From yosimori@translell.tutkie.tut.ac.jp Tue Dec 5 01:10:49 1995 Received: from translell.translell.tutkie.tut.ac.jp for yosimori@translell.tutkie.tut.ac.jp by www.ccl.net (8.6.10/950822.1) id BAA25927; Tue, 5 Dec 1995 01:06:21 -0500 Received: (from yosimori@localhost) by translell.translell.tutkie.tut.ac.jp (8.7+2.6Wbeta/3.3W9) id PAA01438; Tue, 5 Dec 1995 15:09:08 +0900 (JST) Date: Tue, 5 Dec 1995 15:09:08 +0900 (JST) Message-Id: <199512050609.PAA01438@translell.translell.tutkie.tut.ac.jp> To: CHEMISTRY@www.ccl.net Cc: yosimori@translell.tutkie.tut.ac.jp Subject: Peptide interaction From: yosimori@translell.tutkie.tut.ac.jp (Atsushi Yoshimori) X-Mailer: mnews [version 1.19] 1995-07/21(Fri) I'm working on a program for peptide interaction. I would like to compare my result with some factual data. Cuuld any of you please give me a reference,or supply data on the geometry of two peptides at interaction ? Thanks in advance A.Yoshimori yosimori@translell.tutkie.tut.ac.jp From vergoten@POP.univ-lille1.fr Tue Dec 5 04:40:52 1995 Received: from lilserv.univ-lille1.fr for vergoten@POP.univ-lille1.fr by www.ccl.net (8.6.10/950822.1) id EAA28757; Tue, 5 Dec 1995 04:29:32 -0500 Received: from omega.univ-lille1.fr (omega.univ-lille1.fr [134.206.1.35]) by lilserv.univ-lille1.fr (8.7.1/jtpda-5.1) with SMTP id KAA27075 for ; Tue, 5 Dec 1995 10:26:48 +0100 (MET) Received: by omega.univ-lille1.fr; id AA02923; Tue, 5 Dec 1995 10:29:13 +0100 Message-Id: <9512050929.AA02923@omega.univ-lille1.fr> X-Sender: vergoten@pop.univ-lille1.fr Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Date: Tue, 05 Dec 1995 10:32:17 +0100 To: chemistry@www.ccl.net From: vergoten@POP.univ-lille1.fr (Gerard Vergoten) Subject: NATO-ASI on Biomolecular structure and dynamics X-Mailer: "NATO Advanced Study Institute" "BIOMOLECULAR STRUCTURE AND DYNAMICS: RECENT EXPERIMENTAL AND THEORICAL=20 ADVANCES" ASI LOUTRAKI, Greece May 27-June 6,1996 Contact: Professor G. VERGOTEN Address: Universit=E9 des Sciences et Technologies de Lille CRESIMM ( U 279 INSERM ) UFR de Chimie B=E2t C8 - 1er =E9tage 59655 VILLENEUVE D'ASCQ FRANCE FAX : (33) 20 33 72 79 E mail : vergoten@pop.univ-lille1.fr Designated Publisher: KLUWER From owner-chemistry@ccl.net Tue Dec 5 06:40:53 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id GAA29820; Tue, 5 Dec 1995 06:37:52 -0500 Received: from gaia.msicam.co.uk for rnobes@msicam.co.uk by bedrock.ccl.net (8.7.1/950822.1) id GAA19950; Tue, 5 Dec 1995 06:37:49 -0500 (EST) Received: by gaia.msicam.co.uk (940816.SGI.8.6.9/SMI-4.1 (MSI-Cambridge)) id LAA21978; Tue, 5 Dec 1995 11:32:14 GMT From: rnobes@msicam.co.uk (Ross Nobes) Message-Id: <199512051132.LAA21978@gaia.msicam.co.uk> Subject: Re: CCL:G94: B3LYP energy and Charge To: teoulf@pdc.kth.se (Ulf Ryde) Date: Tue, 5 Dec 1995 11:32:14 +0000 (GMT) Cc: chemistry@ccl.net Reply-To: rnobes@msi.com In-Reply-To: <199512011543.QAA34604@struve.pdc.kth.se> from "Ulf Ryde" at Dec 1, 95 04:43:10 pm X-Mailer: ELM [version 2.4 PL23] Content-Type: text Ulf Ryde writes: > > I have just started to use Gaussian, and I have noted two strange things > with G94: (I sent this question to info@gaussian.com two weeks ago, but > I have got no answer) > > 1. Gaussian does not give the same B3LYP energy as IBM:s Mulliken. > Who is right? The answer is that both are right! The Gaussian definition of B3LYP uses the VWN local correlation functional; most other programs use what Gaussian terms VWN5. Cheers, Ross -- +----------------------------------------------------------------+ | Dr Ross Nobes | | Senior Scientist, Quantum Mechanics ! | | | BIOSYM/Molecular Simulations | | 240/250 The Quorum Phone: + 44 1223 413300 | | Barnwell Road Fax: + 44 1223 413301 | | Cambridge CB5 8RE, UK E-mail: rnobes@msicam.co.uk | +----------------------------------------------------------------+ From