From 9702029k@lv.levels.unisa.edu.au Wed Jul 8 00:14:03 1998 Received: from zorba.levels.unisa.edu.au (SYSTEM@Zorba.levels.unisa.edu.au [130.220.17.9]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id AAA11189 Wed, 8 Jul 1998 00:14:01 -0400 (EDT) Received: from xiy205359.unisa.edu.au ("port 1803"@XIY205359.Levels.UniSA.Edu.Au) by Levels.UniSA.Edu.Au (PMDF V5.1-10 #27872) with SMTP id <01IZ5RPFWO0Q986BRE@Levels.UniSA.Edu.Au> for chemistry@www.ccl.net; Wed, 8 Jul 1998 13:43:58 +0930 Received: by xiy205359.unisa.edu.au with Microsoft Mail id <01BDAA77.7EA4C680@xiy205359.unisa.edu.au>; Wed, 08 Jul 1998 13:51:23 +0930 Date: Wed, 08 Jul 1998 13:51:21 +0930 From: Josh Bowden <9702029k@lv.levels.unisa.edu.au> Subject: Mixing basis sets? To: "'chemistry@www.ccl.net'" Message-id: <01BDAA77.7EA4C680@xiy205359.unisa.edu.au> MIME-version: 1.0 Content-type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by www.ccl.net id AAA11189 Hello all, As a continuation of recent discussion on this list about 3-21G vs 6-31G*, can I ask if anyone has information on mixing basis sets in a calculation. Programs such as CRYSTAL 95 and HyperChem (probably others as well) allow you to apply different basis to individual atoms. If the lack of polarization functions ( as stated by cory@chem.ucalgary) is a problem can you not apply a bigger basis set to 'problem' atoms and reduce the basis of others? Has anyone looked at this systematically and is there any referencs on this topic? Are there any problems in this metholodgy (does it have any major downfalls)? Thankyou for your time, I will return a summary. Josh Bowden (hoping this is not a stupid question!) Ian Wark Research Institute University of South Australia E-mail : 9702029k@lv.levels.unisa.edu.au From Harald.Lanig@ccc.uni-erlangen.de Wed Jul 8 03:16:34 1998 Received: from faui45.informatik.uni-erlangen.de (root@faui45.informatik.uni-erlangen.de [131.188.2.45]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id DAA13594 Wed, 8 Jul 1998 03:16:32 -0400 (EDT) Received: from as1200.organik.uni-erlangen.de (as1200-1.organik.uni-erlangen.de [131.188.128.6]) by faui45.informatik.uni-erlangen.de (8.8.8/8.1.16-FAU) with ESMTP id JAA11522 for ; Wed, 8 Jul 1998 09:16:27 +0200 (MET DST) Received: from ccc.uni-erlangen.de (indigo11.organik.uni-erlangen.de [131.188.128.69]) by as1200.organik.uni-erlangen.de (8.8.7/8.1.11-FAU) with ESMTP id JAA08024 for ; Wed, 8 Jul 1998 09:15:04 +0200 (MET DST) Sender: Harald.Lanig@ccc.uni-erlangen.de Message-ID: <35A31CCA.F1AD55DA@ccc.uni-erlangen.de> Date: Wed, 08 Jul 1998 09:16:26 +0200 From: Harald Lanig Organization: Computer-Chemie-Centrum Uni Erlangen/Nbg X-Mailer: Mozilla 4.04 [en] (X11; I; IRIX 5.3 IP22) MIME-Version: 1.0 To: CHEMISTRY@www.ccl.net Subject: AMBER optimization of metalloenzymes Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear netters, optimizing metalloenzymes (e.g. Zn) with AMBER needs parameters not included in the original 95 parameter set. Has anybody out there experiences about how to perform such calculations? Any help is highly appreciated! Regards H Lanig -- --------------------------------------------------------------------- Dr. Harald Lanig Computer Chemie Centrum der Universitaet Erlangen/Nuernberg Institut fuer Organische Chemie I, Naegelsbachstr. 25 D-91052 Erlangen, Germany Phone +49(0)9131-85 6581 Fax -85 6565 mailto:lanig@ccc.uni-erlangen.de http://www.ccc.uni-erlangen.de/clark/lanig --------------------------------------------------------------------- From bioinfo.ernet.in!sangeeta@bioinfo.ernet.in Wed Jul 8 07:14:23 1998 Received: from naveen.ncst.ernet.in (naveen.ncst.ernet.in [202.41.110.35]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id HAA16671 Wed, 8 Jul 1998 07:14:06 -0400 (EDT) Received: from iucaa (iucaa.ernet.in [202.141.155.1]) by naveen.ncst.ernet.in (8.6.12/8.6.6) with SMTP id QAA11801 for ; Wed, 8 Jul 1998 16:46:21 +0530 Received: from iucaa by iucaa (5.65v3.2/SMI-4.1) id AA27356; Wed, 8 Jul 1998 16:40:57 +0500 Received: by (5.x/SMI-SVR4) id AA12841; Wed, 8 Jul 1998 16:34:09 -0500 Date: Thu, 9 Jul 1998 02:34:09 +0500 (GMT-5) From: Sangeeta Sawant To: CHEMISTRY@www.ccl.net Subject: Is there any script to convert ARC -> CAR or ARC -> pdb? Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi everybody, Has anyone written a script/code for converting the Biosym ARC format to the Biosym CAR format or from ARC to pdb format? I am interested in getting it if possible (or before I start writing one). I am aware that Babel can convert from CAR to other formats but it does not have ARC to other format utility. Thanks a lot for help. Regards, Sangeeta +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Mrs. Sangeeta Sawant + + Research Fellow email : sangeeta@bioinfo.ernet.in + + Bioinformatics Centre phone : +91-212-355039 + + University of Pune fax : +91-212-350087 + + Ganeshkhind + + Pune - 411007 + + India. + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From bioinfo.ernet.in!sangeeta@bioinfo.ernet.in Wed Jul 8 07:43:41 1998 Received: from naveen.ncst.ernet.in (naveen.ncst.ernet.in [202.41.110.35]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id HAA17127 Wed, 8 Jul 1998 07:43:33 -0400 (EDT) Received: from iucaa (iucaa.ernet.in [202.141.155.1]) by naveen.ncst.ernet.in (8.6.12/8.6.6) with SMTP id RAA13967 for ; Wed, 8 Jul 1998 17:16:13 +0530 Received: from iucaa by iucaa (5.65v3.2/SMI-4.1) id AA24457; Wed, 8 Jul 1998 17:10:50 +0500 Received: by (5.x/SMI-SVR4) id AA12859; Wed, 8 Jul 1998 16:43:06 -0500 Date: Thu, 9 Jul 1998 02:43:05 +0500 (GMT-5) From: Sangeeta Sawant To: Computational Chemistry List Subject: Summary :Superimposition Program Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi all, Thanks to everyone who sent a reply to my query regarding superimposition of several structures of peptides in batch mode. The suggestions are extremely useful. Here is the summary of the replies along with the query: +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Mrs. Sangeeta Sawant + + Research Fellow email : sangeeta@bioinfo.ernet.in + + Bioinformatics Centre phone : +91-212-355039 + + University of Pune fax : +91-212-350087 + + Ganeshkhind + + Pune - 411007 + + India. + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ -----Original Query------- >Hi all! >I would like to know if there is any software/program (preferably >shareware/public-domain) which allows to superimpose several >protein/peptide conformations onto one (say, template confo.) in a batch >mode. The program may be for either IRIX or OS2 (DEC-ALPHA) or SOLARIS or >LINUX or DOS (No Mac-OS please). Any help will be appreciated. -----------Responses--------- I am not sure if this helps; but did you take a look at swisspdb viewer http://www.expasy.ch Sasidhar - Sasidhar ____________________________________________________________________________ Dr. Y. U. Sasidhar, Associate Professor, Department of Chemistry Indian Institute of Technology, Powai, Mumbai 400 076, INDIA ____________________________________________________________________________ e-mail : chyusia@ether.chem.iitb.ernet.in Fax : (+91-22 ) 578 3480 (IIT Main ), (+91-22 ) 576 7152 ( Chemistry ) _____________________________________________________________________________ Tel : (+91-22 ) 578 2545 Ext.7179(O), 8198(Lab), 7151(Message), 8179(R) : (+91-22 ) 576-Ext. Number ____________________________________________________________________________ ---------- Hi Sangeeta, You can use the CCP4 program PolyPose for the purpose. If you don't have CCP4 (which, I believe you don't). You can use Gerard's program LSQMAN which is the most versatile superimposition program I've seen, but requires some inspired script writing. Lastly I've got a fast superimposer, which is a debugged and improved version of the one I wrote in Pune. For more info. see the following: LSQMAN http://alpha2.bmc.uu.se/~gerard/manuals/lsqman_man.html CCP4 (PolyPose and many other useful programs) http://www/dl.ac.uk/CCP/CCP4/main.html super_duper.c (That's mine) Can superimpose using the whole molecule or any sub-set which you define. The algo. is the same as the one I wrote in Pune, but now re-written and de-bugged. I can send you OSF1 Version 4.0 (DEC-ALPHA) executable, or the C-sources. Finally if you want any special things to be done, it may be possible to incorporate them. Hope this helps. deva ---------------------------------------------------------------------------- Devapriya Choudhury Office: Home: Deptt. of Molecular Biology Oskar Arpis Vag 2,2 Box 590, BMC, S75650, Uppsala S75124, Uppsala Sweden Sweden Tel: +46 18 4714524 +46 18 400314 FAX: +46 18 536971 e-mail deva@xray.bmc.uu.se ----------------------------------------------------------------------------- ---------- it's called profit and does exactly what ou want! cheers, gerald ---------------------------------------------------------------------- Gerald Loeffler - Bioinformatics Scientist Boehringer Ingelheim R&D Vienna, Molecular Biology Department Email: Gerald.Loeffler@vienna.at Phone: +43 676 3289588 (and +43 1 80105 634) Fax: +43 1 80105 683 Smail: Bender+Co, Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria ---------- You may try the molecular modelling package MOLMOL from ETH Zuerich. It is a graphical program which can also be run in batch-mode (without graphics-display. It can be controlled from shellscripts or directly at the commandline. It is able to superimpose as many molecules as you wish in several modes (to first, to mean, circular), and you can choose, which atoms or residues to consider for superposition. And!!!! It is freeware! Take a look at http://www.mol.biol.ethz.ch/wuthrich/software/molmol/ There are versions for UNIX (IRIX, DEC OSF, SOLARIS, LINUX), VMS, and Windows95/NT. You can also get the source and adapt it to whatever you want. -- Bye, Marc Saric Lehrstuhl fuer Biophysik Projektgruppe Theoretische Biophysik http://www.bph.ruhr-uni-bochum.de/ Ruhr-Universitaet Bochum Germany ---------- Dear Sangeeta, Try MOLMOL: There is a nice way to run it in batch as well. http://www.mol.biol.ethz.ch/wuthrich/software/molmol Hope it helps, Jurgen -- Drs Jurgen F. Doreleijers NMR spectroscopy, Utrecht University, The Netherlands mailto:jurgen@nmr.chem.uu.nl http://www-nmr.chem.uu.nl/~jurgen ---------- Hi , make a search in the web for a programm Profit, it is a powerfull unix programm that allow you to make a protein superimposition also in batch mode. Maybe you can find it at http://www.biochem.ucl.ac.uk/~martin/swreg.html Hope this helps. -- Rino Ragno ++----------------------------------------------------------------------++ ++----------------------------------------------------------------------++ || || || Dr. Rino Ragno E-mail: ragno@uniroma1.it || || Institute for Biomedical Computing or: rino@gpc.wustl.edu || || Center for Molecular Design or: ragno@axcasp.caspur.it || || Box8036, Washington University Phone : 314-362-2272 || || 700 South Euclid Avenue FAX : 314-362-0234 || || St. Louis, Missouri 63110 || || U. S. A. || || || || WEB PAGE : www.ibc.wustl.edu/cmd/people/rino/rino.html || || || ++----------------------------------------------------------------------++ ++----------------------------------------------------------------------++ ---------- Have a look at the Molecular Modelling toolkit at: http://starship.skyport.net/crew/hinsen/mmtk.html It contains the necessary superposition code, and making a batch mode program that uses it is a simple matter (maybe 10 lines of code). I could even write you that small piece of code, if I knew what exactly you want the program to do with the superposed structure! -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@cnrs-orleans.fr Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.55.69 Rue Charles Sadron | Fax: +33-2.38.63.15.17 45071 Orleans Cedex 2 | Deutsch/Esperanto/English/ France | Nederlands/Francais ------------------------------------------------------------------------------- -------------- Sangeeta, You might look into a program called MOE, by the Chemical Computing Group. It has very nice 3D homology modeling capabilities and will run in batch mode. _____________________________________________________________________ Abby Parrill, Ph.D. Currently: Chemistry Department Michigan State University East Lansing, MI 48824-1322 parrill@argus.cem.msu.edu Soon: Chemistry Department University of Memphis Memphis, TN 38152 Computational Research on Materials Institute at University of Memphis (CROMIUM) ______________________________________________________________________ ---------- Hi Sangeeta, I'd highly recommend VMD. It's available for many platforms (SGI, Linux, AIX, HPUX), it's free and very flexible due to a (TCL-like?) scripting language. Check http://www.ks.uiuc.edu/Research/vmd/ for more. Cheers, Chris -- Dr. Christoph Steinbeck (mailto:steinbeck@ice.mpg.de - http://seneca.ice.mpg.de/~stein) Max-Planck-Institute of Chemical Ecology (http://www.ice.mpg.de) Tatzendpromenade 1a, 07745 Jena, Germany Tel: int + (49) 3641 