From dsmith@CTCnet.Net Thu Aug 14 02:17:31 1997 Received: from home.ctcnet.net.CTCnet.Net for dsmith@CTCnet.Net by www.ccl.net (8.8.3/950822.1) id BAA11324; Thu, 14 Aug 1997 01:43:00 -0400 (EDT) Received: from fock by home.ctcnet.net.CTCnet.Net (SMI-8.6/SMI-SVR4) id BAA10669; Thu, 14 Aug 1997 01:42:26 -0400 Message-Id: <3.0.1.32.19970814014052.009b2008@pop.dasgroup.com> X-Sender: dsmith@pop.dasgroup.com X-Mailer: Windows Eudora Light Version 3.0.1 (32) Date: Thu, 14 Aug 1997 01:40:52 -0400 To: Jian Wang From: "Douglas A. Smith Ph.D." Subject: Re: Empirical solvation models Cc: CHEMISTRY@www.ccl.net In-Reply-To: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" This is not a direct answer but may be of interest. A few years ago we published a comparison of the use of molecular mechanics (AMBER* force field) plus the GBSA solvation model versus the use of ab initio plus Monte Carlo simulations for estimating conformational equilibria in aqueous solution for four test cases: 1,2-ethanediol, 2-hydroxybenzoic acid, and both the neutral and protonated forms of histamine. The GBSA relative solvation free energies were consistently smaller than the values obtained in the MC simulations when using the charges from the AMBER* forceifield, and up to 30 percent underestimated when using the charge sets from the MC simulation. Comparisons were also made to experimental data. We ascribed the differences in the two approaches as due to the application of torsional parameters and atomic charges developed in the AMBER* forcie field for monofunctional polar systems, while we were looking at difunctional molecules with the possibility of intramolecular hydrogen bonding. The reference: P. I. Nagy, J. E. Bitar, D. A. Smith, J. Comput. Chem. 15, 1994, 1228-1240. Doug Smith At 02:24 PM 8/13/97 -0700, you wrote: > >Dear CCL netters > >Could someone points to me some empirical methods to >estimate free solvation energy of a molecule in >aqueous solution? > >There are many solvation models to calculate free >solvation energy such as QM SCRF methods, AMSOL, PB, >GBSA, MD, MC and etc. What we would like to know is >the performance of empirical methods, i.e., what are >their standard errors over a large set of experimental >data or over other theoretical results, where an empirical >approach will break down. > >I will summarize the replies if there are enough >interests. > >Thanks, > >Jian Wang, Ph.D >Department of Pharmaceutical Chemistry Tel: (415)-476-2597 (O) >Box 0446, Room S-1019 (415)-752-2256 (H) >University of California Fax: (415)-476-0688 (O) >San Francisco, CA94143-0446 >U.S.A. Email: jianwang@cgl.ucsf.edu > > >-------This is added Automatically by the Software-------- >-- Original Sender Envelope Address: jianwang@cgl.ucsf.EDU >-- Original Sender From: Address: jianwang@cgl.ucsf.edu >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 > > > -- Dr. Douglas A. Smith, President and CEO | voice: (814) 255-7859 The DASGroup, Inc. | fax: (814) 255-3517 1732 Lyter Drive, 2nd Floor | email: dsmith@dasgroup.com Johnstown, PA 15905 | WWW: http://www.dasgroup.com Contract R&D specialists in modeling, simulation, and synthesis for chemistry, materials science, and biotechnology. From schiffer@h1tw0036.hoechst.com Thu Aug 14 03:17:33 1997 Received: from backup.hoechst.com for schiffer@h1tw0036.hoechst.com by www.ccl.net (8.8.3/950822.1) id DAA11632; Thu, 14 Aug 1997 03:16:44 -0400 (EDT) Received: by backup.hoechst.com id JAA16386; Thu, 14 Aug 1997 09:12:48 +0200 Received: from unknown(134.81.76.36) by backup id sma016368; Thu