From jkl@ccl.net Mon Apr 7 00:34:29 1997 Received: from bedrock.ccl.net for jkl@ccl.net by www.ccl.net (8.8.3/950822.1) id AAA24238; Mon, 7 Apr 1997 00:10:17 -0400 (EDT) Received: from krakow.ccl.net for jkl@ccl.net by bedrock.ccl.net (8.8.3/950822.1) id AAA19002; Mon, 7 Apr 1997 00:10:12 -0400 (EDT) From: Jan Labanowski Received: for jkl@ccl.net by krakow.ccl.net (8.8.3/920428.1525) id AAA02389; Mon, 7 Apr 1997 00:10:12 -0400 (EDT) Date: Mon, 7 Apr 1997 00:10:12 -0400 (EDT) Message-Id: <199704070410.AAA02389@krakow.ccl.net> To: chemistry@www.ccl.net Subject: Q-CHEM Software released Cc: jkl@ccl.net, gene@q-chem.com Dear Netters, Q-Chem, Inc. has just released Q-Chem(TM) 1.0, a quantum chemistry software package capable of HF, DFT, and Hybrid HF-DFT methods with a focus on very large molecular systems. Q-Chem is available on a number of computer platforms, but for more information please see: http://www.ccl.net/cca/info/software-packages/q-chem/QPress.html and visit Q-Chem's website at: http://www.q-chem.com Jan Labanowski jkl@ccl.net From schiffer@h1tw0036.hoechst.com Mon Apr 7 03:34:33 1997 Received: from backup.hoechst.com for schiffer@h1tw0036.hoechst.com by www.ccl.net (8.8.3/950822.1) id DAA25868; Mon, 7 Apr 1997 03:03:14 -0400 (EDT) Received: by backup.hoechst.com (SMI-8.6/SMI-SVR4) id JAA11595; Mon, 7 Apr 1997 09:00:48 +0200 Received: from unknown(134.81.79.248) by backup via smap (V1.3) id sma011578; Mon Apr 7 08:59:53 1997 Received: from 134.81.76.36 by fra28.hiserv.de with SMTP (Microsoft Exchange Internet Mail Connector Version 4.0.994.63) id H8703CRA; Mon, 7 Apr 1997 09:06:22 +0200 Received: from h1tw0024 by h1tw0036 via SMTP (940816.SGI.8.6.9/940406.SGI.AUTO) id JAA04518; Mon, 7 Apr 1997 09:01:10 +0200 Message-ID: <33489BB5.167E@h1tw0036.hoechst.com> Date: Mon, 07 Apr 1997 09:01:09 +0200 From: "Dr. Heinz Schiffer" Organization: Hoechst Corporate Research & Technology X-Mailer: Mozilla 2.0 (X11; I; IRIX 5.3 IP22) MIME-Version: 1.0 To: Computational Chemistry List Subject: [Fwd: Re: CCL:H2 dissociation by UHF and DFT in G94?] Content-Type: multipart/mixed; boundary="------------2781446B794B" This is a multi-part message in MIME format. --------------2781446B794B Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit -- Dr. Heinz Schiffer Phone ++49-69-305-2330 Hoechst CR&T Fax ++49-69-305-81162 Scientific Computing, G864 Email schiffer@h1tw0036.hoechst.com 65926 Frankfurt am Main schiffer@msmwia.hoechst.com --------------2781446B794B Content-Type: message/rfc822 Content-Transfer-Encoding: 7bit Content-Disposition: inline Received: from h1tw0036 by h1tw0024 via ESMTP (940816.SGI.8.6.9/940406.SGI.AUTO) for id JAA21417; Mon, 7 Apr 1997 09:00:45 +0200 Received: from h1tw0024 by h1tw0036 via SMTP (940816.SGI.8.6.9/940406.SGI.AUTO) id JAA04515; Mon, 7 Apr 1997 09:00:38 +0200 Sender: schiffer@h1tw0036 Message-ID: <33489B96.41C6@h1tw0036.hoechst.com> Date: Mon, 07 Apr 1997 09:00:38 +0200 From: "Dr. Heinz Schiffer" Organization: Hoechst Corporate Research & Technology X-Mailer: Mozilla 2.0 (X11; I; IRIX 5.3 IP22) MIME-Version: 1.0 To: ccluser@chu.chem.nthu.edu.tw Subject: Re: CCL:H2 dissociation by UHF and DFT in G94? References: <9703270251.AA18249@chu.chem.nthu.edu.tw> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mozilla-Status: 0000 ccluser@chu.chem.nthu.edu.tw wrote: > > Dear CCL members, > I tried to get energies of h2 (H atoms are seperated by 2 and 10 > angstrom) by UHF/6-31g**, b3lyp/6-31g** and svwn/6-31g**, > and all are set in singlet state, then I got energies as following, > 2 angstrom, > UHf/6-31g** -0.9167408 > b3lyp/6-31g** -0.9959347 > svwn/6-31g** -0.9167408 > > 10 angstrom, > UHf/6-31g** -0.7241629 > b3lyp/6-31g** -0.8923662 > svwn/6-31g** -0.4588643 > I am so surprising at these results, does it mean these three > methods can't describe the PES of h2 dissociation exactly? and > we can't calculate TS involving H2 formation or dissociation? Hi Chiu-Ling ! No! The problem is another one. I guess you used the converged MOs of the 2 Angstrom calculation as a start for the 10 Angstrom calculation. At 2 Angstrom the UHF and RHF