643644 --- Fax: int + (49) 3641 643665 What is man but that lofty spirit -- that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. From laaksone@csc.fi Wed Jul 8 08:38:47 1998 Received: from pobox.csc.fi (pobox.csc.fi [128.214.46.62]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id IAA17941 Wed, 8 Jul 1998 08:38:47 -0400 (EDT) Received: from laaksonen.csc.fi (laaksonen.csc.fi [193.166.1.75]) by pobox.csc.fi (8.9.0.Beta5/8.9.0.Beta5/CSC/Rtrs-1.22) with SMTP id PAA09145 for ; Wed, 8 Jul 1998 15:38:46 +0300 (EET DST) Date: Wed, 8 Jul 1998 15:35:35 +0300 (GFT Daylight Time) From: Leif Laaksonen Reply-To: Leif Laaksonen To: CHEMISTRY@www.ccl.net Subject: Do the Windows NT have any impact on the comp chem field? Message-ID: X-X-Sender: laaksone@laaksonen.csc.fi MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL members, Over the last years I have regularly asked the CC list the same question whether PCs and Windows NT are of any value in molecular modelling or the comp chem field in general. We now have the 400 MHz Intel processors with 100 MHz buses and OpenGL supported graphics cards in our PCs. The lowend, and possible already midrange, graphics workstations are totally dominated by Windows and Linux PC boxes. Both Linux and Windows NT are strongly entering the heavy "number crunching" field trough multiprocessor boxes. There are a lot of articles about building supercomputers out of inexpensive Intel or Alpha processors. My question is now whether Windows NT and Linux already play a significant role in the computation chemistry field? Are the Windows NT and Linux interesting platforms for the comp chem software companies? Will the recent SGI announcement of NT-based machines make much impact on the chemistry market? Are there any new ideas in software development? I do not want, once again, to start a Unix - Windows war. I just want to know in which direction you think we are going. Yours, -leif laaksonen ------------------------------------------------------------------- Center for Scientific Computing | Phone: 358 9 4572378 P.O. Box 405 | Mobile: 358 400425203 FIN-02101 Espoo | Telefax: 358 9 4572302 FINLAND | Mail: Leif.Laaksonen@csc.fi -------- URL: http://laaksonen.csc.fi/leif.laaksonen.html --------- From topper@cooper.edu Wed Jul 8 11:38:34 1998 Received: from magnum.cooper.edu (magnum.cooper.edu [199.98.16.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id LAA21101 Wed, 8 Jul 1998 11:38:34 -0400 (EDT) Received: from zeus.cooper.edu by magnum.cooper.edu with SMTP id AA16830 (5.65c/IDA-1.4.4 for ); Wed, 8 Jul 1998 11:23:27 -0400 Received: by zeus.cooper.edu id AA17474 (5.67b/IDA-1.5 for CHEMISTRY@www.ccl.net); Wed, 8 Jul 1998 11:32:08 -0400 From: TOPPER ROBERT Message-Id: <199807081532.AA17474@zeus.cooper.edu> Subject: CCL:Summary: Visualization of molecules and arbitrary geometric objects To: CHEMISTRY@www.ccl.net Date: Wed, 8 Jul 1998 11:32:08 -0400 (EDT) Cc: topper@cooper.edu (TOPPER ROBERT) X-Mailer: ELM [version 2.4 PL24alpha3] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Thanks to Jonathan for his summary. I am writing to seek clarification one one point. > 2. Import and display multiple small molecules in various styles (tube, > wireframe, etc.). I interpret this feature as the ability to display multiple molecules in various styles simultaneously. For example; a wireframe model of a protein surrounded by tube models of water molecules. What program(s) have this particular feature? This is a useful thing to be able to do, certainly. I will be glad to summarize for the list. ******************************************************************************** Robert Q. Topper email: topper@cooper.edu Asst. Professor of Chemistry fax: (212) 353-4341 The Cooper Union phone: (212) 353-4378 51 Astor Place subway: take the 6 to Astor Place New York, NY 10003 or the N/R to 8th St/NYU http://www.cooper.edu/engineering/chemechem/ ******************************************************************************** The Cooper Union, established by Peter Cooper in 1859, is a private engineering/ architecture/art college where all students receive full scholarships. ******************************************************************************** From jean.brion@univ-reims.fr Wed Jul 8 11:47:47 1998 Received: from cleo.univ-reims.fr (cleo.univ-reims.fr [193.50.208.