From batra@urz.unibas.ch Wed Apr 20 04:29:56 1994 Received: from chx400.switch.ch for batra@urz.unibas.ch by www.ccl.net (8.6.4/930601.1506) id EAA13669; Wed, 20 Apr 1994 04:25:02 -0400 X400-Received: by mta chx400.switch.ch in /PRMD=switch/ADMD=arcom/C=CH/; Relayed; Wed, 20 Apr 1994 10:23:20 +0200 X400-Received: by /PRMD=SWITCH/ADMD=ARCOM/C=CH/; Relayed; Wed, 20 Apr 1994 11:22:36 +0200 Date: Wed, 20 Apr 1994 11:22:36 +0200 X400-Originator: batra@urz.unibas.ch X400-Recipients: non-disclosure:; X400-MTS-Identifier: [/PRMD=SWITCH/ADMD=ARCOM/C=CH/;940420102236] X400-Content-Type: P2-1984 (2) Content-Identifier: 91 Conversion: Prohibited Alternate-Recipient: Allowed From: Rohit Batra Message-ID: <91*/S=batra/OU=urz/O=unibas/PRMD=SWITCH/ADMD=ARCOM/C=CH/@MHS> To: CHEMISTRY Subject: PARALLEL ab initio Dear Netters, Does anyone know about ab initio packages which can optimize open shell species (UHF-, UMP2-Wavefunctions) **PARALLEL** on distributed memory machines? Should there be any responses please reply to me personally I will summarize and send the summary to the list. Thanks a lot, Rohit Batra ========================================================================== Rohit Batra Institute for Organic Chemistry email: batra@urz.unibas.ch University of Basel St. Johanns-Ring 19 fax: 061/322 66 17 4056 Basel Switzerland voice: 061/322 60 60 ========================================================================== From chp1aa@surrey.ac.uk Wed Apr 20 05:30:01 1994 Received: from mail-server.surrey.ac.uk for chp1aa@surrey.ac.uk by www.ccl.net (8.6.4/930601.1506) id FAA14083; Wed, 20 Apr 1994 05:28:36 -0400 Received: from central.surrey.ac.uk by mail-server.surrey.ac.uk with SMTP using (PP) id <26573-0@mail-server.surrey.ac.uk>; Wed, 20 Apr 1994 10:27:57 +0100 Received: by central.surrey.ac.uk (1.37.109.8/16.2) id AA05578; Wed, 20 Apr 1994 10:27:56 +0100 From: Mr Andrew D Allen Message-Id: <9404200927.AA05578@central.surrey.ac.uk> Subject: Crystal structures of Ribonuclease To: chemistry@ccl.net Date: Wed, 20 Apr 94 10:27:56 BST Mailer: Elm [revision: 70.85] My colleague and I have been trying to find well resolved x-ray structures of Ribonuclease A or S, with or without bound inhibitors. The Brookhaven database has only three structures with bound inhibitors, and of these teo are retro- bound. I ask if anyone on the net knows of any other structures that have not been published and are in the public domain or otherwise. We need as many different structures as possible for a QSAR study. Thank Andy. PS. QM - MM or Semi-Emp, I say horses for courses. -- ############################################################################### Structural and Computation Chemistry Group_________chp1aa@uk.ac.surrey - JANET. Department of Chemistry____________________________phone_______+44(483)-259591. University of Surrey_______________________________fax_________+44(483)-300803. Guildford, Surrey, GU2 5XH, UK_____________________ftp____________131.227.110.2 ############################################################################### From DURRAN@chem.surrey.ac.uk Wed Apr 20 06:30:30 1994 Received: from mail-server.surrey.ac.uk for DURRAN@chem.surrey.ac.uk by www.ccl.net (8.6.4/930601.1506) id GAA14388; Wed, 20 Apr 1994 06:05:23 -0400 Received: from central.surrey.ac.uk by mail-server.surrey.ac.uk with SMTP using (PP) id <26689-0@mail-server.surrey.ac.uk>; Wed, 20 Apr 1994 10:57:16 +0100 Received: from chemcharon.chem.surrey.ac.uk by central.surrey.ac.uk with SMTP (1.37.109.8/16.2) id AA09740; Wed, 20 Apr 1994 10:57:12 +0100 Received: From CHEMISTRY-1/WORKQUEUE by chemcharon.chem.surrey.ac.uk via Charon-4.0-VROOM with IPX id 100.940420105704.384; 20 Apr 94 11:00:39 +500 Message-Id: To: chemistry@ccl.net From: Michael