: "Glover, Jonathan (ELS)" To: "'chemistry@ccl.net'" Subject: Computational Drug Design Date: Mon, 8 May 2000 09:27:24 -0400 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2448.0) Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id JAA31109 Dear CCL'ers: <<...>> 2nd Annual Computational Drug Design The Interface of Library Design, Bioinformatics, Structure Based Drug Design and Virtual Screening July 19-21, 2000 * Hyatt Regency San Francisco Key leaders in the biotechnological, pharmaceutical and academic communities recognize the need to utilize innovative computational approaches to guide the synthesis of combinatorial libraries, to analyze the growing volume of screening data, and to focus highthroughput screening resources to minimize discovery time and cost. The Institute for International Research proudly presents the 2nd Annual Computational Drug Design: The Interface of Library Design, Bioinformatics, Structure Based Drug Design and Virtual Screening. This program is specifically designed for the biopharmaceutical industry and includes practical and innovative ways to maximize the value of chemical lead compounds, develop protocols that integrate bioinformatics and chemoinformatics, and enhance computational chemistry and computer aided drug design programs. At this conference you learn how to: * Discover a novel approach to identifying a preferred ligand-binding motif * Examine high throughput virtual screening for lead discovery * Implement more cost-effective protocols for large scale virtual screening * Utilize molecular pharmacophores for faster, more efficient molecular docking * Integrate eADMET and chemical synthesis * Learn about a more efficient and effective means of visualizing protein-protein interactions This program features presentations & case studies from these leading industry experts: Juan Alvarez Paul LaBute Johann Gasteiger Genetics Institute Chemical Computing Group Computer Chemistry Center Andreas Bergner Jin Li Brian Goldman Cambridge Crystallographic Data Center Protherics Vertex Pharmaceuticals Vijay Bhargava Eric Martin Andrew Good Hoescht Marion Roussel, Inc Chiron Corp Bristol Myers-Squibb Regine Bohacek Jennifer Miller Michael Siani Ariad Pharmaceuticals DuPont Pharmaceuticals Kosan Biosciences Arthur Doweyko Garrett Morris Matthew Stahl Bristol Meyers-Squibb The Scripps Institute OpenEye Scientific Jacque Fetrow Michael Pique Michael Vieth GeenFormatics The Scripps Institute Eli Lilly & Co Wayne Guida Schrödinger, Inc Program Schedule Wednesday, July 19th, 2000 8:30-12:00 Pre-conference Workshop Computer Aided Design of Novel Molecules using the 3-D Structures of the > > Target Receptor > > 1:45-2:30 Optimizing Affinity in a Shallow Binding Site: The Design of Low Nanomolar Inhibitors of the Src SH2 Domain 2:30-3:15 Oriented Substituent Pharmacophore PRopErtY Space (OSPPREYS): A Substituent-Based Calculation that Describes Combinatorial Library Products Better than the Corresponding Product-Based Calculation 3:30-4:15 The Discovery Engine (tm) In Action: Demonstration of Rapid Lead Evolution 4:15-5:00 Focused Virtual Screening for More Efficient Exploration of Chemical Space 5:00-6:30 Cocktail Reception Thursday, July 20th, 2000 8:30-9:15 Computer-Aided Design of Novel Polyketides and Polyketide Synthase Genes 9:15-10:00 Virtual Screening: Bridging the Gap Between Structural Genomics and Lead Discovery 10:30-11:15 Data Mining for Drug Design 11:15-12:00 Using 3D-QSAR Methodology to Identify Preferred Ligand Binding