Aug 14 09:12:10 1997 Received: from h1tw0024 by h1tw0036 via SMTP (940816.SGI.8.6.9/940406.SGI.AUTO) id JAA04275; Thu, 14 Aug 1997 09:15:45 +0200 Message-ID: <33F2B09D.3F54@h1tw0036.hoechst.com> Date: Thu, 14 Aug 1997 09:15:41 +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: David Young CC: Computational Chemistry List Subject: Re: CCL:HF Limit References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit David Young wrote: > What I am looking for is a proof of the existence of the > Hartree-Fock limit. Is it possible that this is an observed result for > which no derivation has ever been done? Hi David, if I understand you correctly, then there are 2 questions. The 1st is the one about the existence of solutions of the Hartree-Fock equations (do they have any solution at all !). The 2nd is about convergence of basis set expansions. The 1st questions might be answered with yes (but not conclusively, as far I understand ), see e.g. Elliott H. Lieb, Barry Simon The Hartree-Fock Theory for Coulomb Systems Commun. math. Phys. 53 (1977) 185-194 Elliott H. Lieb, Barry Simon On solutions to the Hartree-Fock problem for atoms and molecules J. Chem. Phys. 61(2) (1974) 735-736 G. Fonte, R. Mignani, G. Schiffrer Solution of the Hartree-Fock Equations Coomun. math. Phys. 33 (1973) 293-304 The 2nd question is very difficult to answer. People like Bob Hill, John D. Morgan, and Werner Kutzelnigg had a hard time thinking of it, here a few references : Werner Kutzelnigg Theory of the Expansion of Wave Functions in a Gaussian Basis Int. J. Quantum Chem. 51 (1994) 447-463 John D. Morgan III The analytic structure of atomic and molecular wavefunctions and its impact on the rate of convergence of variational calculations in : M. Defranceschi, J. Delhalle (eds.), Numerical Determination of the Electronic Structure of Atoms, Diatomic and Polyatomic Molecules, Kluwer, 1989, pp. 49-84 Robert Nyden Hill Rates of convergence and error estimation formulas for the Rayleigh-Ritz variational method J. Chem. Phys. 83(3) (1985) 1173-1196 Hope, this helps 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@CRT.hoechst.com From HOEFER@dacmza.chemie.Uni-Mainz.DE Thu Aug 14 04:17:34 1997 Received: from MZDMZA.ZDV.UNI-MAINZ.DE for HOEFER@dacmza.chemie.Uni-Mainz.DE by www.ccl.net (8.8.3/950822.1) id DAA11944; Thu, 14 Aug 1997 03:55:13 -0400 (EDT) Received: from decnet-daemon (HOEFER@DACMZA) by MZDMZA.ZDV.UNI-MAINZ.DE (PMDF V5.0-4 #10401) id <01IMFBRU6Q4G9KMKLJ@MZDMZA.ZDV.UNI-MAINZ.DE> for chemistry@www.ccl.net; Thu, 14 Aug 1997 09:56:37 +0100 Date: Thu, 14 Aug 1997 09:56:37 +0100 From: ANDREAS HOEFER Subject: output of frequency calculations in G94 To: chemistry@www.ccl.net Message-id: <01IMFBRUAEXE9KMKLJ@MZDMZA.ZDV.UNI-MAINZ.DE> X-VMS-To: BITNET"chemistry@www.ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Hi does anybody have an idea , how to get additional output of frequency calculations in Gaussian94 ? Especially we are interested in : Force constants in internal coordinates composition of the normal modes concerning internal coord.s or at least a transformation matrix to convert the cartesian force constants to internals. Some calculations on small molecules contain the internal forces in their P output, but large molecules do not ! Is there an internal flag ( IOp ) to be set for this output ?? Thanks a lot in advance. Andreas Hoefer Inst. fuer Anorgan. und Analyt. Chemie Joh. Gutenberg Universitaet Mainz Germany email: hoefer@dacmza.chemie.uni-mainz.de From elazhary@theochem.uni-stuttgart.de Thu Aug 14 