From chemistry-request@server.ccl.net Fri Oct 13 05:35:18 2000 Received: from tigris.klte.hu (tigris.klte.hu [193.6.138.33]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA08329 for ; Fri, 13 Oct 2000 05:35:17 -0400 Received: from anti07 (193.6.133.59) by tigris.klte.hu (MX V5.1-A Vn6f) with SMTP for ; Fri, 13 Oct 2000 11:34:47 +0200 Message-ID: <001f01c034f9$253f9980$3b8506c1@chem.klte.hu> From: "Tamas E. Gunda" To: Subject: New Mol2mol 3.5 Date: Fri, 13 Oct 2000 11:37:03 +0200 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-2" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2615.200 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id FAA08330 Dear CCL Members, The new 3.50 version of the molecule file conversion, manipulation and utility program Mol2Mol is now available from CompuChem Ltd. The current version of Mol2Mol recognizes, and interconverts more than 30 different file formats. It contains a simple graphic display module to inspect the currently loaded molecule. It possesses some chemical intelligence for recognizing detailed atom types, hybridization and chemical environments, which is necessary for converting simpler formats (like X-ray crystallographic files) to more advanced ones, or when hydrogen atoms are automatically to be added to the heavy atoms. Multiple-to-multiple multiple-to-many conversions. Calculation of pyramidalities, ring puckerings. Some of the new features of Mol2Mol ver 3.50: New file formats have been added: Molecule-3D (m3d), crystal Shelx read and edit/write, MDL SD file read and write. Adding hydrogens to PDB (type) files: mimic pH; New graphical utility: show the distances to nearest atoms, browse multiple structures. Several features for POV-Ray files. For more info see: http://www.compuchem.com/mol2mol.htm (demo version is available.) and/or http://dragon.klte.hu/~gundat/mol2mola.htm POV-Ray users may also have a look at: http://dragon.klte.hu/~gundat/povraya.htm ------------------ Dr Tamas E. Gunda University of Debrecen, POBox 36 H-4010 Debrecen, Hungary e-mail: tamasgunda@tigris.klte.hu home-page: www.klte.hu/~gundat/gunda.htm From chemistry-request@server.ccl.net Fri Oct 13 09:09:15 2000 Received: from lipid.biocomp.unibo.it (ivan@lipid.biocomp.unibo.it [137.204.193.11]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA09946 for ; Fri, 13 Oct 2000 09:09:15 -0400 Received: from localhost (ivan@localhost) by lipid.biocomp.unibo.it (8.9.3/8.9.3) with ESMTP id PAA27198 for ; Fri, 13 Oct 2000 15:24:15 +0200 Date: Fri, 13 Oct 2000 15:24:15 +0200 (CEST) From: Ivan Rossi To: CompChem Mailing List Subject: Bologna Winter school announcement Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CLL'ers, This is to announce the Bologna Winter school on Biotechnology This year's topic will be : In Silico Biomolecular Recognition More information can be found on the school web page at http://www.biocomp.unibo.it/school/html2000/index.html Ivan --------------------------------------------------- University of Bologna CIRB INTERDEPARTMENTAL CENTER FOR BIOTECHNOLOGY CINECA, CIB, CNR MARINO GOLINELLI FOUNDATION O.N.L.U.S. Organization :ALTA srl BOLOGNA WINTER SCHOOL on Biotechnology IN SILICO BIOMOLECULAR RECOGNITION 4-10 February 2001 Bologna - Italy Main topics will be: ligand-protein interaction, peptide-protein interaction, protein-protein interaction, docking programs. Round table discussions will focus on "hot" topics of proteomics. TEACHERS: Geoff Barton European Bioinformatics Institute, Hinxton, UK Alessandro Desideri Universita' Tor Vergata, Roma, IT Manuela Helmer Citterich Universita' Tor Vergata, Roma, IT