sanja@indigo.irb.hr Tue Dec 5 09:10:56 1995 Received: from indigo.irb.hr for sanja@indigo.irb.hr by www.ccl.net (8.6.10/950822.1) id IAA01099; Tue, 5 Dec 1995 08:57:04 -0500 Received: by indigo.irb.hr (940816.SGI.8.6.9/930416.SGI.AUTO) for CHEMISTRY@www.ccl.net id OAA15118; Tue, 5 Dec 1995 14:56:59 -0800 From: "sanja" Message-Id: <9512051456.ZM15116@indigo.irb.hr> Date: Tue, 5 Dec 1995 14:56:49 -0800 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: CHEMISTRY@www.ccl.net Subject: NBO-summary Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Recently I posted a question: > Hello all, > > I am interested in the NBO program, version4.0, written by Glendening, Reed, > Carpenter and Weinhold. Some info how I can obtain it will be helpful. > Thanks!!! > > Best regards, > > Sanja the answer I got is: >Sanja, > >Contact Frank Weinhold at the University of Wisconsin >(weinhold@chem.wisc.edu). NBO 4.0 is copyrighted there and Frank >should have details on how you can obtain the code. > >Eric Glendening thanks to Eric Elendening for giving me this information. Sanja -- *~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~* Sanja Sekusak e-mail: sanja@indigo.irb.hr Rudjer Boskovic Institute phone: (385-1) 456 10 89 HR-10001 Zagreb, CROATIA fax: (385-1) 27 26 48 *~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~* From duanx@Picard.ml.wpafb.af.mil Tue Dec 5 09:41:01 1995 Received: from riker.ml.wpafb.af.mil for duanx@Picard.ml.wpafb.af.mil by www.ccl.net (8.6.10/950822.1) id JAA01729; Tue, 5 Dec 1995 09:34:57 -0500 Received: from picard.ml.wpafb.af.mil by riker.ml.wpafb.af.mil (5.65/Ultrix3.0-C) id AA03431; Tue, 5 Dec 1995 09:34:56 -0500 Received: by Picard.ml.wpafb.af.mil (4.1/version) id AA01924; Tue, 5 Dec 95 09:34:54 EST Date: Tue, 5 Dec 1995 09:34:53 -0500 (EST) From: Xiaofeng Duan To: CHEMISTRY@www.ccl.net Subject: help with compiling TCGMSG Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, there! I was trying to compile TCGMSG (version 4.04) toolkit for parallel GAMESS on SGI (operating system version 6.01) machine. But I never got it done. The error message says "-I/user/include/bsd" and "-I/usr/include/sun" do not refer to a valid directory. and the FATAL error is that there is no such file or directory for "-lsun". I searched /user/include directory and nerver found "bsd" and "sun" files there. Does anyone have any experience to compile TCGMSG on SGI and know how to overcome these problems? Thanks in advance! **************************************** Xiaofeng Duan, Ph. D. WL/MLBP, Bldg. 654 2941 P St. Ste. 1 Wright-Patterson AFB, OH 45433 (513)255-9164 duanx@Picard.ml.wpafb.af.mil **************************************** From owner-chemistry@ccl.net Tue Dec 5 11:10:57 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id LAA03384; Tue, 5 Dec 1995 11:00:39 -0500 Received: from struve.pdc.kth.se for teoulf@pdc.kth.se by bedrock.ccl.net (8.7.1/950822.1) id LAA22399; Tue, 5 Dec 1995 11:00:37 -0500 (EST) Received: (from teoulf@localhost) by struve.pdc.kth.se (8.6.10/8.6.9) id RAA34794 for chemistry@ccl.net; Tue, 5 Dec 1995 17:00:25 +0100 Date: Tue, 5 Dec 1995 17:00:25 +0100 From: Ulf Ryde Message-Id: <199512051600.RAA34794@struve.pdc.kth.se> To: chemistry@ccl.net Subject: Summary B3LYP energy and G94 Charge Dear netters, here is the answer to my two questions about Gaussian-94 (and Mulliken). 