Organization: Chemistry Department, Uni of Surrey Date: Wed, 20 Apr 1994 10:56:51 GMT Subject: GIAO reference Priority: normal X-Mailer: WinPMail v1.0 (R1) Hello, Does anybody know if a there is an english translation in the literature of the reference by London : F. London, J. Phys. Radium 8, 397, (1937). Thanks, Mike. (DURRAN@CHEM.SURREY.AC.UK) From CUNDARIT@MSUVX1.MEMST.EDU Wed Apr 20 08:29:59 1994 Received: from msuvx1.memst.edu for CUNDARIT@MSUVX1.MEMST.EDU by www.ccl.net (8.6.4/930601.1506) id HAA15484; Wed, 20 Apr 1994 07:39:35 -0400 Received: from MSUVX1.MEMST.EDU by MSUVX1.MEMST.EDU (PMDF V4.2-14 #5958) id <01HBE00RWLE88X07SK@MSUVX1.MEMST.EDU>; Wed, 20 Apr 1994 06:39:27 CST Date: Wed, 20 Apr 1994 06:39:27 -0600 (CST) From: CUNDARIT@MSUVX1.MEMST.EDU Subject: Re: CCL:PARALLEL ab initio To: batra@urz.unibas.ch Cc: chemistry@ccl.net Message-id: <01HBE00RZ9UA8X07SK@MSUVX1.MEMST.EDU> X-VMS-To: IN%"batra@urz.unibas.ch" X-VMS-Cc: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Hi, Parallel-GAMESS will do the UHF optimization in parallel on a bunch of different parallel platforms. To date, we have run it on an IBM SP1, KSR-1, CM-5, Paragon, iPSC/860, and the Iowa State folks have run it across heterogeneous Ethernetworks of UNIX workstations. I believe there exists a version for the nCUBE. The above refers t the US version of GAMESS. I also believe there is good parallel capability in the UK version, although I have not used it. Tom From jpleiss@orgch01.chemie.uni-stuttgart.de Wed Apr 20 08:46:26 1994 Received: from noc.BelWue.DE for jpleiss@orgch01.chemie.uni-stuttgart.de by www.ccl.net (8.6.4/930601.1506) id HAA15504; Wed, 20 Apr 1994 07:46:42 -0400 Received: from orgch01.chemie.uni-stuttgart.de by noc.BelWue.DE with SMTP id AA02229 (5.65c8/IDA-1.4.4 for ); Wed, 20 Apr 1994 13:46:33 +0200 Received: by orgch01.chemie.uni-stuttgart.de (920330.SGI/BelWue-1.0SG(subsidiary)) (for chemistry@ccl.net) id AA22171; Wed, 20 Apr 94 13:52:34 +0200 Date: Wed, 20 Apr 94 13:52:34 +0200 From: jpleiss@orgch01.chemie.uni-stuttgart.de (Jurgen Pleiss) Message-Id: <9404201152.AA22171@orgch01.chemie.uni-stuttgart.de> To: chemistry@ccl.net Subject: Spectroscopy database Dear colleagues: Can anyone give me a hint where to find a database on spectroscopic data of small molecules, e.g. the wavelength of the absorption and emission maximum of fluorescence. Thanks for your help, Jurgen ================================================================================ Jurgen Pleiss Email:jpleiss@orgch01.chemie.uni-stuttgart.de Institute for Organic Chemistry Phone:(49)-711-6854260 University of Stuttgart Fax: (49)-711-6854269 D-70569 Stuttgart Germany From ipcakc@vigyan.iisc.ernet.in Wed Apr 20 08:50:04 1994 Received: from relay1.UU.NET for ipcakc@vigyan.iisc.ernet.in by www.ccl.net (8.6.4/930601.1506) id HAA15520; Wed, 20 Apr 1994 07:51:03 -0400 From: Received: from iisc.ernet.in (via iisc.iisc.ernet.in) by relay1.UU.NET with SMTP (5.61/UUNET-internet-primary) id AAwmlb14667; Wed, 20 Apr 94 07:50:56 -0400 Received: by iisc.ernet.in (ERNET-IISc/AT&T UNIX SYS V.3.2) id AA18288; Wed, 20 Apr 94 16:47:41 EDT Received: by vigyan.iisc.ernet.in (smail2.3) id AA21480; 20 Apr 94 16:14:53 EST (Wed) To: CHEMISTRY@ccl.net Subject: imaginary frequencies Date: 20 Apr 94 16:14:53 EST (Wed) Message-Id: <9404201614.AA21480@vigyan.iisc.ernet.in> Dear netters, I have done frequency calculations along the potential energy surface right from the reactants to the transition state. At the reactants, as expected, I get all Positive Frequencies and at the Transition State, as again expected, I get one and only one imaginary frequency. But, interestingly, along the surface, with respect to the reaction coordinate of my choice, I get a negative (imaginary) frequency and it develops to a larger imaginary frequency (i.e. for ex. -300.00 cm-1 to -1800.00 cm-1). Now the question is, any point along the surface is a neither a maxima nor a minima with respect to the other reaction coordinate (unlike transition state which is THE maxima along the reaction coordinate). So why do we observe the imaginary frequency along the surface? These frequencies are calculated for a metathetical reaction like R-H + R' ----> R + H-R' where R and R' are alkyl substrates. Please mail your answers to the following address : ipcakc@ipc.iisc.ernet.in Thanks in advance, V. Sridhar, Dept. of I.P.C., I.I.Sc., Bangalore - 560 012 - India. P.S: The Program used is Gaussian92. From burkhart@goodyear.com Wed Apr 20 09:30:03 1994 Received: from goodyear.com for burkhart@goodyear.com by www.ccl.net (8.6.4/930601.1506) id JAA16687; Wed, 20 Apr 1994 09:28:16 -0400 Received: from rdsrv2 by goodyear.com (4.1/SMI-4.1) id AA09535; Wed, 20 Apr 94 09:28:12 EDT Received: from rds325 by rdsrv2 (4.1/SMI-4.1) id AA08925; Wed, 20 Apr 94 09:28:12 EDT Received: by rds325 (920330.SGI/920502.SGI.AUTO) for @rdsrv2:chemistry@ccl.net id AA25170; Wed, 20 Apr 94 09:28:11 -0400 Date: Wed, 20 Apr 94 09:28:11 -0400 From: burkhart@goodyear.com (Craig W. Burkhart) Message-Id: <9404201328.AA25170@rds325> To: chemistry@ccl.net Subject: Latest Feud... Netters: Joe Golab is right when he says that the debate about REAL CHEMISTRY is inane. As a matter of fact, one could argue that all of science is nothing more than model building (yes, experimentalists construct models, too). Von Neumann said about 40 years ago that the best we can expect out of science in general is modelbuilding. It is a great human achievement, because it gives us a framework to test our ideas for their strengths and shortcomings. Without models, we would be stuck in the first stage of understanding--the trial and error phase. Or worse yet, we could be stuck, as the modern philosophical movement is, with words and nothing to test them against. Without waxing too much, models are what we should always be trying to build and use. It is what we as scientists do (hopefully) well. I will, however, not bend to people who spout their region of chemistry to be REAL CHEMISTRY, and everyone else's is just function-fitting. To me, that is the worst kind of elitism because it is not justified. Let's not get into the game of "my model is better than your model", unless we are comparing apples with apples. -------------------------------------------------------------------------- Craig W. Burkhart, Ph.D. Senior Research Chemist E-mail: cburkhart@goodyear.com The Goodyear Tire & Rubber Co. Fone: 216.796.3163 Research Center Fax: 216.796.3304 142 Goodyear Boulevard Akron, OH 44305 -------------------------------------------------------------------------- For a successful technology, reality must take precedence over public relations, for Nature cannot be fooled - Feynman -------------------------------------------------------------------------- From JKONG@ac.dal.ca Tue Apr 19 23:29:53 1994 Received: from SYSWRK.UCIS.DAL.CA for JKONG@ac.dal.ca by www.ccl.net (8.6.4/930601.1506) id WAA11690; Tue, 19 Apr 1994 22:41:08 -0400 Received: from AC.Dal.Ca by SYSWRK.UCIS.DAL.CA (PMDF V4.2-14 #2545) id <01HBDLEVQD34006IQW@SYSWRK.UCIS.DAL.CA>; Tue, 19 Apr 1994 23:38:58 -0400 Received: from AC.DAL.CA by AC.DAL.CA (PMDF V4.2-14 #2545) id <01HBDLCTQDOW00HE71@AC.DAL.CA>; Tue, 19 Apr 1994 23:38:50 -0300 Date: Tue, 19 Apr 1994 23:38:50 -0300 From: JING KONG Subject: More flame? Was: Semiempirical parameterization ... To: chemistry@ccl.net Message-id: <01HBDLCTRPXE00HE71@AC.DAL.CA> X-VMS-To: IN%"chemistry@ccl.net" X-VMS-Cc: MORE FLAME? WAS: SEMIEMPIRICAL PARAMETERIZATION ... MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Dear netters, The discussion raised from parameterization of semiempirical methods seemingly becomes more or less about the philosophies behind different approaches. I would like to add some comments to what Holder, Letner and Burkhart wrote. But most time I will use E.R. Davidson's words since he is one of the few who made major contributions to the mainstream QM ab initio methods (and thus is more authoritive :-).) His words are in quotation marks. Holder wrote: > I can safely say that MM has nothing to do with chemistry, > but is more or less a fit to a convenient set of functions. It > does have chemical validity in that it gives us good answers to some > questions. Letner replied, >However MM force fields do have terms that model chemical phenomenon. >Examples include bond angles, bond lengths, etc. Granted, these are Bond angles and bond lengths were in Chemistry many, many years ago (100?). Can MM say more about bond angles and bond lengths than numbers? Holder wrote: > QM is an entirely different situation, in that the actual arbiters of > chemistry, the electrons, are treated directly by mathematical functions. > The chemistry come OUT of a model that describes the electrons. Unfortunately, not much chemistry have come out so far from mainstream QM methods. "Finally, with most modern programs, the user is left with exactly the same information that Pauling started with 60 years ago." Letner wrote: > Further, is not any mathmatical fomalism a model? This is to >include QM, a more detailed and complicated model of atomic events. Yes, I agree. QM approach (I mean mainstream such as ab initio and DFT) based on the same philosophy as MM: use mathematical models derived approximately from physical laws to produce numbers. Does this approach work? "It will be noticed that the Nobel prizes in quantum chemistry have gone to Pauling, Mulliken, Hoffmann, Fukui, and Lipscomb. All of these people are noted for the models of the chemical bond that they have developed and used to explain important chemical phenomena. Even in the computer age, they focused on incorrect, but useful, empirical wavefunctions. The insights that they obtained were not found on any computer pritout." Simply, Chemistry is neither Physics nor Mathematics. One may hope that QM would work quantitatively. "Atomic orbitals do not work. The error in a wave function is largest where the wavefunction is largest. The computer cost, at fixed accuracy, grows like N!." I feel that an optimal solution should be good both quantitatively and qualitatively. All of these are concerned only by method developers and those who want to understand more about the chemistry part of the nature. For those practical users, take what Burkhart wrote: >The faith comes in the numbers...the better the numbers, the >better the faith. No more, no less. And, be happy. Jing Kong Dalhousie Last quote: "Computers do not solve problems, people do." in Reviews in Computational Chemistry, Kenny B. Lipkowitz and Donald B. Boyd Eds., VCH 1990. From ferenc@rchsg8.chemie.uni-regensburg.de Wed Apr 20 10:34:34 1994 Received: from comsun.rz.uni-regensburg.de for ferenc@rchsg8.chemie.uni-regensburg.de by www.ccl.net (8.6.4/930601.1506) id KAA17732; Wed, 20 Apr 1994 10:28:09 -0400 Received: from rchsg8.chemie.uni-regensburg.de by comsun.rz.uni-regensburg.de with SMTP id AA21043 (5.65c/IDA-1.4.4 for ); Wed, 20 Apr 1994 16:27:56 +0200 Received: by rchsg8.chemie.uni-regensburg.de (920330.SGI/URRZ-Sub-1.5-irix) (for CHEMISTRY@ccl.net) id AA19463; Wed, 20 Apr 94 16:25:56 +0200 Date: Wed, 20 Apr 94 16:25:56 +0200 From: Ferenc.Molnar@chemie.uni-regensburg.de (Ferenc Molnar) Message-Id: <9404201425.AA19463@rchsg8.chemie.uni-regensburg.de> To: CHEMISTRY@ccl.net Subject: force fields Dear Netters: A few days ago I posted the following request: >I was wondering if anybody out there could give me >a reference to a good review or book covering the >following topics: >1) Where to find a good (and complete) compilation > of empirical force field parameters > (AMBER, MMX, etc.) >2) How to derive forces acting on individual atoms > from a given empirical force field, > consisting of e.g.: bond stretch, > angle bending, torsional potential terms etc. I would like to thank everbody who answered and especially Dr. Eberhard von Kitzing for his list of references! Here is the summary: ________________________________________________________________________________ From lipkowitz@chem.iupui.edu Tue Apr 12 19:53:34 1994 Received: from comsun.rz.uni-regensburg.de by rchsg8.chemie.uni-regensburg.de via SMTP (920330.SGI/URRZ-Sub-1.5-irix) (for ferenc) id AA02838; Tue, 12 Apr 94 19:53:34 +0200 Received: from indyvax.iupui.edu by comsun.rz.uni-regensburg.de with SMTP id AA09430 (5.65c/IDA-1.4.4 for ); Tue, 12 Apr 1994 19:55:29 +0200 Received: from macgw.chem.iupui.edu by INDYVAX.IUPUI.EDU (PMDF V4.2-12 #5862) id <01HB36VAA300003YHQ@INDYVAX.IUPUI.EDU>; Tue, 12 Apr 1994 12:54:21 -0500 Date: Tue, 12 Apr 1994 12:51:37 +0000 (U) From: Lipkowitz Subject: RE: CCL:force fields and forces To: Ferenc Molnar Message-Id: <01HB36VAACNM003YHQ@INDYVAX.IUPUI.EDU> Content-Transfer-Encoding: 7BIT Status: R A compilation of MM2 parameters that have been published can be found in: K.B.Lipkowitz "MM2 Parameters" QCPE Bulletin, 12(1), 6-11, 1992 and a list of published parameters for all force fields in: E.Osawa and K.B.Lipkowitz "Enlarged table of ad hoc parameters for molecular mechanics" JCPE Newsletter, 5(1), 3-23, 1993. JCPE is the Japanese Chemistry Program Exchange. ________________________________________________________________________________ From dew01@xray5.chem.louisville.edu Tue Apr 12 20:42:15 1994 Received: from comsun.rz.uni-regensburg.de by rchsg8.chemie.uni-regensburg.de via SMTP (920330.SGI/URRZ-Sub-1.5-irix) (for ferenc) id AA02858; Tue, 12 Apr 94 20:42:15 +0200 Received: from xray5.chem.louisville.edu by comsun.rz.uni-regensburg.de with SMTP id AA09760 (5.65c/IDA-1.4.4 for ); Tue, 12 Apr 1994 20:43:48 +0200 Received: by xray5.chem.louisville.edu (930416.SGI/930416.SGI) for ferenc.molnar@chemie.uni-regensburg.de id AA12371; Tue, 12 Apr 94 14:43:37 -0400 Date: Tue, 12 Apr 94 14:43:37 -0400 From: dew01@xray5.chem.louisville.edu (D. E. Williams) Message-Id: <9404121843.AA12371@xray5.chem.louisville.edu> To: ferenc.molnar@chemie.uni-regensburg.de Status: R Dear Dr. Molnar: Accurate net atomic charges are needed for force fields. Reliable net atomic charges can be found by fitting the molecular electric potential obtained by ab initio quantum mechanical methods. In addition to charges, program PDM93 also allows atomic dipoles/quadrupoles, bond dipoles, and addition of lone pair electron sites if necessary in order to fit the electric potential. A particularly useful feature of the program is the transparent way in which dependency conditions are specified. As distributed the program can handle 1000 atoms, but this can easily be increased if necessary. I append information about this program. -Don Williams Program PDM93, Potential Derived Multipoles The following is a brief description of this program. Molecules interact with each other via their electric potential. PDM93 finds optimized net atomic charges and other site multipole representations of the molecular electric potential based on a variety of models. The program is easy to use, flexible and powerful. Results are obtained in a single iteration and a complete error treatment is made which