Motifs: The Multiple Conformer Protocol 1:00-1:45 Robustness and Resistance: Evolutionary and Coevolutionary Methods in Docking and Drug Design 1:45-2:30 Developing Methods for Pharmacophore-Based Molecular Docking 2:30-3:15 Relibase+: The Easy Way To Search Protein-Ligand Complexes 3:30-4:15 Which Sequence Should I Target? Use of Structure to Find the Important Needle in the Haystack of Protein Sequences 4:15-5:00 Q&A Panel Discussion Friday, July 21st, 2000 8:30-9:15 Visualizing Protein-Protein Interactions 9:15-10:00 Docking-Based QSAR: A Novel Approach to Directing Lead Optimization 10:30-11:15 A Widely Applicable Set of 2½ D Descriptors 11:15-12:00 Integration of eADMET and Chemistry 1:00-1:45 Rapid 3D Database Searching 1:45-2:30 Validation and Optimization of Structure-Based Virtual Screening: Putting the Horse before the Cart 2:30-3:15 Next Generation Flexible Docking: Low-Mode Conformational Search For further information, please call (888) 670-8200 US; (941) 951-7885 Int'l. Visit our website at http://www.IIR-ny.com/conference.cfm?EventID=P0568&CFID=71675&CFTOKEN=11563 We look forward to greeting you in San Francisco on July 19th! From chemistry-request@server.ccl.net Mon May 8 11:09:49 2000 Received: from alpha.luc.ac.be (alpha.luc.ac.be [193.190.2.30]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA31556 for ; Mon, 8 May 2000 11:09:47 -0400 Received: from sbg-ts (sbg-ts.luc.ac.be [193.190.1.15]) by alpha.luc.ac.be (8.9.3/8.9.3) with SMTP id RAA20848 for ; Mon, 8 May 2000 17:09:31 +0200 (MET DST) Date: Mon, 8 May 2000 17:09:31 +0200 (MET DST) Message-Id: <200005081509.RAA20848@alpha.luc.ac.be> X-Sender: skwasnie@mail.luc.ac.be X-Mailer: Windows Eudora Pro Version 2.1.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@ccl.net From: sergiusz kwasniewski Subject: g98 => because of confusion Hi, I'm reposting my mail because of some confusions about my input file: >>>>> $rungauss %scr=/scratch/skwasnie/name.chk %mem=50000000 #n MP2 guess=read geom=checkpoint GFINPUT ChkBasis name 0 1 <<<<< while the output looks like: >>>>> No Z-matrix found on checkpoint file. Cartesian coordinates read from the checkpoint file: /scratch/skwasnie/Gau-21150.chk FileIO operation on non-existent file. FileIO: IOper= 2 IFilNo(1)=-20997 Len= 140008 IPos= 0 Q= 43980 02523400 <<<<< hope this clears out some mistakes serge ___________________________________________________ Sergiusz Kwasniewski LUC SBG/TS Universitaire Campus Gebouw D 3590 Diepenbeek BELGIUM tel(direct): 032 (0)11/268315 fax : 032 (0)11/268301 email : sergiusz.kwasniewski@luc.ac.be http://www.luc.ac.be/Research/TheoChem ___________________________________________________ From chemistry-request@server.ccl.net Mon May 8 13:56:40 2000 Received: from mail.science.siu.edu (mail.science.siu.edu [131.230.107.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA32397 for ; Mon, 8 May 2000 13:56:40 -0400 Received: from tapas (131.230.99.83) by mail.science.siu.edu with SMTP (Eudora Internet Mail Server 2.2.2); Mon, 8 May 2000 12:56:27 -0500 Message-ID: <004701bfb916$5eea5da0$5363e683@thchem.siu.edu> From: "Tapas Kar" To: , "sergiusz kwasniewski" References: <200005081509.RAA20848@alpha.luc.ac.be> Subject: Re: CCL:g98 => because of confusion Date: Mon, 8 May 2000 12:53:51 -0500 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 > $rungauss > %scr=/scratch/skwasnie/name.chk > %mem=50000000 In stead of %scr use %chk - this will solve your problem. ---------------------------------------------------- Tapas Kar, Ph. D