Joel Janin LEBS, CNRS, Gif sur Yvette, FR David T. Jones Brunel University, West London, UK Thomas Lengauer SCAI, GMD Sankt Augustin, DE Ruth Nussinov Seckler Inst. of Molecular Medicine, Tel Aviv, IL Arthur J. Olson The Scripps Research Institute La Jolla , USA Michael Sternberg Imperial Cancer Research Fund, London, UK Alfonso Valencia National Center of Biotechnology, Cantoblanco, ES -- Dr. Ivan Rossi - CIRB Biocomputing Unit e-mail: ivan@biocomp.unibo.it Web: http://www.biocomp.unibo.it/ivan From chemistry-request@server.ccl.net Fri Oct 13 10:09:31 2000 Received: from interlock.herc.com (interlock.herc.com [199.221.7.2]) by server.ccl.net (8.8.7/8.8.7) with SMTP id KAA10208 for ; Fri, 13 Oct 2000 10:09:31 -0400 From: Goutam.Das@betzdearborn.com Received: from csdnsg1.herc.com ([147.116.14.51]) by interlock.herc.com with SMTP id KAA09731 (InterLock SMTP Gateway for ); Fri, 13 Oct 2000 10:09:19 -0400 Subject: DFT To: chemistry@ccl.net X-Mailer: Lotus Notes Release 5.0.2b December 16, 1999 Message-Id: Date: Fri, 13 Oct 2000 09:07:56 -0500 X-Priority: 3 (Normal) X-Mimetrack: Serialize by Router on CSDNSG1/Servers/Herc(Release 5.0.1b|September 30, 1999) at 10/13/2000 09:59:34 AM Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hello CCLers, Can anyone of you suggest an introduction to DFT suitable for advanced undergraduates (texts, references, websites) This is mainly for students to get a "working idea" for DFT. Thanx to all of you in anticipation. Happy Friday the 13th! Goutam Das Research Scientist BetzDearborn Division of Hercules The Woodlands, TX 77380 281.367.6201 ext 425 From chemistry-request@server.ccl.net Fri Oct 13 15:06:54 2000 Received: from kodakr.kodak.com (kodakr.kodak.com [192.232.119.69]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA11459 for ; Fri, 13 Oct 2000 15:06:53 -0400 Received: from copernicus.rl.kodak.com (copernicus.rl.kodak.com [150.220.89.97]) by kodakr.kodak.com (8.9.1/8.9.1) with ESMTP id PAA00724 for ; Fri, 13 Oct 2000 15:06:47 -0400 (EDT) Received: from kodak.com (berlioz [150.220.89.22]) by copernicus.rl.kodak.com (8.9.3+Sun/8.9.1) with ESMTP id PAA15793 for ; Fri, 13 Oct 2000 15:05:26 -0400 (EDT) Sender: giesen@copernicus.rl.kodak.com Message-ID: <39E756ED.AD4A532D@kodak.com> Date: Fri, 13 Oct 2000 14:39:41 -0400 From: David Giesen Organization: Eastman-Kodak X-Mailer: Mozilla 4.05C-SGI [en] (X11; U; IRIX64 6.5 IP25) MIME-Version: 1.0 To: chemistry@ccl.net Subject: G98 SMP on a Sun Machine Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi - I apologize for the 'software' content of this note rather than 'chemistry'. I've tried sending this question to help@gaussian.com (no response) and a thorough search of the CCl archives gave no helpful information. I am having trouble running G98 rev a7 in parallel using SMP on a multi-processor Sun machine. Jobs requesting multiple processors (%nproc>1) die in link 101 immediately after printing out the route. This is the same place the SMP jobs died on a linux machine before I upped the value of SHMMAX (thanks to a note from Doug Fox of Gaussian which I found in the CCL archive). I've been assured by the Sun sysadmin that the value of SHMMAX is at 1GB, much higher than I'm attempting to use. Serial jobs run just fine. Any idea what else could be causing this problem? Also, if anyone knows how I can double check the value of SHMMAX on a Sun machine (not to imply that I don't trust my sysadmin....), that'd be useful. Thanks in advance for any help - Dave More info - I have successfully gotten this version to run using smp on an SGI and a linux machine. After some problems, I