06:17:42 1997 Received: from artemis.rus.uni-stuttgart.de for elazhary@theochem.uni-stuttgart.de by www.ccl.net (8.8.3/950822.1) id FAA12423; Thu, 14 Aug 1997 05:44:16 -0400 (EDT) Received: from tc8.theochem.uni-stuttgart.de (tc8.theochem.uni-stuttgart.de [129.69.55.128]) by artemis.rus.uni-stuttgart.de with SMTP id LAA06141 (8.6.13/IDA-1.6 for ); Thu, 14 Aug 1997 11:44:16 +0200 Message-ID: <199708140944.LAA06141@artemis.rus.uni-stuttgart.de> Received: by tc8.theochem.uni-stuttgart.de (1.38.193.4/16.2/BelWue-2.1) id AA02459; Thu, 14 Aug 1997 11:44:15 +0200 From: "Dr. Adel El-Azhary" Subject: personal workstations To: chemistry@www.ccl.net Date: Thu, 14 Aug 97 11:44:15 METDST Mailer: Elm [revision: 70.85] Dear CCL members: Did anyone have and idea how the digital new workstations, a- and i-serie would compare in speed with the alpha workstation for example 500/500. Thank you very much in advance for your answers. Best regards, Adel El-Azhary From shenkin@still3.chem.columbia.edu Thu Aug 14 09:17:42 1997 Received: from mailrelay1.cc.columbia.edu for shenkin@still3.chem.columbia.edu by www.ccl.net (8.8.3/950822.1) id JAA13570; Thu, 14 Aug 1997 09:06:56 -0400 (EDT) Received: from still3.chem.columbia.edu (still3.chem.columbia.edu [128.59.112.36]) by mailrelay1.cc.columbia.edu (8.8.5/8.8.5) with SMTP id JAA29098; Thu, 14 Aug 1997 09:06:48 -0400 (EDT) Received: by still3.chem.columbia.edu (950413.SGI.8.6.12/930416.SGI.AUTO) id JAA06396; Thu, 14 Aug 1997 09:06:47 -0400 Date: Thu, 14 Aug 1997 09:06:47 -0400 From: shenkin@still3.chem.columbia.edu (Peter Shenkin) Message-Id: <199708141306.JAA06396@still3.chem.columbia.edu> To: chemistry@www.ccl.net, Verschelde Jean-Luc Subject: Re: CCL:cluster > From chemistry-request@www.ccl.net Wed Aug 13 19:15:56 1997 > I am looking for a program that clusters structures by calculating the > RMS deviation and is able to read PDB files. > Who can help me? See the URL listed below for a description of our XCluster program. It's part of the MacroModel package, and MacroModel does read PDB files. XCluster then reads the resulting MacroModel-format files. XCluster is described in a J. Comp. Chem. article of a few years back. The reference is in the on-line bibliography also accessible >from the URL in my .signature. Hope this helps, -P. "Making Barbie smart is like making GI Joe a conscientious objector" M.Dowd * Peter S. Shenkin; Chemistry, Columbia U.; 3000 Broadway, Mail Code 3153 * ** NY, NY 10027; shenkin@columbia.edu; (212)854-5143; FAX: 678-9039 *** *MacroModel WWW page: http://www.columbia.edu/cu/chemistry/mmod/mmod.html * From jkl@ccl.net Thu Aug 14 10:17:35 1997 Received: from bedrock.ccl.net for jkl@ccl.net by www.ccl.net (8.8.3/950822.1) id JAA13815; Thu, 14 Aug 1997 09:45:18 -0400 (EDT) Received: from krakow.ccl.net for jkl@ccl.net by bedrock.ccl.net (8.8.6/950822.1) id JAA22068; Thu, 14 Aug 1997 09:45:18 -0400 (EDT) From: Jan Labanowski Received: for jkl@ccl.net by krakow.ccl.net (8.8.3/920428.1525) id JAA04753; Thu, 14 Aug 1997 09:45:16 -0400 (EDT) Date: Thu, 14 Aug 1997 09:45:16 -0400 (EDT) Message-Id: <199708141345.JAA04753@krakow.ccl.net> To: chemistry@www.ccl.net Subject: Sorry for the "Why not allow advertising on the Internet" message Cc: jkl@ccl.net Dear CCL, I want to apologize to the German speaking membership of the CCL for the spam which appeared on the list. I updated my filters with a number of keywords in German, and included paths to the origin for header checking. I hope that messages from at least this source will not spam the list again, but