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id LAA21284 Wed, 8 Jul 1998 11:47:46 -0400 (EDT) Received: from centre01.univ-reims.fr (centre01.univ-reims.fr [193.50.208.1]) by cleo.univ-reims.fr with SMTP (8.7.1/8.7.1) id RAA05980 for ; Wed, 8 Jul 1998 17:45:26 +0200 (METDST) Message-Id: <199807081545.RAA05980@cleo.univ-reims.fr> Received: by centre01.univ-reims.fr (1.38.193.4/16.2) id AA21805; Wed, 8 Jul 1998 16:39:35 +0100 From: BRION Jean Subject: problem with g94 casscf77 under linux To: chemistry@www.ccl.net Date: Wed, 8 Jul 98 16:39:35 WETDST Mailer: Elm [revision: 70.85] Hello, We have installed the Gaussian 94 package on a Linux machine and we meet now one problem when trying a CASSCF(7,7) (generating 784 configurations)... The problem is in link 510, when the program begins "Generating Lanczos Guess". At this moment, we establish that the running does not create any output more... (even with a long calculation time about 3000 minutes !). -We have a PII 400 machine, with 256Mo of memory and a 9Go hard disk. -Gaussian version is D.4 -Linux version is S.u.S.e 1998 -the memory used for this calculation was 8MW -The previous CASSCF(5,5) has worked very well in 5 minutes for 75 generated CONFIGURATIONS. -When adding the FULLDIAG keyword in the CASSCF options list, the calculation works ! (but takes a long time) - on a HP755 machine: * The same CASSCF(5,5) calculations takes about 10 minutes * The same CASSCF(7,7) works very well, and takes about 12 minutes We have tried another thing to try to solve our problem: i.e add the -malign-double in the compilator options. => Although other jobs (than the casscf(7,7) one) run faster, our problem on the CASSCF(7,7) remains the same (that means this job never stops without output and without error). Has someone already met this difficulty ? Is this a gaussian environement problem or a machine configuration problem ? We have also tried to drop the -O2 option in the source's compilation with gcc. We have no idea any more at this time ... Thank you in advance for your help. E. Henon From smithja@ucarb.com Wed Jul 8 12:59:15 1998 Received: from hscmg02.hou.ucarb.com ([144.68.4.25]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id MAA22770 Wed, 8 Jul 1998 12:59:14 -0400 (EDT) Received: by hscmg02.hou.ucarb.com with Internet Mail Service (5.0.1458.49) id ; Wed, 8 Jul 1998 09:57:00 -0500 Message-ID: From: "Smith JA (Jack)" To: chemistry@www.ccl.net Subject: RE: Summary: Visualization of molecules and arbitrary geometric o bjects Date: Wed, 8 Jul 1998 09:55:58 -0500 X-Priority: 3 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.0.1458.49) Content-Type: text/plain > 3. Import and display multiple geometric objects, such as triangulated > meshes, iso-surfaces of a field, spheres of arbitrary radius, lines. > These should be arbitrary data specified by the user, not something > computed from the molecule by the tool itself. I find this deficiency (mainly lack of user-defined objects) in almost all modeling packages somewhat strange. It seems like such a relatively minor, yet useful, enhancement to such otherwise complex applications. We're just talking about basic geometry stuff - not chemistry, physics or quantum mechanics. This reminds me of a related feature I've always wanted to see in modeling packages. I'd like to be able to select a subset of atoms in a structure and have the program (or let the user) determine the principle axes (mass-weighted or not), construct/display your choice of a variety of geometric enclosures (sphere, ellipsoid, cone, cylinder, cube, and other polyhedra, including the 7 crystallographic cell types), with or without using VdW/covalent/ionic contacts, and report/export the dimensions, angles, surface area, volume, density, etc. I'd also like to see the 'inverse' feature (athough, somewhat more ambiguous) for characterizing cavities. A similar feature would be to fit/display a 2D surface (simple plane, quadratic surface, plane wave, etc.) through a selected subset of atoms - again, relative to the principle or user-defined axes. The fit could be mass-weighted or plain least-squares. The coordinate system could be rectilinear, curvilinear, oblique, etc. Fitting a 3D surface would be a bit more challenging, but also potentially useful. I think that quantifying the shape and size of molecular fragments (cavities) is an important, useful and often overlooked aspect of most molecular modeling packages. - Jack -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- Jack A. Smith || Union Carbide || Phone: (304) 747-5797 Catalyst Skill Center || FAX: (304) 747-4672 P.O. Box 8361 || S. Charleston, WV 25303 || smithja@ucarb.com -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- From herbert.homeier@chemie.uni-regensburg.de Wed Jul 8 13:44:07 1998 Received: from rrzs2.rz.uni-regensburg.de (rrzs2.rz.uni-regensburg.de [132.199.1.