From jtgolab@amoco.com Wed Feb 4 13:09:47 1998 Received: from interlock.amoco.com for jtgolab@amoco.com by www.ccl.net (8.8.3/950822.1) id MAA23552; Wed, 4 Feb 1998 12:32:44 -0500 (EST) Message-Id: <199802041732.AA19607@interlock.amoco.com> From: jtgolab@amoco.com (Joe Golab) Date: Wed, 4 Feb 1998 11:40:00 -0600 X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: CHEMISTRY@www.ccl.net Subject: Theoretical Spectra Cc: jtgolab@amoco.com Does anyone know of a program or subroutine that will take spectral data, for example (X,Y) where X is frequency and Y is intensity, and plot it like an experimental spectrum, i.e. Not A Simple Line Diagram. Even the "core" of a program, would be ok; I'm trying to avoid (re)work and parting with my money. -- :Joe jtgolab@amoco.com (630) 961-7878 +-------------------------------------------------+ | It took a while for the Romans to realize | | that it was best to pillage BEFORE they burned. | +-------------------------------------------------+ From comartin@wicc.weizmann.ac.il Thu Feb 5 03:32:17 1998 Received: from winston.weizmann.ac.il for comartin@wicc.weizmann.ac.il by www.ccl.net (8.8.3/950822.1) id CAA00119; Thu, 5 Feb 1998 02:57:07 -0500 (EST) Received: from localhost by winston.weizmann.ac.il; (5.65v3.2/1.1.8.2/28Jul95-1212AM) id AA04429; Thu, 5 Feb 1998 09:56:44 +0200 Date: Thu, 5 Feb 1998 09:56:42 +0200 (IST) From: "Jan M.L. Martin" X-Sender: comartin@winston.weizmann.ac.il To: "S. Parthiban" Cc: chemistry@www.ccl.net Subject: Re: CCL:G:Normal Coordinate Analysis In-Reply-To: <199802041913.LAA03991@pegasus.arc.nasa.gov> Message-Id: On Wed, 4 Feb 1998, S. Parthiban wrote: > Dear Netters: > I need to perform Normal Coordinate Analysis from the force constants > calculated using Gaussian94. I would appreciate if somebody can share > their program or any pointer on the net would be helpful. Perhaps you can try gar2ped (by C. Van Alsenoy and myself) in ftp://www.ccl.net/pub/chemistry/software/SOURCES/FORTRAN/gar2ped It should compile on more or less any Unix box. JM > Thank you > Parthi --------------------------------------------------------------------------- dr. Jan M.L. Martin Senior Lecturer, Computational Chemistry Department of Organic Chemistry/Kimmelman Building, Room 262 Weizmann Institute of Science/Rechovot 76100/ISRAEL FAX +972(8)9344142 Phone +972(8)9342533 E-mail comartin@wicc.weizmann.ac.il *** research group WWW home page http://theochem.weizmann.ac.il/ *** ---- kol ha-olam kulo gesher tzar me'od, v'ha-ikar lo l'hitpached k'lal --- From seabra@NPD.UFPE.BR Thu Feb 5 15:10:02 1998 Received: from NPD1.NPD.UFPE.BR for seabra@NPD.UFPE.BR by www.ccl.net (8.8.3/950822.1) id OAA06538; Thu, 5 Feb 1998 14:29:18 -0500 (EST) Received: from danon (danon.dqf.ufpe.br) by NPD.UFPE.BR (PMDF V5.1-4 #20469) with SMTP id <01IT86TAXQWW005OWC@NPD.UFPE.BR> for chemistry@www.ccl.net; Thu, 5 Feb 1998 16:26:40 GMT-3 Date: Thu, 05 Feb 1998 16:35:10 -0300 From: Gustavo de Miranda Seabra Subject: Crystal Information To: Computational Chemistry List Message-id: <003601bd326d$2bfc48e0$7d05a196@danon.dqf.ufpe.br> Dear Netters, Could anybody help me finding some properties of beta-PbF2 such as: elastic, dieletric and piezoeletric constants or experimental vibrational frequencies? Thank you very much. Sincerely, -------------------------------------------------------------------------= Gustavo de Miranda Seabra MSc Student in Chemistry E-Mail: seabra@npd.ufpe.br