Department of Chemistry 1245 Lincoln Dr. # 146F Southern Illinois University Carbondale, IL 62901-4409 Tel: 618-453-6485(Off)/6433(Lab) Fax: 618-453-6408 email: tapaskar@siu.edu tapas@risky3.thchem.siu.edu ----- Original Message ----- From: sergiusz kwasniewski To: Sent: Monday, May 08, 2000 10:09 AM Subject: CCL:g98 => because of confusion > Hi, > > I'm reposting my mail because of some confusions about my input file: > > >>>>> > $rungauss > %scr=/scratch/skwasnie/name.chk > %mem=50000000 > #n MP2 guess=read geom=checkpoint GFINPUT ChkBasis > > name > > 0 1 > > > <<<<< > > while the output looks like: > > >>>>> > No Z-matrix found on checkpoint file. > Cartesian coordinates read from the checkpoint file: > /scratch/skwasnie/Gau-21150.chk > FileIO operation on non-existent file. > FileIO: IOper= 2 IFilNo(1)=-20997 Len= 140008 IPos= 0 Q= 43980 > 02523400 > <<<<< > > hope this clears out some mistakes > > serge > > > ___________________________________________________ > > Sergiusz Kwasniewski > LUC SBG/TS > Universitaire Campus Gebouw D > 3590 Diepenbeek > BELGIUM > > tel(direct): 032 (0)11/268315 > fax : 032 (0)11/268301 > email : sergiusz.kwasniewski@luc.ac.be > http://www.luc.ac.be/Research/TheoChem > ___________________________________________________ > > > -= 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 8 16:30:43 2000 Received: from aspirin.dii.utk.edu (root@ASPIRIN.DII.UTK.EDU [128.169.76.123]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA00557 for ; Mon, 8 May 2000 16:30:42 -0400 Received: from utk.edu (RHODIUM.CHEM.UTK.EDU [128.169.96.18]) by aspirin.dii.utk.edu (8.10.0/8.10.0) with ESMTP id e48KUfY15369 for ; Mon, 8 May 2000 16:30:42 -0400 Sender: hinde@utkux.utcc.utk.edu Message-ID: <3917235F.AD69C95B@utk.edu> Date: Mon, 08 May 2000 16:28:15 -0400 From: Robert Hinde Organization: Univ. of Tenn. Chemistry Dept. X-Mailer: Mozilla 4.61 [en] (X11; I; IRIX64 6.2 IP26) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: G98 A.7 Linux QCISD(T)/6-311G(d,p) failure Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers: I have a Linux box with: Red Hat 6.2 kernel 2.2.14-5.0smp gcc-2.95-2 compilers G98 revision A.7 I find that a G2 calculation on the OH- ion hangs in the QCISD(T)/ 6-311G(d,p) job step. The final lines printed by G98 before hanging are: E2= -0.2127464516E+00 EUMP2= -0.75573464702091E+02 Iterations= 50 Convergence= 0.100E-06 Iteration Nr. 1 ********************** Running the job within the gdb debugger reveals the following execution stack: #0 0x400dc8e9 in __wait4 () from /lib/libc.so.6 #1 0x4013b1ec in ?? () from /lib/libc.so.6 #2 0x4008bcec in __libc_system at ../sysdeps/posix/system.c:136 #3 0x400248cc in system at wrapsyscall.c:120 #4 0x804cb32 in gsyst_ at bsd/mdutil.c:2428 #5 0x804a70a in MAIN__ () #6 0x805d081 in main (argc=1, argv=0xbffff9c4) I've traced the problem to the p polarization functions on the hydrogen atom. The following jobs fail in the same fashion: OH- at QCISD(T)/6-311G(d,p) OH- at CCSD(T)/6-311G(d,p) but the following jobs finish to normal completion: OH- at QCISD(T)/6-311G OH- at CCSD(T)/6-311G OH- at QCISD(T)/aug-cc-pvdz and a QCISD(T) calculation with 6-311G(d,p) on oxygen and 6-311G on hydrogen also works. Finally, I browsed the CCL repositories and found a suggestion to try the route specification # g2 tran=conven (see posting by Qadir K. Timerghazin on July 8, 1999). With this addition, the original G2 job runs to completion. I'm not in the habit of running G2 jobs much, but this is a bit troubling. Does anyone