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id NAA24028 Wed, 8 Jul 1998 13:44:04 -0400 (EDT) Received: from rchs4.chemie.uni-regensburg.de (rchs4.chemie.uni-regensburg.de [132.199.48.4]) by rrzs2.rz.uni-regensburg.de (8.8.8/8.8.8) with SMTP id TAA11465 for ; Wed, 8 Jul 1998 19:44:02 +0200 (MET DST) Date: Wed, 8 Jul 1998 19:46:05 +0200 From: Herbert Homeier t4720 Message-Id: <9807081746.AA26286@rchs4.chemie.uni-regensburg.de> To: chemistry@www.ccl.net Subject: G: chkmove error Hi CCL readers, when trying to use the Gaussian 94 chkmove utility, it produced besides a core file an error message as follows: chkmove f UHF.chk UHF.xfr IFile= 501 LenFil= 1000 LenFix= 47. Error termination in NtrErr: NtrErr called from Fatal. Segmentation fault (core dumped) The files after the call are -rw------- 1 hoh05008 che 3334144 Jul 2 12:01 UHF.chk -rw------- 1 hoh05008 che 0 Jul 8 19:21 UHF.xfr -rw------- 1 hoh05008 che 1119388 Jul 8 19:21 core Thus, the .chk file is pretty large. Does anybody know the meaning of this message? Thanks a lot for your attention. Best regards Herbert Homeier -- Priv.-Doz. Dr. Herbert H. H. Homeier Institut fuer Physikalische und Theoretische Chemie Universitaet Regensburg, D-93040 Regensburg, Germany Phone: +49-941-943 4720 FAX: +49-941-943 4719 email: herbert.homeier@na-net.ornl.gov WWW: http://www.chemie.uni-regensburg.de/~hoh05008 From nowak@chemie.uni-halle.de Tue Jul 7 03:31:28 1998 Received: from mailserv.rz.fh-merseburg.de (mailserv.rz.fh-merseburg.de [149.205.18.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id DAA21627 Tue, 7 Jul 1998 03:31:27 -0400 (EDT) Received: from localhost (nowak@localhost) by mailserv.rz.fh-merseburg.de (8.8.8/8.8.7) with SMTP id JAA27271 for ; Tue, 7 Jul 1998 09:33:58 +0200 (METDST) X-Authentication-Warning: mailserv.rz.fh-merseburg.de: nowak owned process doing -bs Date: Tue, 7 Jul 1998 09:33:58 +0200 (METDST) From: Thomas Nowak X-Sender: nowak@mailserv.rz.fh-merseburg.de To: chemistry@www.ccl.net Subject: Energy analysis? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I am looking for program for the analysis of the bond energy. I know there is one implementation of the Morokuma algorithm in ADF, so i looking for other implementations of this or similar algorithm which can be used with other quantum chemistry programs. It would be great, if we can do such analysis on DFT level. Regards, Thomas Nowak Martin-Luther Universitaet Halle FB Chemie (Merseburg) IPC 06099 Halle email: nowak@chemie.uni-halle.de From goeller@pc04.chemie.uni-jena.de Tue Jul 7 04:00:34 1998 Received: from cnve.rz.uni-jena.de (root@cnve.rz.uni-jena.de [141.35.1.32]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id EAA22053 Tue, 7 Jul 1998 04:00:33 -0400 (EDT) Received: from fsuj03.rz.uni-jena.de (root@fsuj03.rz.uni-jena.de [141.35.2.32]) by cnve.rz.uni-jena.de (8.8.7/8.8.7) with ESMTP id KAA05026 for ; Tue, 7 Jul 1998 10:00:30 +0200 (MESZ) Received: from pc04.chemie.uni-jena.de (pc04.chemie.uni-jena.de [141.35.29.60]) by fsuj03.rz.uni-jena.de (8.7.1/8.6.10) with SMTP id KAA12169 for ; Tue, 7 Jul 1998 10:00:27 +0200 (MESZ) Received: from localhost by pc04.chemie.uni-jena.de (5.65v3.2/1.1.10.5/28Jan98-0152PM) id AA11289; Tue, 7 Jul 1998 10:00:46 +0200 Sender: goeller@pc04.chemie.uni-jena.de Message-Id: <35A1D5AE.15FB@pc04.chemie.uni-jena.de> Date: Tue, 07 Jul 1998 10:00:46 +0200 From: Andreas Goeller X-Mailer: Mozilla 3.0Gold (X11; I; OSF1 V4.0 alpha) Mime-Version: 1.0 To: chemistry@www.ccl.net Subject: c70 Content-Type: multipart/mixed; boundary="------------59E21CFB3F54" This is a multi-part message in MIME format. --------------59E21CFB3F54 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Many thanks to the 12 scientists who answered (the first half an hour after my request). Here is the pm3-arc-fiel I got from the calculation: -- Andreas Goeller --------------------------------------------------------------- Dr. Andreas Goeller Institut fuer Physikalische Chemie Friedrich-Schiller-Universitaet Lessingstr. 