includes estimated standard deviation and correlation of variables. The program is written in Fortran 77 and runs on Unix, Vax, and other computers with F77 capability. Program PDM93 has a unique combination of features: o general sites, e.g. united atoms, not necessarily at atomic locations o each site may have any combination of monopole, dipole, or quadrupole o bond dipole model is supported o restricted (along the bond direction) bond dipole model is supported o provision for site dipole vectors in sp2 or sp3 directions o selected fixed atomic charges o selected groups of atoms with fixed charge o atomic charge equalities or symmetry relations o rotational invariance of site charges o provision for optional foreshortening of X-H bonds o comparison with Mulliken charges and Mulliken electric potential o direct input from Gaussian-92 o generalized input from other quantum mechanics programs o automatic generation of electric potential grid points o provision for custom generation of grid points o on-line program manual o comprehensive examples are provided A review of potential-derived charges may be found in Reviews of Computational Chemistry, Vol. II, pp. 219-271 (1991). For further information contact Dr. Donald E. Williams, Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, USA. Tel:(502)588-5975 Fax:(502)588-8149 E-mail:dewill01@ulkyvx.louisville.edu ----------------------------------------------------------------------- Ordering information Program package consisting of manuals, Fortran-77 source files, and demonstration example files....................................$2,000 Special discount price is available to academic institutions ........$495 Choose the preferred method of shipment: Via ftp, purchaser furnishes valid ftp address................n/c Via magnetic media, specify type..............................$20 DC6150 tape cartridge, unix tar format or MP120 tape cartridge (8mm), Vax backup format or 9-track 1600 bpi ascii tape or 9-track 6250 bpi ascii tape Make check payable to the University of Louisville. ------------------------------------------------------------------------- From SUNDIUS@phcu.helsinki.fi Wed Apr 13 14:03:12 1994 Received: from comsun.rz.uni-regensburg.de by rchsg8.chemie.uni-regensburg.de via SMTP (920330.SGI/URRZ-Sub-1.5-irix) (for ferenc) id AA03539; Wed, 13 Apr 94 14:03:12 +0200 Received: from fltf.Helsinki.FI by comsun.rz.uni-regensburg.de with SMTP id AA17415 (5.65c/IDA-1.4.4 for ); Wed, 13 Apr 1994 14:05:02 +0200 Received: from phcu.helsinki.fi by phcu.helsinki.fi (PMDF V4.2-14 #4706) id <01HB4PJ0YJCWC6AXVP@phcu.helsinki.fi>; Wed, 13 Apr 1994 15:04:51 EET Date: Wed, 13 Apr 1994 15:04:51 +0200 (EET) From: Tom Sundius U of Helsinki +358 0 1918339 Subject: Re: CCL:force fields and forces To: Ferenc.Molnar@chemie.uni-regensburg.de Message-Id: <01HB4PJ1058IC6AXVP@phcu.helsinki.fi> X-Vms-To: IN%"Ferenc.Molnar@chemie.uni-regensburg.de" X-Vms-Cc: SUNDIUS Mime-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Content-Transfer-Encoding: 7BIT Status: R A good book about molecular mechanics force fields which I would like to recommend, is the following: Kjeld Rasmussen: Potential Energy Functions in Conformational Analysis, Lecture Notes in Chemistry vol. 37, Springer-Verlag (1985) It contains an evaluation of many published force field (prior to 1985) and has a lot of references. Best regards, Tom Sundius +-----------------------------------------------------------------------+ ! Tom Sundius Decnet: 63569::SUNDIUS, 63539::SUNDIUS ! ! Department of Physics PsiMail: PSI%244203008::SUNDIUS ! ! PL9 (Siltavuorenpenger 20) Bitnet: SUNDIUS@FINUHCB, SUNDIUS@FINUH ! ! SF-00014 UNIVERSITY OF HELSINKI ! ! Finland Internet: sundius@phcu.helsinki.fi ! ! Phone : +358 0 