solutions of the SCF - Procedure are the same, at 10 Angstrom they are not. But RHF is always a solution to the SCF-equations, even if the UHF solution is lower in energy. So, if you start with "RHF" orbitals at 10 Angstrom you always get a RHF solution, and not the UHF one ! To get the UHF solution at 10 Angstrom you have to use proper UHF start orbitals, either creating it by hand, or by doing a so-called triplet instability calculation, or using some other tricks. For references about this problem, see e.g. I. Mayer, On the behaviour of the UHF method near the "critical point", Acta Physica Hungarica 54(3-4) (1983) 246-266. Ciao, Heinz -- Dr. Heinz Schiffer Phone ++49-69-305-2330 Hoechst CR&T Fax ++49-69-305-81162 Scientific Computing, G864 Email schiffer@h1tw0036.hoechst.com 65926 Frankfurt am Main schiffer@msmwia.hoechst.com --------------2781446B794B-- From neuber@exp.bessy.de Mon Apr 7 09:34:43 1997 Received: from metaxa.exp.bessy.de for neuber@exp.bessy.de by www.ccl.net (8.8.3/950822.1) id JAA01518; Mon, 7 Apr 1997 09:00:43 -0400 (EDT) Message-Id: <199704071300.JAA01518@www.ccl.net> Received: from metaxa.bessy.de (bes704.exp.bessy.de) by metaxa.exp.bessy.de (MX V4.1 VAX) with SMTP; Mon, 07 Apr 1997 15:00:28 MET_DST From: "Michael Neuber" To: "ccl-liste" Subject: need help with a translation Date: Mon, 7 Apr 1997 15:02:56 +0200 X-MSMail-Priority: Normal X-Priority: 3 X-Mailer: Microsoft Internet Mail 4.70.1160 MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hello everyone! Please excuse my off-topic help request: can any native English speaking member of the list (perhaps mathematician..) help me with the translation of the German word 'Scharparameter' into the English language ? (Scharparameter means the parameter which is addressed to distinguish between several similar curves in a survey diagramm, e.g., maybe some heater setting value called A, if you consider several different system answers T_A(t) [temperature vs time, dependent on setting for A]. As the German 'Kurvenschar' translates to 'array of curves' or 'family of curves' I thought of something like 'array parameter'. Any better suggestions? Regards Michael @ Berlin From john@xray.bmc.uu.se Mon Apr 7 11:34:44 1997 Received: from XRAY.BMC.UU.SE for john@xray.bmc.uu.se by www.ccl.net (8.8.3/950822.1) id LAA02435; Mon, 7 Apr 1997 11:29:30 -0400 (EDT) Received: from alfasud.bmc.uu.se by XRAY.BMC.UU.SE with SMTP; Mon, 7 Apr 1997 17:03:33 +0300 (MET-DST) Received: by alfasud.bmc.uu.se; id AA04041; Mon, 7 Apr 1997 17:29:24 +0200 Date: Mon, 7 Apr 1997 17:29:22 +0200 (MET DST) From: John Marelius X-Sender: john@alfasud.bmc.uu.se To: chemistry@www.ccl.net Subject: Looking for Connolly surface program In-Reply-To: Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I'm looking for a program to calculate Connolly surfaces of molecules, using pdb files as input and producing output as text that can be fed into another (home-made) program. I hope to find a free program with source code. Anyone have any tips? Thanks, John Marelius +-----------------------------------------------------------------------------+ | John Marelius | | Dept. of Molecular Biology, Uppsala University | | E-mail: john@ibg.uu.se | | www: http://www.ibg.uu.se/~john | +-----------------------------------------------------------------------------+ From rahsjc@rohmhaas.com Mon Apr 7 13:34:44 1997 Received: from nmho05u.rohmhaas.com for rahsjc@rohmhaas.com by www.ccl.net (8.8.3/950822.1) id NAA03070; Mon, 7 Apr 1997 13:03:02 -0400 (EDT) Received: by nmho05u.rohmhaas.com; id NAA17067; Mon, 7 Apr 1997 13:12:41 -0400 (EDT) Received: from fermi.sh.rohmhaas.com(136.141.248.15) by nmho05u.rohmhaas.com via smap (V3.1.1) id xma016996; Mon, 7 Apr 97 13:12:32 -0400 Received: from localhost by fermi.sh.rohmhaas.com (AIX 3.2/UCB 5.64/4.03) id AA25771; Mon, 7 Apr 1997 13:02:42 -0400 Date: Mon, 7 Apr 1997 13:02:42 -0400 (EDT) From: "Subhas J. Chakravorty" X-Sender: rahsjc@fermi.sh.rohmhaas.com To: Michael Neuber Cc: ccl-liste Subject: Re: CCL:need help with a translation In-Reply-To: <199704071300.JAA01518@www.ccl.net> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Scharparameter