10 phone: +49(0)-3641-948352 D-07743 Jena fax: +49(0)-3641-948302 (secretary) Germany email: goeller@pc04.chemie.uni-jena.de http://www.uni-jena.de/chemie/photo/goeller/goeller.html --------------------------------------------------------------- Dr. Andreas Goeller ehemals Computer Chemie Centrum email: goeller@organik.uni-erlangen.de http://www.organik.uni-erlangen.de/clark/goeller/goeller.html --------------------------------------------------------------- --------------59E21CFB3F54 Content-Type: text/plain; charset=us-ascii; name="c70_a.arc" Content-Transfer-Encoding: 7bit Content-Disposition: inline; filename="c70_a.arc" Timestamp: 1998-07-06-17-47-25-0000027082-dec SUMMARY OF PM3 CALCULATION Jul-06-1998 AMPAC Version 6.01 Presented by: Semichem, Inc. 7128 Summit Shawnee KS 66216 (913) 268-3271 (913) 268-3445 (fax) C 70 C70 ahg 060798 GEOMETRY OPTIMISED : ENERGY MINIMISED SCF FIELD WAS ACHIEVED HEAT OF FORMATION = 884.164149 kcal = 3700.226962 kJ TOTAL ENERGY = -8266.478209 eV GRADIENT NORM = 1.076535 UNSTABLE MODE(S) = 0 (ESTIMATE) DIPOLE = 0.000466 DEBYE NO. OF FILLED LEVELS = 140 IONISATION POTENTIAL = 9.011204 eV MOLECULAR POINT GROUP = D5H 0.100000 MOLECULAR WEIGHT = 840.770 COMPUTATION TIME = 535.90 SECONDS FINAL GEOMETRY OBTAINED CHARGE PM3 T=20000 C70 ahg 060798 C 0.000000 0 0.000000 0 0.000000 0 0 0 0 0.0052 C 1.386218 1 0.000000 0 0.000000 0 1 0 0 -0.0108 C 4.168393 1 114.309434 1 0.000000 0 2 1 0 0.0289 C 4.496086 1 126.816351 1 32.936186 1 1 2 3 0.0062 C 2.475050 1 83.150500 1 -135.890692 1 3 2 1 -0.0179 C 1.373843 1 81.210681 1 96.639167 1 4 1 2 0.0062 C 1.425929 1 140.961669 1 30.350674 1 5 3 2 -0.0179 C 1.457155 1 119.688632 1 112.571080 1 1 2 3 0.0053 C 1.386236 1 119.712429 1 0.038472 1 8 1 2 -0.0108 C 1.412381 1 121.523133 1 -33.240021 1 7 5 3 0.0289 C 3.540814 1 52.955977 1 -64.327361 1 4 1 2 0.0062 C 2.474941 1 88.738568 1 138.246505 1 10 7 5 -0.0179 C 1.373842 1 22.817500 1 -154.792768 1 11 4 1 0.0062 C 1.425898 1 140.968684 1 -115.676676 1 12 10 7 -0.0179 C 1.457100 1 108.002049 1 -141.719398 1 8 1 2 0.0052 C 1.386219 1 119.709177 1 141.762873 1 15 8 1 -0.0107 C 1.412398 1 121.517212 1 -33.214501 1 14 12 10 0.0289 C 1.453337 1 120.212298 1 24.514306 1 2 1 3 0.0062 C 2.474929 1 88.740159 1 138.227265 1 17 14 12 -0.0179 C 1.373844 1 120.084863 1 0.202221 1 18 2 1 0.0062 C 1.425879 1 140.971533 1 -115.686468 1 19 17 14 -0.0179 C 1.457092 1 107.999794 1 0.009885 1 15 8 1 0.0052 C 1.386223 1 119.709059 1 141.756821 1 22 15 8 -0.0107 C 1.412408 1 121.517397 1 -33.214615 1 21 19 17 0.0289 C 1.453354 1 120.206798 1 -0.253646 1 9 8 1 0.0063 C 2.474930 1 88.737922 1 138.230007 1 24 21 19 -0.0179 C 1.373821 1 120.085101 1 0.236932 1 25 9 8 0.0062 C 1.425876 1 140.963988 1 -115.675420 1 26 24 21 -0.0179 C 1.457124 1 119.698540 1 -24.699647 1 1 2 3 0.0053 C 1.386225 1 119.713009 1 -0.044689 1 29 1 2 -0.0108 C 1.412388 1 121.519755 1 -33.233857 1 28 26 24 0.0289 C 1.453347 1 120.203825 1 -0.244880 1 16 15 8 0.0062 C 2.476649 1 125.709560 1 -25.781333 1 3 2 1 -0.0179 C 1.373840 1 120.086737 1 0.243539 1 32 16 15 0.0062 C 1.412409 1 145.125360 1 -58.084924 1 3 2 1 -0.0179 C 3.580927 1 78.517275 1 102.465964 1 7 5 3 0.0052 C 1.386214 1 22.806921 1 61.097510 1 36 7 5 -0.0107 C 1.412389 1 31.224740 1 179.999270 1 12 10 7 0.0289 C 1.462714 1 90.247981 1 4.281224 1 26 24 21 0.0062 C 1.462739 1 108.388095 1 -142.521223 1 18 2 1 -0.0179 C 1.373852 1 119.680206 1 -2.465268 1 39 26 24 0.0062 C 1.412398 1 115.704008 1 -12.591088 1 10 7 5 -0.0179 C 1.457102 1 100.989898 1 -151.694532 1 36 7 5 0.0052 C 1.386219 1 119.708986 1 -13.996033 1 43 36 7 -0.0107 C 1.412417 1 121.368145 1 147.956427 1 40 18 2 0.0289 C 1.462720 1 131.418967 1 -98.579441 1 33 3 2 0.0062 C 1.412412 1 115.707523 1 150.838216 1 38 12 10 -0.0179 C 1.373845 1 119.679819 1 122.112263 1 46 33 3 0.0062 C 1.412406 1 115.710105 1 -12.612276 1 17 14 12 -0.0179 C 1.457105 1 107.999198 1 127.758088 1 43 36 7 0.0052 C 1.386223 1 119.708339 1 -141.757651 1 50 43 36 -0.0107 C 1.412386 1 92.436517 1 38.508725 1 33 3 2 0.0289 C 1.453323 1 120.210170 1 -99.340658 1 37 36 7 0.0062 C 1.462730 