1918339 Tom.Sundius@Helsinki.fi ! ! Telex : 122229 nuphu sf sundius@cc.helsinki.fi ! ! Fax : +358 0 1918680 sundius@csc.fi ! +-----------------------------------------------------------------------+ ________________________________________________________________________________ From case@scripps.edu Thu Apr 14 04:35:02 1994 Received: from comsun.rz.uni-regensburg.de by rchsg8.chemie.uni-regensburg.de via SMTP (920330.SGI/URRZ-Sub-1.5-irix) (for ferenc) id AA04410; Thu, 14 Apr 94 04:35:02 +0200 Received: from scripps.edu (riscsm.scripps.edu) by comsun.rz.uni-regensburg.de with SMTP id AA17445 (5.65c/IDA-1.4.4 for ); Thu, 14 Apr 1994 04:36:59 +0200 Received: from lanczos.scripps.edu by scripps.edu (5.61/1.34) id AA18277; Wed, 13 Apr 94 19:36:57 -0700 Received: by lanczos.Scripps.EDU (4.1/SMI-4.1/TSRI1.0) id AA01213; Wed, 13 Apr 94 19:35:59 PDT Date: Wed, 13 Apr 1994 19:33:38 -0700 (PDT) From: David Case Subject: Re: CCL:force fields and forces To: Ferenc Molnar In-Reply-To: <9404121655.AA02784@rchsg8.chemie.uni-regensburg.de> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Status: R You might want to get the public domain package "moil" from the University of Illinois at Chicago. It will show you how to calculate forces on atoms, and has (I believe) AMBER and Charmm force field parameters. ...d.a. case ________________________________________________________________________________ From vkitzing@sunny.mpimf-Heidelberg.mpg.de Wed Apr 20 13:24:19 1994 Received: from comsun.rz.uni-regensburg.de by rchsg8.chemie.uni-regensburg.de via SMTP (920330.SGI/URRZ-Sub-1.5-irix) (for ferenc) id AA19236; Wed, 20 Apr 94 13:24:19 +0200 Received: from foxy.mpimf-heidelberg.mpg.de ([192.109.43.254]) by comsun.rz.uni-regensburg.de with SMTP id AA18899 (5.65c/IDA-1.4.4 for ); Wed, 20 Apr 1994 13:26:00 +0200 Received: from sunny.mpimf-heidelberg.mpg.de by foxy.mpimf-heidelberg.mpg.de (5.65+/1.34) id AA06534; Wed, 20 Apr 94 13:25:36 +0200 Received: from [192.109.43.34] (mac10) by sunny.mpimf-Heidelberg.mpg.de (4.1/SMI-4.1) id AA08625; Wed, 20 Apr 94 13:21:34 +0200 Date: Wed, 20 Apr 94 13:21:34 +0200 Message-Id: <9404201121.AA08625@sunny.mpimf-Heidelberg.mpg.de> To: Ferenc.Molnar@chemie.uni-regensburg.de (Ferenc Molnar) From: vkitzing@sunny.mpimf-Heidelberg.mpg.de (Eberhard von Kitzing) Subject: Re: force fields Status: R Als Einf"uhrung in die Methode und als "Ubersicht eignen sich sicherlich: %0 Book %A Burkert, Ulrich %A Allinger, Norman %D 1982 %T Molecular Mechanics %S ASC Monography 117 %I America Chemical Society %0 Book %A Lipkowitz, K. B. %A Boyd, D. B. %D 1993 %T Reviews in Computational Chemistry %I VCH Publishers %C Weinheim %V 1-4 %K molecular mechanics, introduction Diese Liste ist nat"urlich nicht vollst"andig, aber vielleicht kein schlechter Anfang: %0 Journal Article %A Allinger, Norman L. %A Yuh, Young H. %A Lii, Jen-Huei %D 1989 %T Molecular Mechanics. The MM3 force field for Hydrocarbons. (1) %J Journal of the American Chemical Society %V 111 %N 23 %P 8551-8565 %K molecular mechanics, introduction, force field, MM3, aliphatic hydrocarbons, structural energy, heat of formation %0 Journal Article %A Amodeo, Pietro %A Barone, Vincenzo %D 1992 %T A new general form of molecular force fields. Application to intra- and interresidue interactions in peptides %J Journal of the American Chemical Society %V 114 %P 9085-9093 %K molecular mechanics, force field, potential function, parameter, general %0 Journal Article %A Cannon, J.F. %D 1993 %T Amber force-field parameters for guanosine triphosphate and its imido and methylene analogs %J Journal of Computational Chemistry %V 14 %N N8 %P 995-1005 %K nucleic-acids/ras p21/vibrational frequencies/conformational-analysis/molecular mechanics/gtp hydrolysis/sugar