is a definitely acceptable possibilty. Scarparameter would make it American Scar-parameter would make it English. Scur-parameter would make it Indian English. and just the A-parameter would make it Scientific English. One could choose one of the above or Some of the above. or all of the above or none of the above! As we normally do in Science!. Subhas Chakravorty. On Mon, 7 Apr 1997, Michael Neuber wrote: > Hello everyone! > > Please excuse my off-topic help request: > can any native English speaking member of the list (perhaps > mathematician..) > help me with the translation of the German word > > 'Scharparameter' > > into the English language ? > (Scharparameter means the parameter which is addressed to distinguish > between several similar curves in a survey diagramm, > e.g., maybe some heater setting value called A, if you consider several > different system answers T_A(t) [temperature vs time, dependent on > setting for A]. > > As the German 'Kurvenschar' translates to 'array of curves' or 'family of > curves' > I thought of something like > 'array parameter'. > Any better suggestions? > > Regards > Michael @ Berlin > > > > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: neuber@exp.bessy.de > -- Original Sender From: Address: neuber@exp.bessy.de > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > > Subhas J. Chakravorty, sjchakravorty@rohmhaas.com (215)-619-5481 Rohm and Haas Company Spring House, PA-19447 ************************************************************************** Disclaimer : Opinions in the above text are not of Rohm and Haas Company + ************************************************************************** From raman@indigo1.biomol.uci.edu Mon Apr 7 14:34:47 1997 Received: from indigo1.biomol.uci.edu for raman@indigo1.biomol.uci.edu by www.ccl.net (8.8.3/950822.1) id OAA03652; Mon, 7 Apr 1997 14:26:42 -0400 (EDT) Received: from indigo2.biomol.uci.edu by indigo1.biomol.uci.edu (8.8.5) id SAA29288; Mon, 7 Apr 1997 18:26:36 GMT From: CS Raman Received: by indigo2.biomol.uci.edu (8.8.4) id SAA12098; Mon, 7 Apr 1997 18:26:35 GMT Message-Id: <199704071826.SAA12098@indigo2.biomol.uci.edu> Subject: Re: CCL:Looking for Connolly surface program To: john@xray.bmc.uu.se (John Marelius) Date: Mon, 7 Apr 1997 11:26:35 -0700 (PDT) Cc: chemistry@www.ccl.net In-Reply-To: from "John Marelius" at Apr 7, 97 05:29:22 pm X-Mailer: ELM [version 2.4 PL25] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit John: > > I'm looking for a program to calculate Connolly surfaces of molecules, > using pdb files as input and producing output as text that can be fed into I think you need the Molecular Surface Package written by Mike Connolly. Mike may be reached at: connolly@best.com. MSP does a nice job of tallying Contact, reentrant and molecular surface areas in conjuction with solvent accessible surface areas. You may also want to try: ICM by Ruben Abagyan abagyan@earth.med.nyu.edu - the fastest program I am aware of for calculating surface areas. Frank Eisenhaber (eisenhaber@embl-heidelberg.de) also has program(s) to do what you are interested in. Browse: www.embl-heidelberg.de/~eisenhab/ Cheers -raman ___________________________________________________________________ C.S.Raman Tel: (714) 824-4322 University of California Fax: (714) 824-8540 Dept. MB & B email: raman@indigo1.biomol.uci.edu 3205 Bio Sci II Irvine, CA 92697-3900 ------------------------------------------------------------------- If we really understand the problem, the answer will come out of it, because the answer is not separate from the problem. - J.Krishnamurti ___________________________________________________________________ From bruno@antas.agraria.uniss.it Mon Apr 7 16:34:39 1997 Received: from ssmain.uniss.it for bruno@antas.agraria.uniss.it by www.ccl.net (8.8.3/950822.1) id PAA04111; Mon, 7 Apr 1997 15:58:26 -0400 (EDT) Received: from antas.agraria.uniss.it by ssmain.uniss.it with SMTP (1.39.111.2/16.2) id AA122183114; Mon, 7 Apr 1997 21:58:34 +0200 Date: Mon, 7 Apr 1997 21:58:36 +0100 (NFT) From: "Dr. Bruno Manunza" To: John