else have the same problem and a better diagnosis? My main worry is that something has messed up in the compilation, although there is no obvious error message in the compile log. I know that Gaussian does not support the gcc/g77 compilers, but when I bought the source CDROM this was not stated on the G98 web page. Once I got the CDROM with printed compilation instructions for the Portland compilers, I decided to plunge ahead and try to get it to compile anyway using gcc/g77... am I living dangerously? -- Robert J. Hinde Department of Chemistry University of Tennessee Knoxville, TN 37996 rhinde@utk.edu Preferred e-mail attachment formats: text / RTF / PDF 865-974-4840 voice 865-974-3454 fax From chemistry-request@server.ccl.net Mon May 8 20:40:38 2000 Received: from socrates.cgl.ucsf.edu (socrates.cgl.ucsf.edu [128.218.27.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id UAA01494 for ; Mon, 8 May 2000 20:40:38 -0400 Received: from [128.218.88.227] (mdi-29.ucsf.edu [128.218.88.227]) by socrates.cgl.ucsf.edu (8.9.3/8.9.3/GSC1.6) with ESMTP id RAA144424 for ; Mon, 8 May 2000 17:40:33 -0700 (PDT) X-Sender: jhempel@socrates.ucsf.edu Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Mon, 8 May 2000 18:11:58 -0800 To: chemistry@ccl.net From: "Judith C. Hempel" Subject: UCSFmeetingOCT13-14 Hello -- Please post the following information for this UCSF/MDI scientific meeting. Thanks very much. Judy Hempel --->> UCSF/MDI Symposium on Drug Design and Discovery October 13-14, 2000 San Francisco, California Registration and meeting information at: http://mdi.ucsf.edu/ The Department of Pharmaceutical Chemistry and Molecular Design Institute of the University of California San Francisco announce a two day meeting chaired by Professors Peter Kollman, Ken Dill, and Irwin Kuntz to address drug design and discovery in the post genomics era. The meeting will give many interesting perspectives on how the science and the technology of drug discovery are changing and will continue to change in the era of combinatorial chemistry and genomics. Experts in the field and scientists seeking understanding of the state of the art as it pertains to interrelationships of genomics, macromolecular structure, combinatorial chemistry and drug design are invited to attend. Poster sessions will provide the opportunity for all who attend to present their recent results. Keynote Speaker: Paul Anderson, Senior VP Chemical and Physical Sciences, DuPont Pharmaceuticals Speakers List: Johan Aqvist, Uppsala University Paul Anderson, DuPont Fred Cohen, UCSF Ken Dill, UCSF Robert Fletterick, UCSF Simon Kearsley, Merck Peter Kollman, UCSF Irwin Kuntz, UCSF Jon Mason, Bristol-Myers Squibb Ken Merz, Pharmacopeia David Pearlman, Vertex Tom Scanlan, UCSF Bruce Tidor, MIT Dennis Underwood, DuPont Gennady Verkhivker, Agouron Jim Wells, Sunesis For more information and to register by email (kristina@cgl.ucsf.edu), please contact: Kristina Clarke, UCSF Department of Pharmaceutical Chemistry, 513 Parnassus Avenue, Box 0446, Room S-926, San Francisco, CA 94143-0446 (tel: 415-514-0148; fax: 415-502-4690; email: kristina@cgl.ucsf.edu). Judith C. Hempel, Ph.D. Associate Director, Molecular Design Institute UCSF-Molecular Design Institute 513 Parnassus Ave., S-926 San Francisco, CA 94143-0446 (tel) 415.502.8396 (fax) 415.502-8397 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ For more info, check out the WEB: http://mdi-10.ucsf.edu email: jhempel@cgl.ucsf.edu ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~