was able to compile G98.a7 on the Sun machine and successfully run serial jobs (thanks to Sergei Tretiak at Los Alamos and again without a helpful response from Gaussian getting it to compile) The Sun is running SunOS 5.7, and Gaussian was compiled using the required compilers, libraries etc (as specified on http://www.gaussian.com/g98_req.htm ) Information on the Sun machine: MODEL: SUNW,Ultra-Enterprise CPU: SUNW,UltraSPARC-II @ 400 MHz (x12 cpus) SunOS RELEASE: 5.7 MEMORY: 6144MB SWAP: 17341.5MB total, 216.7MB used, 17124.8MB available Input file: %chk=water.chk %mem=2000000 %nproc=2 #p hf sto-3g scf=(tight,direct) water 0 1 o h 1 b1 h 1 b1 2 a1 b1 = 1.0 a1 = 104. Output file (after header): ************************************************* Gaussian 98: Sun-SVR4-Unix-G98RevA.7 11-Apr-1999 13-Oct-2000 ************************************************* %chk=water.chk %mem=2000000 %nproc=2 Will use up to 2 processors via shared memory. ------------------------------- #p hf sto-3g scf=(tight,direct) ------------------------------- 1/38=1/1; 2/17=6,18=5/2; 3/11=9,25=1,30=1/1,2,3; 4//1; 5/5=2,32=2,38=4/2; 6/7=2,8=2,9=2,10=2,28=1/1; 99/5=1,9=1/99; Leave Link 1 at Fri Oct 13 15:03:26 2000, MaxMem= 2000000 cpu: 0.5 (Enter /packages/g98/l101.exe) Error termination via Lnk1e in /packages/g98/l101.exe. Job cpu time: 0 days 0 hours 0 minutes 0.7 seconds. File lengths (MBytes): RWF= 6 Int= 0 D2E= 0 Chk= 1 Scr= 1 -- Dr. David J. Giesen Eastman Kodak Company david.giesen@kodak.com 2/83/RL MC 02216 (ph) 1-716-58(8-0480) Rochester, NY 14650 (fax)1-716-588-1839 From chemistry-request@server.ccl.net Fri Oct 13 15:31:20 2000 Received: from mailhost.msi.com (fire.msi.com [146.202.0.242]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA11566 for ; Fri, 13 Oct 2000 15:31:19 -0400 Received: (from daemon@localhost) by mailhost.msi.com (980427.SGI.8.8.8/970903.SGI.AUTOCF) id MAA11636; Fri, 13 Oct 2000 12:26:09 -0700 (PDT) Received: from unknown(146.202.29.179) by mailhost.msi.com via smap (V2.0) id xma011634; Fri, 13 Oct 00 12:25:50 -0700 Message-Id: <4.2.0.58.20001013122751.00c32eb0@146.202.6.218> X-Sender: nxg@146.202.6.218 X-Mailer: QUALCOMM Windows Eudora Pro Version 4.2.0.58 Date: Fri, 13 Oct 2000 12:37:14 +0100 To: Goutam.Das@betzdearborn.com, chemistry@ccl.net From: Niri Govind Subject: Re: CCL:DFT In-Reply-To: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Hi Goutam, There's a new text by Frank Jensen "Introduction to Computational Chemistry" which has a chapter on DFT which provides a good basic working introduction and compares it to other electronic structure methods...Its a handy text. Another good reference is Callaway and March (Solid State Physics, 1984) I forget the exact volume number Of course, there is a Parr and Yang and Dreizler and Gross which provide some of the formal definitions. I am sure there are many more. Regards -Niranjan At 09:07 AM 10/13/00 -0500, Goutam.Das@betzdearborn.com wrote: >Hello CCLers, > >Can anyone of you suggest an introduction to DFT suitable for advanced >undergraduates (texts, references, websites) This is mainly for students >to get a "working idea" for DFT. > >Thanx to all of you in anticipation. Happy Friday the 13th! > >Goutam Das >Research Scientist >BetzDearborn Division of Hercules >The Woodlands, TX 77380 >281.367.6201 ext 425 > > >-= 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 > > ___________________________________ Niranjan Govind, Ph.D. Scientist, Materials Science Molecular Simulations, Inc 9685 Scranton Road, CA 92121-3752 Tel: 858-799-5337, Fax: 858-458-0136 Email: nxg@msi.com Web: http://www.msi.com