Marelius Cc: chemistry@www.ccl.net Subject: Re: CCL:Looking for Connolly surface program In-Reply-To: Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Mon, 7 Apr 1997, John Marelius wrote: > I'm looking for a program to calculate Connolly surfaces of molecules, > using pdb files as input and producing output as text that can be fed into > another (home-made) program. I hope to find a free program with source > code. > Anyone have any tips? > Thanks, > > John Marelius Dear John, there are a few programs free on the net which do what you are looking for, we keep an updated list on the software page of our site at: http://antas.agraria.uniss.it hope it helps Dr Bruno Manunza DISAABA (Dept. of Agricultural Environm. Sci) University of Sassari V.le Italia 39 07100 Sassari, ITALY phone: 39 79 229215 fax: 39 79 229276 e-mail: bruno@antas.agraria.uniss.it e-mail: bruno@tharros.dipchim.uniss.it e-mail: gx6bot81@cray.cineca.it web: http://antas.agraria.uniss.it From tvd@msi.com Mon Apr 7 16:40:23 1997 Received: from bioc1.msi.com for tvd@msi.com by www.ccl.net (8.8.3/950822.1) id PAA04033; Mon, 7 Apr 1997 15:47:53 -0400 (EDT) Received: by bioc1.msi.com (5.64/0.0) id AA21841; Mon, 7 Apr 97 12:47:21 -0700 Received: from iris69.msi.com(146.202.3.69) by bioc1.msi.com via smap (V2.0) id xma021837; Mon, 7 Apr 97 12:47:20 -0700 Received: by iris69.msi.com (940816.SGI.8.6.9/930416.SGI) for CHEMISTRY@www.ccl.net id MAA05654; Mon, 7 Apr 1997 12:47:56 -0700 Date: Mon, 7 Apr 1997 12:47:56 -0700 From: tvd@msi.com (Ton van Daelen) Message-Id: <199704071947.MAA05654@iris69.msi.com> To: CHEMISTRY@www.ccl.net Subject: ACS seminar on Cerius2 software developer's kit (reminder) To all software developers out there... This is the final announcement of the seminar that MSI is organizing at the ACS on the Cerius2 Software Developer's Kit. There is a small numbers of places still available, but please sign up soon as space is unfortunately limited. With best regards - Ton van Daelen ---------------------------------------------- Cerius2 Software Developer's Kit Seminar ACS San Francisco Rm 276, Moscone Convention Center 9:00am-11:00am, April 14, 1997 During the ACS meeting in San Francisco MSI is organizing a seminar on the Cerius2 software developer's toolkit (C2.SDK). C2.SDK allows you to plug your own chemistry applications into MSI's Cerius2 modeling environment. You can link in existing software or develop entirely new applications. You concentrate on the scientific side of your program and C2.SDK takes care of the molecular graphics, window management, and data visualization. C2.SDK is used to develop scientific applications that solve research problems in fields including polymer science, rational drug design, combinatorial chemistry, catalysis, chemical reactions, and protein chemistry. The C2.SDK toolkit consists of a rich API set dealing with all aspects of interfacing chemistry codes, including GUI design, structure visualization, graphing, and volumetric display. Applications can be written in FORTRAN, C, or C++. The seminar will also discuss imminent SDK extensions that allow you to run applications through the internet, or an intranet, from a web browser interface on your desktop computer (PC, or MAC). In addition, we will demonstrate the use of C2.Tcl, the scripting language for the Cerius2 interface, for simple customization of routine modeling operations. C2.Tcl is based on the standard tcl scripting language, it lets you put together a simple application with its own graphical user interface in a matter of minutes. C2.Tcl aids in all aspects of molecular modeling, in particular in drug design and protein analysis. For more information about C2.SDK and C2.Tcl: http://www.msi.com/support/sdk/ The seminar is offered free of charge. Because space is limited, attendance is by registration only. The deadline for advanced registration is April 7. You can sign up at the following URL: http://www.acs.org/meetings/sanfran/exhwksp.html Ton van Daelen Product Manager Software Developer's Kit __o E: tvd@msi.com _`\<,_ Molecular Simulations P: -1-619-546-5329 (*)/ (*) 9685 Scranton