Universidade Federal de Pernambuco - Recife - Pernambuco - Brazil -------------------------------------------------------------------------= From uucp@msi.com Thu Feb 5 14:05 EST 1998 Received: from bioc1.msi.com for uucp@msi.com by www.ccl.net (8.8.3/950822.1) id OAA06450; Thu, 5 Feb 1998 14:05:14 -0500 (EST) Received: by bioc1.msi.com (931110.SGI/930416.SGI) for CHEMISTRY@www.ccl.net id AA24774; Thu, 5 Feb 98 10:45:35 -0800 Received: from news.msi.com(146.202.0.224) by bioc1.msi.com via smap (V2.0) id xma024766; Thu, 5 Feb 98 10:45:16 -0800 Received: by news.msi.com (4.1/SMI-4.1) id AA18769; Thu, 5 Feb 98 10:41:55 PST From: bobf@msi.com (Bob Funchess) Subject: Re: CCL:neutral glycine in CHARMM ? Message-Id: Organization: Molecular Simulations Inc. References: Date: Thu, 5 Feb 1998 18:41:49 GMT To: CHEMISTRY@www.ccl.net Petr Belsky (belsky@indy.jh-inst.cas.cz) wrote: > Dear netters, > This is to ask how to build neutral glycine in CHARMM, it means > NH2-CH2-COOH. We are working with CHARMM 23 and only zwitterion of > glycine is present there. > Many thanks in advance > Petr Belsky > belsky@indy.jh-inst.cas.cz The easiest way is to apply the neutral terminus patches. In MSI's version those are COOH and NH2; I don't know off the top of my head if they're the same for the academic version or not but you could look in the RTF file for "PRES" records and see what's available there. read sequ card * Glycine * 1 GLY gene SEG1 setup patch NH2 SEG1 1 setup patch COOH SEG1 1 setup -- Robert B. Funchess, Ph.D. bobf@msi.com Senior Scientist, Scientific Support Voice (619) 458-9990 x738 Molecular Simulations Inc. FAX (619) 458-0431 9685 Scranton Road San Diego, CA 92121-3752 http://www.msi.com/ From fabien@piimsdm8.univ-mrs.fr Fri Feb 6 06:10:11 1998 Received: from piimsdm8.univ-mrs.fr for fabien@piimsdm8.univ-mrs.fr by www.ccl.net (8.8.3/950822.1) id FAA10390; Fri, 6 Feb 1998 05:58:44 -0500 (EST) Received: by piimsdm8.univ-mrs.fr (920330.SGI/920502.SGI) for chemistry@www.ccl.net id AA19988; Fri, 6 Feb 98 11:58:23 -0800 Date: Fri, 6 Feb 98 11:58:23 -0800 From: fabien@piimsdm8.univ-mrs.fr (Borget Fabien) Message-Id: <9802061958.AA19988@piimsdm8.univ-mrs.fr> To: chemistry@www.ccl.net Subject: Ozone and complexes Hi, i'm Fabien BORGET from the University of Provence in France. my e-mail: fabien@piimsdm8.univ-mrs.fr I will begin some quantic calculations about Ozone and some charge transfert complexes between ozone and compounds containing nitrogen. I'm searching some references. Thanks Fabien BORGET From BARANSKA@Trurl.ch.uj.edu.pl Fri Feb 6 08:10:14 1998 Received: from info.cyf-kr.edu.pl for BARANSKA@Trurl.ch.uj.edu.pl by www.ccl.net (8.8.3/950822.1) id HAA10720; Fri, 6 Feb 1998 07:23:36 -0500 (EST) Received: from kinga.cyf-kr.edu.pl (0@kinga.cyf-kr.edu.pl [149.156.2.32]) by info.cyf-kr.edu.pl (8.8.8/8.8.8) with ESMTP id NAA10937 for ; Fri, 6 Feb 1998 13:22:49 +0100 (MET) Received: from Trurl.ch.uj.edu.pl (trurl.ch.uj.edu.pl [149.156.71.254]) by kinga.cyf-kr.edu.pl (8.8.8/8.8.8) with ESMTP id NAA05683 for ; Fri, 6 Feb 1998 13:22:48 +0100 (MET) Received: from TRURL/MAILQUEUE by Trurl.ch.uj.edu.pl (Mercury 1.31); 6 Feb 98 13:16:16 GMT+2 Received: from MAILQUEUE by TRURL (Mercury 1.31); 6 Feb 98 13:16:11 GMT+2 From: "Malgorzata Baranska, p.253, tel. 265" Organization: Faculty of Chemistry, UJ To: chemistry@www.ccl.net Date: Fri, 6 Feb 1998 13:16:10 MET+2 Subject: CCL:PEDs X-Confirm-Reading-To: "Malgorzata