1. The B3LYP energies in G94 and Mulliken differs since they use different forms of the VWN functional: From: rnobes@msicam.co.uk (Ross Nobes) Subject: Re: CCL:G94: B3LYP energy and Charge Date: Tue, 5 Dec 1995 11:32:14 +0000 (GMT) The answer is that both are right! The Gaussian definition of B3LYP uses the VWN local correlation functional; most other programs use what Gaussian terms VWN5. Cheers, Ross +----------------------------------------------------------------+ | Dr Ross Nobes | | Senior Scientist, Quantum Mechanics ! | | | BIOSYM/Molecular Simulations | | 240/250 The Quorum Phone: + 44 1223 413300 | | Barnwell Road Fax: + 44 1223 413301 | | Cambridge CB5 8RE, UK E-mail: rnobes@msicam.co.uk | +----------------------------------------------------------------+ Similar answers also from Douglas J. Fox help@gaussian.com and Byron H Lengsfield, III bbyron@almaden.ibm.com 2. The Charge problem was a bug that is fixed in the current C.3 revision of Gaussian-94 (I used Rev. B.1). Thank you to all who has answered the questions. Ulf --------------------------------------------------------------- Dr. Ulf Ryde teoulf@garm.teokem.lu.se Assistant professor Department of Theoretical Chemistry University of Lund Chemical centre, P. O. Box 124 Tel: +46-46-2224502 S-221 00, Lund, SWEDEN Fax: +46-46-2224543 --------------------------------------------------------------- From dhr@chem.iupui.edu Tue Dec 5 11:25:57 1995 Received: from nitro.chem.iupui.edu for dhr@chem.iupui.edu by www.ccl.net (8.6.10/950822.1) id LAA03853; Tue, 5 Dec 1995 11:25:11 -0500 Received: by nitro.chem.iupui.edu (940816.SGI.8.6.9/MSU-2.04) id QAA22201; Tue, 5 Dec 1995 16:23:12 GMT Date: Tue, 5 Dec 1995 11:23:12 -0500 (EST) From: "Daniel H. Robertson" Subject: Return of the MacroModel List To: CHEMISTRY@www.ccl.net Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Announcing the return of the MacroModel list discribed below. Send requests for subscribing to mmod-request@chem.iupui.edu ** MacroModel List ** ------------------------------------------------------------------------------ The MacroModel mailing list is an uncensored e-mail exploder that allows MacroModel users to communicate with other users of MacroModel. This list is maintained by and for MacroModel users and is not supported directly by the MacroModel Development Group. However, some of the MacroModel developers may be members of the list and might be listening. 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URL: http://www.cc.columbia.edu/cu/chemistry/mmod/mmod.html academic inquires: other inquires: Contact: Joan Horgan Carol Parish E-Mail: jqh@still3.chem.columbia.edu carol@still3.chem.columbia.edu VOICE: (212) 854-8665 (212) 854-5143 or (718) 981-7875 FAX: (212) 854-5429 (718) 981-7875 technical questions: The Still Group E-Mail: mmod@still3.chem.columbia.edu VOICE: (212) 854-5143 or 8402 FAX: (212) 678-9039 ----------------------------------------------------------------------------- F | Dan Robertson, Ph.D., Assistant Scientist & Manager | I C | Facility for Computational Molecular and Biomolecular Science | U M | Department of Chemistry http://chem.iupui.edu | P B | Indiana University - Purdue University Indianapolis | U S | robertson@chem.iupui.edu (317) 278-2202 | I From owner-chemistry@ccl.net Tue Dec 5 11:55:58 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id LAA04345; Tue, 5 Dec 1995 11:43:19 -0500 Received: from QUCDN.QueensU.CA for dickson@chem.QueensU.CA by bedrock.ccl.net (8.7.1/950822.1) id LAA23025; Tue, 5 Dec 1995 11:43:11 -0500 (EST) Received: from chem.QueensU.CA by QUCDN.QueensU.CA (IBM VM SMTP V2R2) with TCP; Tue, 05 Dec 95 11:38:27 EST Received: by chem.QueensU.CA (4.1/SMI-4.0) id AA19595; Tue, 5 Dec 95 11:50:35 EST Date: Tue, 5 Dec 95 11:50:35 EST From: dickson@chem.QueensU.CA (Ross Dickson) Message-Id: <9512051650.AA19595@chem.QueensU.CA> To: chemistry@ccl.net Subject: G94 LSDA confusion Ulf Ryde writes: > 1. Gaussian does not give the same B3LYP energy as IBM:s Mulliken. > Who is right? Ross Nobes replies: >The answer is that both are right! The Gaussian definition of B3LYP >uses the VWN local correlation functional; most other programs use >what Gaussian terms VWN5. I think this is worth amplifying. Those of you who started using density functional theory when Gaussian brought it out will want to pay