you never know how clever they are. It is encouraging that Internet is really international {:-(} and the spam is not only restricted to English. Jan Labanowski jkl@ccl.net From genghis@darkwing.uoregon.edu Thu Aug 14 11:17:37 1997 Received: from darkwing.uoregon.edu for genghis@darkwing.uoregon.edu by www.ccl.net (8.8.3/950822.1) id KAA14068; Thu, 14 Aug 1997 10:29:47 -0400 (EDT) Received: from localhost (genghis@localhost) by darkwing.uoregon.edu (8.8.7/8.8.7) with SMTP id HAA29073; Thu, 14 Aug 1997 07:29:42 -0700 (PDT) Date: Thu, 14 Aug 1997 07:29:42 -0700 (PDT) From: "Dale A. Braden" To: ANDREAS HOEFER cc: chemistry@www.ccl.net Subject: Re: CCL:G:output of frequency calculations in G94 In-Reply-To: <01IMFBRUAEXE9KMKLJ@MZDMZA.ZDV.UNI-MAINZ.DE> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Andreas, There is a size-based cutoff in G94 for printing of certain kinds of information, such as internal force constants, etc. Using IOp(7/33=1) will override this, and should give you the additional information you want. Best wishes, Dale Dale Braden Department of Chemistry University of Oregon Eugene, OR 97403-1253 genghis@darkwing.uoregon.edu From elazhary@theochem.uni-stuttgart.de Thu Aug 14 11:22:20 1997 Received: from artemis.rus.uni-stuttgart.de for elazhary@theochem.uni-stuttgart.de by www.ccl.net (8.8.3/950822.1) id KAA14091; Thu, 14 Aug 1997 10:34:28 -0400 (EDT) Received: from tc8.theochem.uni-stuttgart.de (tc8.theochem.uni-stuttgart.de [129.69.55.128]) by artemis.rus.uni-stuttgart.de with SMTP id QAA11602 (8.6.13/IDA-1.6 for ); Thu, 14 Aug 1997 16:34:25 +0200 Message-ID: <199708141434.QAA11602@artemis.rus.uni-stuttgart.de> Received: by tc8.theochem.uni-stuttgart.de (1.38.193.4/16.2/BelWue-2.1) id AA02567; Thu, 14 Aug 1997 16:34:25 +0200 From: "Dr. Adel El-Azhary" Subject: personal workstation To: chemistry@www.ccl.net Date: Thu, 14 Aug 97 16:34:25 METDST Mailer: Elm [revision: 70.85] Dear CCL members: I sent today morning a question about the speed of the new digital workstations a- and i-series. I just have been told that there is a new product call au-series and uses the unix operation system. So does anyone know how fast these workstation compared to the normal alpha workstations and whether the gaussian program would support them. Best regards, Adel El-Azhary From basmith@pollux.chem.umn.edu Thu Aug 14 12:17:45 1997 Received: from pollux.chem.umn.edu for basmith@pollux.chem.umn.edu by www.ccl.net (8.8.3/950822.1) id LAA14518; Thu, 14 Aug 1997 11:33:28 -0400 (EDT) Received: from localhost by pollux.chem.umn.edu via SMTP (950413.SGI.8.6.12/950213.SGI.AUTOCF) for id KAA12807; Thu, 14 Aug 1997 10:33:28 -0500 Date: Thu, 14 Aug 1997 10:33:27 -0500 (CDT) From: "Bradley A. Smith" To: chemistry@www.ccl.net Subject: xvibs Version 4.0.1 In-Reply-To: <199708141345.JAA04753@krakow.ccl.net> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII A maintenance release of xvibs is available in the CCL archive. The new version has these bug fixes: - Fixed bug in g94ReadFrequencies() which would only read frequencies if there were no negative frequencies. (Affected transition state calculations) - Correction for when energy not found. (Affected Gaussian94 MCSCF calculations) - Fixed bug which always wrote vectors for first frequency. (Thanks to Peter Freunscht) This new version is available at ftp://ftp.ccl.net/pub/chemistry/software/SOURCES/C/xvibs -- Bas ----- Bradley A. Smith basmith@pollux.chem.umn.edu Chemistry Department http://pollux.chem.umn.edu/~basmith/ University of Minnesota (612) 624-1535 From