Baranska, p.253, tel. 265" X-pmrqc: 1 Priority: normal X-mailer: Pegasus Mail v3.22 Message-ID: <1BB0AE319C@Trurl.ch.uj.edu.pl> Dear Netters, I calculate vibrational spectra of some complicated molecules (-S-, -SO2-,-NCN- groups) and their complexes with Cu, Cd, Ni using Gaussian 94. I need to obtain potential energy distributions (PEDs) so I've tried GAR2PED program , but my molecules are too complicated for this program. I would be very grateful for any sugestion.Is there a program which can handle wich my problem? Second Question: Is anybody know a parametrisation for semiempirical methods for copper? Malgorzata Baranska Jagiellonian University,Cracow,Poland e-mail: baranska@trurl.ch.uj.edu.pl From aguado@jmlopez.fam.cie.uva.es Fri Feb 6 08:22:00 1998 Received: from jmlopez.fam.cie.uva.es for aguado@jmlopez.fam.cie.uva.es by www.ccl.net (8.8.3/950822.1) id HAA10697; Fri, 6 Feb 1998 07:13:50 -0500 (EST) Received: (from aguado@localhost) by jmlopez.fam.cie.uva.es (8.8.3/8.8.3) id NAA03892 for chemistry@www.ccl.net; Fri, 6 Feb 1998 13:24:45 +0100 Date: Fri, 6 Feb 1998 13:24:45 +0100 From: Andres Aguado Message-Id: <199802061224.NAA03892@jmlopez.fam.cie.uva.es> To: chemistry@www.ccl.net Subject: Summary of polarizabilities... Dear netters, A few days ago I posted a question on ionic polarizabilities. The original message was: ............................................................................ Dear All: I need to know if there is any experimental (or good theoretical) determination of the polarizability of ions in ionic crystals. Specifically, I would like to know the polarizabilities of the following anions: F- Cl- Br- I- O-- S-- Se-- Te-- and of the following cations: Li+ Na+ K+ Rb+ Cs+ Be++ Mg++ Ca++ Sr++ Ba++ in the stoichiometric crystals like LiCl or MgO (all possible combinations), and in the "nonstoichiometric" crystals like MgF_2 or Li_2O (also all the known combinations). I would like to know also the polarizabilities of these ions in the diatomic molecules. Any help will be very appreciated. Of course, I will make a summary of all the responses received. Thank in advance!! Andres Aguado aguado@jmlopez.fam.cie.uva.es http:\\jmlopez.fam.cie.uva.es~aguado ........................................................................... Thanks to all the people who responded!!! Below I give a list of references on the subject: Int.J.Quantum Chem.Quantum.Chem.Symp.29 (1995) 523 Chem.Phys. 59(1981) 341 van Dujen & Swart,J.Phys.Chem., in press See the many papers by Pyper, Madden and Fowler. A recent one, from which many previous papers can be traced, is J. Phys. Condens. Matter 9, 471. Have a look at: P. C. Schmidt, A. Weiss, T. P. Das Phys.Rev.B. 1979, 19, 5525. Regards, Martin Kaupp David Feller, email:d3e102@emsl.pnl.gov, has calculated recently the polarizabilities of Li+,Na+,K+,Rb+,Cs+,Mg2+,Ca2+,Sr2+,and Ba2+ cations with MP ab initio methods. His results are near the complete basis set limit. Contact him if you are interested. ........................................................................... Best regards from Spain!! Andres Aguado aguado@jmlopez.fam.cie.uva.es http:\\jmlopez.fam.cie.uva.es~aguado From rochaj@rpi.edu Fri Feb 6 13:10:16 1998 Received: from mail1.its.rpi.edu for rochaj@rpi.edu by www.ccl.net (8.8.3/950822.1) id NAA14756; Fri, 6 Feb 1998 13:05:51 -0500 (EST) Received: from rpi.edu (rochaj@ri404.rcs.rpi.edu [128.113.31.76]) by mail1.its.rpi.edu (8.8.8/8.8.6) with ESMTP id MAA50362 for ; Fri, 6 Feb 1998 12:37:42 -0500 Sender: rochaj@rpi.edu Message-ID: <34DB4A60.81CCC054@rpi.edu> Date: Fri, 06 Feb 1998 12:37:36 -0500 From: "John-David R. Rocha" Organization: RPI X-Mailer: Mozilla 4.03 [en] (X11; I; AIX 4.1) MIME-Version: 1.0 To: "Comp. Chem. List" Subject: CCL:Compiling Viewmol Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I've been trying to compile Viewmol2.1 on an IBM RS/6000 with AIXv4.1. I am getting the following message during the final linking: /bin/sh getmachine viewmol cc -o viewmol annotate.o basisform.o bondorder.o calcmo.o coledit.o cylinder.o distort.o draw.o drawel.o drawform.o drawop.o drawsp.o ellipse.o feedback.o fileselect.o getmem.o getrc.o hardcopy.o hpgl.o inert.o init.o input.o insint.o intern.o makemenu.o maketics.o manual.o marcub.o matrix.o messgb.o mkconn.o mo.o mkunitc.o moform.o mouseaction.o mousecb.o normod.o optiform.o osname.o postscript.o printform.o ray.o raytracer.o redraw.o resource.o runprog.o save.o saveform.o specform.o viewmol.o waveform.o window.o xfont.o zoom.o -L/usr/lpp/OpenGL/lib -L/afs/rpi.edu/home/16/rochaj/tiff-v3.4/lib -ltiff -lXGLW -lGLU -lGL -lXm -lXmu -lXext -lXt -lX11 -lm ld: 0711-317 ERROR: Undefined symbol: .__eprintf ld: 0711-345 Use the -bloadmap or -bnoquiet option to obtain more information. make: 1254-004 The error code from the last command is 8. I noticed that Steve Bennet from Delaware also had a similar problem. Post reply to the list or directly to my e-mail below. Thanks in advance, John-David -- John-David Ray Rocha Rensselaer Polytechnic Institute rochaj@rpi.edu http://www.rpi.edu/~rochaj From tapas@risky3.thchem.siu.edu Fri Feb 6 17:10:18 1998 Received: from risky3.thchem.siu.edu for tapas@risky3.thchem.siu.edu by www.ccl.net (8.8.3/950822.1) id QAA15753; Fri, 6 Feb 1998 16:35:09 -0500 (EST) Received: (from tapas@localhost) by risky3.thchem.siu.edu (AIX4.2/UCB 8.7/8.7) id PAA14176; Fri, 6 Feb 1998 15:38:43 -0600 (CST) Date: Fri, 6 Feb 1998 15:38:43 -0600 (CST) From: Tapas Kar To: ComputerChemistryList Subject: ScH and NiH bond length Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I am looking for experimental and thoretical bond lengths of ScH and NiH. Thanks for your attention, Tapas ----------------- Tapas Kar, Ph. D Asst. Scientist Department of Chemistry Southern Illinois University at Carbondale Illinois 62901-4409 Fax: (618) 453 6408 Tel: (618) 453 6433 From hartmann@ccc.uni-erlangen.de Fri Feb 6 09:10:28 1998 Received: from faui45.informatik.uni-erlangen.de for hartmann@ccc.uni-erlangen.de by www.ccl.net (8.8.3/950822.1) id IAA11366; Fri, 6 Feb 1998 08:58:33 -0500 (EST) Received: from derioc1.organik.uni-erlangen.de (derioc1.organik.uni-erlangen.de [131.188.128.1]) by faui45.informatik.uni-erlangen.de (8.8.8/8.1.16-FAU) with ESMTP id OAA21771 for ; Fri, 6 Feb 1998 14:58:26 +0100 (MET) Received: from picard (hartmann@picard.organik.uni-erlangen.de [131.188.128.100]) by derioc1.organik.uni-erlangen.de (8.8.7/8.1.30-FAU) with SMTP id OAA13559 for ; Fri, 6 Feb 1998 14:58:25 +0100 (GMT-1:00) Sender: hartmann@organik.uni-erlangen.de Message-ID: <34DB2583.640E537C@ccc.uni-erlangen.de> Date: Fri, 06 Feb 1998 16:00:19 +0100 From: Michael Hartmann Organization: Computer-Chemie-Centrum To: CHEMISTRY@www.ccl.net Subject: DFT_on_PCs_summary My original question was: > > Dear Netters, > > does anybody know something about ab-initio and/or > DFT programs