Road F: -1-619-458-0136 /\/\/\/\/\/\ San Diego, CA 92121 W: http://www.msi.com Check out What's New in SDK on the SDK web pages at http://www.msi.com/support/sdk/ From gaussian.com!moses@lorentzian.com Mon Apr 7 18:34:45 1997 Received: from relay5.UU.NET for gaussian.com!moses@lorentzian.com by www.ccl.net (8.8.3/950822.1) id SAA04946; Mon, 7 Apr 1997 18:17:50 -0400 (EDT) Received: from uucp3.UU.NET by relay5.UU.NET with SMTP (peer crosschecked as: uucp3.UU.NET [192.48.96.34]) id QQckhl25698; Mon, 7 Apr 1997 18:18:06 -0400 (EDT) Message-Id: Received: from m10.UUCP by uucp3.UU.NET with UUCP/RMAIL ; Mon, 7 Apr 1997 18:17:49 -0400 Received: by m10.lorentzian.com; Mon, 7 Apr 1997 18:16:02 -0400 Received: by mousse.gaussian.com; Mon, 7 Apr 1997 15:25:49 -0500 From: gaussian.com!moses@lorentzian.com (David Moses) Subject: Product Announcement: GaussView To: CHEMISTRY@www.ccl.net Date: Mon, 7 Apr 1997 15:25:49 -0500 (EST) X-Mailer: ELM [version 2.4 PL24] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Gaussian, Inc. is pleased to introduce GaussView, an affordable graphical interface, customized for use with Gaussian. GaussView provides Gaussian users with graphical structure input, calculation setup, and visualization of results. The initial release of GaussView runs on Digital Unix for Alpha 4.0b, Silicon Graphics Irix 6.2, and IBM AIX 4.1 systems using OpenGL, and while running on these systems can display on any X-windows terminal. Future platforms will be announced as they become available. GaussView is compatible with Revision E of G94. Check with us about compatibility with your hardware/software configuration. If you would like to obtain a license for GaussView, or if you desire additional information, please contact us at the e-mail address or fax or telephone numbers given below. GaussView will be on display at the ACS meeting in San Francisco, April 14-16. Visit us in the Digital Equipment booth (#1039) for a personal demonstration. *------------------------*------------------------*-----------------------* | David J. Moses, Ph.D. | Carnegie Office Park | info@gaussian.com | | Vice President, C.O.O. | Building Six | 412-279-6700 (Voice) | | Gaussian, Inc. | Pittsburgh, PA 15106 | 412-279-2118 (FAX) | *------------------------*------------------------*-----------------------* | Be sure to visit our Website at http://www.gaussian.com | *------------------------*------------------------*-----------------------* This notice is sent without warranty of any kind, expressed or implied. Gaussian and GaussView are trademarks of Gaussian, Inc. All other trademarks are the property of their respective holders. From genghis@darkwing.uoregon.edu Mon Apr 7 19:34:39 1997 Received: from darkwing.uoregon.edu for genghis@darkwing.uoregon.edu by www.ccl.net (8.8.3/950822.1) id TAA05249; Mon, 7 Apr 1997 19:17:17 -0400 (EDT) Received: from localhost (genghis@localhost) by darkwing.uoregon.edu (8.8.5/8.8.5) with SMTP id QAA06756 for ; Mon, 7 Apr 1997 16:16:31 -0700 (PDT) Date: Mon, 7 Apr 1997 16:16:31 -0700 (PDT) From: Dale Andrew Braden To: cclpost Subject: geometry optimization methods Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL, A brief question: Are there any circumstances in which a geometry optimization in Cartesian coordinates would be *faster* than in redundant internal coordinates? The reason I am asking is because I am trying to optimize the geometry of a hydrogen-bonded dimer in a solvent medium using Gaussian 94, and the change in the two intermolecular Z-matrix coordinates (distance and angle) remains large for many, many iterations. The geometry isn't exactly oscillating between two structures, but it isn't settling down, either, and I thought that perhaps by changing the optimization method from redundant internal coordinates (the default method in G94) to cartesians, the optimization might proceed more smoothly to a converged minimum. I don't want to try this unless it can work, because the calculation is expensive. Best wishes to all, Dale Braden Department of Chemistry University of Oregon Eugene, OR 97403-1253 genghis@darkwing.uoregon.edu