1 108.389741 1 -142.479818 1 32 16 15 -0.0178 C 1.373847 1 120.084710 1 -0.231891 1 53 37 36 0.0062 C 1.412395 1 115.708901 1 -12.614494 1 24 21 19 -0.0179 C 1.457090 1 108.001298 1 0.001244 1 50 43 36 0.0052 C 1.386218 1 119.707581 1 -141.755324 1 57 50 43 -0.0107 C 1.412385 1 31.223954 1 -180.011953 1 26 24 21 0.0289 C 1.453338 1 120.201077 1 0.247901 1 44 43 36 0.0062 C 1.412400 1 115.706065 1 150.833228 1 59 26 24 -0.0179 C 1.373850 1 120.088876 1 -0.246457 1 60 44 43 0.0062 C 1.412394 1 115.707703 1 -12.598290 1 31 28 26 -0.0179 C 1.457103 1 120.848134 1 -32.836871 1 36 7 5 0.0052 C 1.386223 1 119.709407 1 26.442422 1 64 36 7 -0.0108 C 1.412392 1 121.368846 1 147.963398 1 54 32 16 0.0288 C 1.453360 1 120.201064 1 0.250395 1 51 50 43 0.0062 C 1.412402 1 115.705498 1 12.587994 1 52 33 3 -0.0179 C 1.373847 1 120.090670 1 -0.252571 1 67 51 50 0.0062 C 1.412402 1 60.560677 1 35.431355 1 3 2 1 -0.0179 0 0.000000 0 0.000000 0 0.000000 0 0 0 0 --------------59E21CFB3F54-- From ivan.oleinik@materials.oxford.ac.uk Tue Jul 7 09:07:48 1998 Received: from oxmail4.ox.ac.uk (oxmail4.ox.ac.uk [163.1.2.33]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id JAA26181 Tue, 7 Jul 1998 09:07:46 -0400 (EDT) Received: from ermine.ox.ac.uk by oxmail4 with SMTP (PP) with ESMTP; Tue, 7 Jul 1998 14:07:39 +0100 Received: from localhost (oums0054@localhost) by ermine.ox.ac.uk (1.1/8.8.3) with SMTP id OAA00784 for ; Tue, 7 Jul 1998 14:07:36 +0100 (BST) Date: Tue, 7 Jul 1998 14:07:36 +0100 (BST) From: "Ivan I. Oleinik" To: chemistry@www.ccl.net Subject: Dmol efficiency: frosen core & basis sets Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello all, I am trying to tune MSI DMol3 to get maximum efficiency in calculations of the large systems, containing H, C, Si, Ge. The obvious choice would be to reduce atomic basis set to the necessary minimum (especially for Si and Ge). There was an option in previus version of Dmol 96.0/4.0.0 to use frozen core approximation to remove core orbitals from SCF procedure. Does anybody know are there any ways to use frozen core approximation in the new version DMol3. An attempt to use "basis" keyword with the flags to froze the core, eg Basis user 6 7 1 0 0 2 0 2 2 for carbon results in error message; too many wave functions, val, core 1 16 1 0 Leave Status 13 Another question in this connection. Is there a possibility to assign the different basis sets to atoms of the same element but located at different parts of the system. Any other comments on increasing efficiency of DMol calculations (with primary concern with geometry optimisation, not energetics) would be very welome. Ivan Oleinik. ------------------------------------------------------------------------ Dr. Ivan I. Oleinik E-mail : ivan.oleinik@materials.ox.ac.uk Department of Materials University of Oxford Parks Road Oxford OX1 3PH Tel : +44 (0)1865 283325 United Kingdom Fax : +44 (0)1865 273764 ------------------------------------------------------------------------ From sichelj@UMoncton.ca Tue Jul 7 14:26:12 1998 Received: from bosoleil.ci.umoncton.ca (sichelj@bosoleil.ci.umoncton.ca [139.103.2.5]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id OAA03089 Tue, 7 Jul 1998 14:26:11 -0400 (EDT) Received: from localhost (sichelj@localhost) by bosoleil.ci.umoncton.ca (8.8.6/8.8.6) with SMTP id PAA21950; Tue, 7 Jul 1998 15:25:18 -0300 (ADT) X-Authentication-Warning: bosoleil.ci.umoncton.ca: sichelj owned process doing -bs Date: Tue, 7 Jul 1998 15:25:17 -0300 (ADT) From: "J. Sichel" X-Sender: sichelj@bosoleil.ci.umoncton.ca To: "E. Lewars" cc: chemistry@www.ccl.net Subject: Re: CCL:QUESTIONS:ELECTRON CORRELATION In-Reply-To: <199807071542.LAA20023@alchemy.chem.utoronto.ca> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by www.ccl.net id OAA03089 On Tue, 7 Jul 1998, E. Lewars wrote: > SOME QUESTIONS ABOUT ELECTRON CORRELATION AND THE > HARTREE-FOCK METHOD > > 5) Is there a way to see *intuitively* that the HFM must overestimate > electron-electron repulsion and underestimate electron kinetic energy? The exact and HF wave function both obey the virial theorem (Levine Quantum Chem 4/e p.441) That is, = -2 and therefore = + = - . So since the variational theorem guarantees that E(HF) > E(exact), we must have T(HF) < T(exact) and V(HF) > V(exact). John Sichel Université de Moncton, NB, Canada