running on WinNT/Win95 - PCs. > > I will post a list of all replies. I want to thank all of you who gave me a reply... Micha and now the answers: ------------------------ TURBOMOLE (with various DFT schemes: S-VWN, B-VWN, B-LYP, B3-LYP, etc. ) is running under LINUX on PCs. Ask people at BASF (Horst Weiss) or at Karlsruhe or visit the TURBOMOLE home page. -- Dr. Heinz Schiffer Phone ++49-69-305-2330 Hoechst Research & Technology Fax ++49-69-305-81162 Scientific Computing, G864 Email schiffer@h1tw0036.hoechst.com 65926 Frankfurt am Main Schiffer@CRT.hoechst.com ------------------------- Sure ! GoTO : http://www.theochem.uni-hannover.de/AllChem We are working on the current release 0.11. The WindosNT/Win95 (32 Bit) Version will be released soon after, but I highly recommand to use Linux as operating system, because of much better memory performance and file handling. In the current release 0.11 we have : variational coulomb integral expansion, adaptive numerical integration of the xc energy and potential, the Minmax SCF procedure for Hartree calculations, full geometry optimization (Z-Matrix and cartesian), frequency analysis, property package (see visualization with VU). Best regards, Bernd ------------------------------------------------------------------------------- ___ EMail: berni@theochem.uni-hannover.de / / _______ / /_/ ____/ REAL : Dipl. Chem. Bernd Zimmermann \___ __/ Theoretische Chemie, Universtit"at Hannover ==== \_/ ====== Am Kleinen Felde 30 LOGOUT FASCISM! D-30167 Hannover, Germany WWW : http://www.theochem.uni-hannover.de/ Phone: (int. acc.)+511+762-5448 ------------------------------------------------------------------------------- Hallo, ich glaube mit NT siehts nicht ganz so gut aus obwohl: fuer ab initio gibt es Gamess/NT (kostenlos, nur ab initio & MP2) Gaussian-94W (ab initio, MP2-n, DFT, $750) PC-Spartan-Plus (ab initio, nur Organik, langsam) Hyperchem (ab initio, geruechteweise sehr langsam) zusaetzlich meines Wissens demnaechst Crays/Oxford Moleculars Unichem (habe ich schon als Demo gesehen) Fuer Linux gibt es obengenannte Programme sowie Turbomole (DFT, ab initio, MP2, 1200 DM, sehr schneller Code) DEFT (DFT-code von St. Amand, kostenlos - bin mir nur nicht ganz sicher ob das auch unter Linux laeuft) Jaguar-3.0 (Schroedinger Inc., $1200) Qchem (angekuendigt) welches ich im wesentlichen benutze. Letzteres soll es irgendwann auch mal als NT Version geben. Viele Gruesse Peter --------------------------------- Dr. Peter Burger Anorg.-Chem. Institut Uni Zuerich Winterthurerstr. 190 8057 Zuerich chburger@aci.unizh.ch ---------------------------------- I am sure you know about Gaussian 94 for Windows 95/NT. If not, just look at their home page, http://www.gaussian.com. Hope this helps. Oscar ......................................................................... Prof. Dr. Oscar N. Ventura Head, MTC-Lab, Avda. Gral. Flores 2124, P.O.Box 1157, 11800 Montevideo, Uruguay Tel:+598-2-9248396 Fax:+598-2-9241906 E-Mail:oscar@bilbo.edu.uy Web:http://bilbo.edu.uy/MTC-Labs/ TMMeC:http://bilbo.edu.uy/tmmec/ ......................................................................... ---------------------------------- Hi, Michael! You have group of programs running on Windows, the most popular is Gaussian, Hyperchem, Spartan, ... ---------------------------------- Gaussian 94W does both ab initio and DFT calculations under Windows 95 and NT 4.0. More details on the G94W package