attention. Sorry if this takes a few moments: The most common local spin-density approximation (LSDA) functional used these days is that of Vosko, Wilk and Nusair (VWN). Everybody knows that. Unfortunately, what some people don't realize is that there's more than one "VWN functional" out there. Look in your Gaussian 94 (or G92/DFT) manual and you'll see them both. In their famous paper [S. H. Vosko, L. Wilk, and M. Nusair, Can. J. Phys. 58(8), 1200 (1980)] VWN describe a number of different functionals as they search for the "best fit" to the homogeneous electron gas correlation energy -- i.e., the LSDA correlation functional. Along the way they include parameters for fitting their Pade approximant expression to an RPA description of the electron gas, a well-established-but-not-state-of-the-art approximation. Then in a table caption (!) they give the parameters which fit the same form to Ceperley & Alder's quantum Monte Carlo calculations on the electron gas. The Ceperley & Alder data is considered the "last word" on LSDA correlation by most experts in the field, so of these two sets of parameters, the latter ones are preferred. Unfortunately, the folks at Gaussian chose to implement the former as the default LSDA correlation functional -- though the latter functional *is* available under the keyword "VWN5". I haven't put a lot of effort into determining why they did things this way, but it may have something to do with the fact that in Appendix E of Parr & Yang's "Density Functional Theory of Atoms and Molecules", the RPA-fitting parameters are given "as the most accurate available for the uniform-gas correlation energy". If you don't know whether to believe Robert Parr and the Gaussian programmers or this post-doc from Canada on this point, you have a couple of choices: (1) You can read the VWN paper yourself -- and good luck, it's not an easy read. You'll understand why there's some confusion. (2) If you have access to G94, you can appeal to a third party: John Perdew, author of a couple of LSDA-fits of his own. Perdew & Zunger's 1981 fit [Phys. Rev. B 23(10), 5048 (1981)] to the same Ceperley & Alder quantum Monte Carlo data is included in Gaussian under the keyword "PL". If you run Gaussian jobs on, say, the hydrogen atom, 6-31G*, you will find: E (hartrees) "VWN" -.493937 "VWN5" -.476044 "PL" -.476230 This clearly indicates that "VWN5" and "PL" are fits to the same data, while "VWN" is something else. Unfortunately, what Gaussian has called "VWN5" is what such people as John Perdew and Axel Becke call "LSDA", while what Gaussian calls "LSDA" or "VWN" is something they don't use anymore. How much difference does all this make? I don't know. Not much, I suspect. Despite the startling difference in total energies above, the dissociation energy of the hydrogen molecule differs by only 0.2 kcal/mol among the three LSDA methods. But this inconsistency in naming between Gaussian and every other density functional program in the business is potentially quite troublesome. Ross M. Dickson, Ph.D. dickson@chem.queensu.ca Dept. of Chemistry, Queen's University at Kingston, Ontario, Canada From owner-chemistry@ccl.net Tue Dec 5 12:40:58 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id MAA05448; Tue, 5 Dec 1995 12:28:58 -0500 Received: from relay5.UU.NET for frisch@lorentzian.com by bedrock.ccl.net (8.7.1/950822.1) id MAA23397; Tue, 5 Dec 1995 12:28:56 -0500 (EST) Received: from uucp3.UU.NET by relay5.UU.NET with SMTP id QQzsvd05176; Tue, 5 Dec 1995 12:28:49 -0500 (EST) Received: from m10.UUCP by uucp3.UU.NET with UUCP/RMAIL ; Tue, 5 Dec 1995 12:28:51 -0500 Received: from mjf by m10.lorentzian.com; Tue, 5 Dec 1995 12:30:57 -0500 Received: by mjf (AIX 4.1/UCB 5.64/4.03) id AA14738; Tue, 5 Dec 1995 12:30:57 -0500 From: frisch@lorentzian.com (Mike Frisch) Message-Id: <9512051730.AA14738@mjf> Subject: Re: CCL:G:G94: B3LYP energy and Charge To: chemistry@ccl.net Date: Tue, 5 Dec 1995 12:30:57 -0500 (EST) In-Reply-To: <199512051132.LAA21978@gaia.msicam.co.uk> from "" at Dec 5, 95 11:32:14 am X-Mailer: ELM [version 2.4 PL24] Content-Type: text Ross Nobes writes: > > Ulf Ryde writes: > > > > I have just started to use Gaussian, and I have noted two strange things > > with G94: (I sent this question to info@gaussian.com two weeks ago, but > > I have got no answer) > > > > 1. Gaussian does not give the same B3LYP energy as IBM:s Mulliken. > > Who is right? > > The answer is that both are right! The Gaussian definition of B3LYP > uses the VWN local correlation functional; most other programs use > what Gaussian terms VWN5. > No, B3LYP was defined to use VWN3. Using the same name for two different functionals is a disservice to everyone and makes reproducing other peoples results impossible. This used to be a major problem in the DFT area, and things are finally improving with regard to terminology. To take a name for something that is specified in the literature and use it for something different is a major step backwards. Published and in-press tests of B3LYP all use VWN3; an assumption that the same conclusions apply to a different functional just because it has the same name are not valid. Mike Frisch frisch@lorentzian.com From Omar.Stradella@sgibos.boston.sgi.com Tue Dec 5 15:26:02 1995 Received: from sgigate.sgi.com for Omar.Stradella@sgibos.boston.sgi.com by www.ccl.net (8.6.10/950822.1) id PAA08262; Tue, 5 Dec 1995 15:15:47 -0500 Received: from sgihub.corp.sgi.com by sgigate.sgi.com via ESMTP (950911.SGI.8.6.12.PATCH825/940406.SGI) id MAA24964; Tue, 5 Dec 1995 12:15:44 -0800 Received: from sgibos.boston.sgi.com by sgihub.corp.sgi.com via SMTP (950511.SGI.8.6.12.PATCH526/911001.SGI) id MAA15143; Tue, 5 Dec 1995 12:15:42 -0800 Received: from arkham.boston.sgi.com by sgibos.boston.sgi.com via SMTP (931110.SGI/940406.SGI) for @sgihub.corp.sgi.com:duanx@Picard.ml.wpafb.af.mil id AA07420; Tue, 5 Dec 95 15:15:39 -0500 Received: by arkham.boston.sgi.com (940816.SGI.8.6.9/940406.SGI.AUTO) id PAA29426; Tue, 5 Dec 1995 15:15:35 -0500 From: "Omar G. Stradella" Message-Id: <9512051515.ZM29424@arkham.boston.sgi.com> Date: Tue, 5 Dec 1995 15:15:12 -0500 In-Reply-To: Xiaofeng Duan "CCL:help with compiling TCGMSG" (Dec 5, 9:34am) References: Organization: Silicon Graphics, Inc. Reply-To: Omar.Stradella@sgibos.boston.sgi.com X-Mailer: Z-Mail (3.2.2 10apr95 MediaMail) To: Xiaofeng Duan , CHEMISTRY@www.ccl.net Subject: Re: CCL:help with compiling TCGMSG Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii On Dec 5, 9:34am, Xiaofeng Duan wrote: > Subject: CCL:help with compiling TCGMSG > Hi, there! > I was trying to compile TCGMSG (version 4.04) toolkit for parallel GAMESS > on SGI (operating system version 6.01) machine. But I never got it done. > The error message says "-I/user/include/bsd" and "-I/usr/include/sun" do > not refer to a valid directory. and the FATAL error is that there is no > such file or directory for "-lsun". I searched /user/include directory > and nerver found "bsd" and "sun" files there. Does anyone have any > experience to compile TCGMSG on SGI and know how to overcome these problems? > Thanks in advance! Those directories/libraries aren't needed anymore. You'll need a 64 or n32 version of TCGMSG to take advantage of the R8000 architecture, you can get one from the anonymous ftp at: ftp.sgi.com:/pub/tcgmsg.4.04.r8k.tar.Z Omar. -- +-------------------------------------------------------------------+ Omar G. Stradella, Ph.D. Silicon Graphics, Inc. E-mail: omar@boston.sgi.com Computational Chemistry Phone: +1-(508) 567-2258 http://www.sgi.com/ChemBio FAX: +1-(508) 562-4755 http://reality.sgi.com/employees/omar +------ Ph-nglui mglw'nafh Cthulhu R'lyeh wgah'nagl fhtagn -------+