dsmith@CTCnet.Net Thu Aug 14 12:29:53 1997 Received: from home.ctcnet.net.CTCnet.Net for dsmith@CTCnet.Net by www.ccl.net (8.8.3/950822.1) id LAA14345; Thu, 14 Aug 1997 11:20:24 -0400 (EDT) Received: from fock by home.ctcnet.net.CTCnet.Net (SMI-8.6/SMI-SVR4) id LAA13167; Thu, 14 Aug 1997 11:19:54 -0400 Message-Id: <3.0.1.32.19970814111823.009d6cc0@pop.dasgroup.com> X-Sender: dsmith@pop.dasgroup.com X-Mailer: Windows Eudora Light Version 3.0.1 (32) Date: Thu, 14 Aug 1997 11:18:23 -0400 To: Jan Labanowski From: "Douglas A. Smith Ph.D." Subject: Re: CCL:Sorry for the "Why not allow advertising on the Internet" message Cc: CHEMISTRY@www.ccl.net In-Reply-To: <199708141345.JAA04753@krakow.ccl.net> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Jan: A warning to us all lest we succumb to the internet lingo... Did you see the newscript article on page 60 of the 11 August 1997 C&E News? spamming has led to legal action both by internet access providers as well as by Hormel Foods, makers of Spam. Doug At 09:45 AM 8/14/97 -0400, you wrote: >Dear CCL, > >I want to apologize to the German speaking membership of the CCL for the >spam which appeared on the list. I updated my filters with a number of >keywords in German, and included paths to the origin for header checking. >I hope that messages from at least this source will not spam the list >again, but you never know how clever they are. >It is encouraging that Internet is really international {:-(} and >the spam is not only restricted to English. > >Jan Labanowski >jkl@ccl.net > > >-------This is added Automatically by the Software-------- >-- Original Sender Envelope Address: jkl@ccl.net >-- Original Sender From: Address: jkl@ccl.net >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 > > > -- Dr. Douglas A. Smith, President and CEO | voice: (814) 255-7859 The DASGroup, Inc. | fax: (814) 255-3517 1732 Lyter Drive, 2nd Floor | email: dsmith@dasgroup.com Johnstown, PA 15905 | WWW: http://www.dasgroup.com Contract R&D specialists in modeling, simulation, and synthesis for chemistry, materials science, and biotechnology. From bruno@antas.agraria.uniss.it Thu Aug 14 14:17:38 1997 Received: from ICINECA.CINECA.IT for bruno@antas.agraria.uniss.it by www.ccl.net (8.8.3/950822.1) id NAA15780; Thu, 14 Aug 1997 13:56:57 -0400 (EDT) Received: from cinymp.cineca.it by ICINECA.CINECA.IT (IBM VM SMTP V2R2) with TCP; Thu, 14 Aug 97 19:58:11 ITA Received: from antas.agraria.uniss.it by cinymp.cineca.it with SMTP (5.61/CRI-80.1) id AA39369; Thu, 14 Aug 97 19:57:06 +0200 Date: Thu, 14 Aug 1997 19:56:22 +0100 (NFT) From: "Dr. Bruno Manunza" To: David Young Cc: CHEMISTRY@www.ccl.net Subject: Re: CCL:HF Limit In-Reply-To: Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Wed, 13 Aug 1997, David Young wrote: > > Hi, > > I've searched a number of sources and not come up with anything, > so I'm hoping someone can send me a reference or point me in the right > direction. > > What I am looking for is a proof of the existence of the > Hartree-Fock limit. Is it possible that this is an observed result for > which no derivation has ever been done? > > Dave Young > youngd2@mail.auburn.edu > Dear Dave, if you are looking for a mathematical proof of the variational theorem on which the Hartree-Fock theory is based, you may have a look to: H. Margenau, G.M. Murphy. The Mathematics of Physics and Chemistry. Van Nostrand. Toronto. 1956. The theorem is discussed in the chapter 11.18 (Quantum Mechanics-Variational Method). Bye Bruno 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