are available on our web site www.gaussian.com. Douglas J. Fox Director of Technical Support help@gaussian.com ------------------------- If you have a source license, Gaussian compiles on Linux using f2c/gcc. It does not compile using g77 or eg77 (which would be faster) due to some very ugly and invalid equivalences done in some of the utility functions. ( I gave up when I say a routine with ~100 arguments, some of which had been unsafely equivalenced. ) I have a patch file to convert the source tree into a Debian/hamm package for installation on our PC's, but can't distribute the .debs due to the commercial nature of Gaussian. Some versions of the C libraries were incompatible with the Gaussian code. Earlier Libc5's and the current libc6 work though - later libc5's had an incompatibility. Specifying alignment flags might also boost it's performance, but I haven't experimented there (it's difficult enough to compile Gaussian without playing with optional flags). WinNT/win95 ... if you can't get precompiled binaries, you could do it yourself from your source code. Some fortran compilers will object to the gaussian code- so you may need to try multiple compilers or use f2c/wingcc to get it to work. If it were me, I'd just put Linux on a small extra disk and set up the machine to dual boot, since you won't be able to use Word while gaussian is running anyway. By specifying an upper memory limit in either the job file or the site configuration file, you can leave Linux enough memory to continue using the machine interactively. -Drake -- Dr. Drake Diedrich, Research Officer - Computing, (02)6279-8302 John Curtin School of Medical Research, Australian National University 0200 Replies to other than Drake.Diedrich@anu.edu.au will be routed off-planet --------------------------- Hallo! Warum installierst Du nicht ein Betriebssystem (z.B. Linux), dann kannst Du ALLES (z.B. Gaussian, oder, wenn es beliebt, DFT wie deMon, ADF etc.) benutzen. Thomas ch glaube, es gibt eine Spartan-Version, wo soetwas drin ist. Zumindestens HF-MP2. Ich kenne die Windows nicht, aber wenn Du einen vernuenftigen Fortran-Compiler hast, koenntest Du damit auch deMon (oder das 'neue' Cache) installieren. Kostet beides 1000 Dollar, wenn ich nicht irre, koennte ich mich sogar drum kuemmern, ich kenne beide Gruppen. Ciao Thomas -------------------------- Dear Sir, In first of all, I'd like know if you can run ab-intio or DFT programs on UNIX or LINUX. On the other hand, Do you have a group in DFT or no?, if the answer is yes, What's the main purpose of your DFT's group?. I realize you this questions because we want contact with some grups in DFT. Regards. MANUEL. Dear Michael: With respect to question about packages in DFT available for PCs, my first suggestion is a comertial package of D.R. Salahub. His address is: Departement de chimie, Universite de Montreal, C.P. 6210, Succ. A, Montreal, Quebec H3C 3V1, Canada. I don't know his e-mail but if you need it, please send me a e-mail and i'd find out it. Regards. Manuel Pereiro. ---------------------------- -- ******************************************************************* * Michael Hartmann Computer-Chemie-Centrum and * * Dipl.-Chem. (univ.) Institut.fuer.Anorganiche Chemie * * Univ. Erlangen-Nuernberg * * Tel.: (0)9131-856938 Fax : (0)9131-856565 * * URL: http://www.ccc.uni-erlangen.de/clark/hartmann/ * *******************************************************************