ring/proteins/gdp/nucleosides %X %O FORCE FIELD; %0 Journal Article %A Casewit, C. J. %A Colwell, K. S. %A Rappe, A. K. %D 1992 %T Application of a universal force field to organic molecules %J Journal of the American Chemical Society %V 114 %P 10035-10046 %K molecular mechanics, force field, potential function, parameter, general %0 Journal Article %A Clementi, Enrico %D 1989 %T Computer Simulations of Hydrated Proteins %J Journal of Molecular Liquids %V 41 %P 233-239 %K molecular dynamics, interaction potentials, force field, quantum mechanics, ab initio, protein, B-DNA, Z-DNA, water potential, Hartee-Fock approximation, configuration interaction, MCY water model, MCYL water model, water cluster, Monte Carlo, fluid dynamics, solvation, counterions, gramicidin A %O review %0 Journal Article %A Garcia, Angle E. %A Krumhansl, J. A. %D 1987 %T Agreement between Single Crystal X-Ray and Molecular Mechanical Sugar Ring Conformations %J Journal of Biomolecular Structure & Dynamics %V 5 %N 3 %P 513-537 %K ribose sugar puckering, AMBER force field, fitting of force field parameter %0 Journal Article %A Glennon, T.M. %A Merz, K.M. %D 1993 %T Applications of a new carbohydrate force-field %J Biophysical Journal %V 64 %N N2 %P A 183-183 %K %X %O FORCE FIELD; %0 Journal Article %A Grootenhuis, P.D.J. %A Haasnoot, C.A.G. %D 1993 %T A charmm based force-field for carbohydrates using the cheat approach - carbohydrate hydroxyl-groups represented by extended atoms %J Molecular Simulation %V 10 %N N2-6 %P 75-95 %K carbohydrates/force field/molecular mechanics, conformational analysis/solvation/hydrogen bonding/molecular-dynamics simulations/intramolecular hydrogen-bonds/nuclear magnetic-resonance/alpha-d-glucose/conformational-analysis/aqueous-solution/ ethylene-glycol/d-glucopyranose/oligosaccharides/energy %X %O FORCE FIELD; %0 Journal Article %A Hall %A Pavitt %D 1984 %T Comparisons of force fields %J Journal of Computational Chemistry %V 5 %N 5 %P 441-450 %K force fields, comparison %0 Journal Article %A Hwang, M.J. %A Stockfisch, T. %A Hassan, M. %A Nguyen, D. %A Hagler, A.T. %D 1993 %T Class-ii force-fields for peptides and proteins %J Biophysical Journal %V 64 %N N2 %P A 12-12 %K %X %O FORCE FIELD; %0 Journal Article %A Kini, R. M. %A Eveans, J. E. %D 1992 %T Comparison of Protein Models Minimized by the All-Atom and United-Atom Models in the AMBER Force Field: Correlation of RMS deviation with Crystallographic R Factor and Size %J Journal of Biomolecular Structure & Dynamics %V 10 %N 2 %P 265-279 %K comparison of force fields %0 Journal Article %A Kollman, Peter %A Dill, Ken %D 1991 %T Decisions in Force Field Development: An Alternative to those Described by Roterman et al. %J Journal of Biomolecular Structure & Dynamics %V 8 %P 1103-1107 %K comparison of force fields %0 Journal Article %A Kouwijzer, M.L.C.E. %A Vaneijck, B.P. %A Kroes, S.J. %A Kroon, J. %D 1993 %T Comparison of 2 force-fields by molecular-dynamics simulations of glucose crystals - effect of using ewald sums %J Journal of Computational Chemistry %V 14 %N N11 %P 1281-1289 %K %X %O FORCE FIELD; %0 Journal Article %A Levitt, Michael %D 1989 %T Molecular Dynamics of Macromolecules in Water %J Chemica Scripta %V 29A %P 197-203 %K molecular dynamics, force field, water model %0 Journal Article %A Lii, Jenn-Huei %A Allinger, Norman L. %D 1989 %T Molecular Mechanics. The MM3 Force Field for Hydrocarbons. (2) Vibrational Frequencies and Thermodynamics %J Journal of the American Chemical Society %V 111 %P 8566-8575 %K molecular mechanics, emperical force field, MM3, vibrational frequencies, hydrocarbons %0 Journal Article %A Lii, Jenn-Huei %A Allinger, Norman L. %D 1989 %T Molecular Mechanics. The MM3 Force Field for Hydrocarbons. (3) The van der Waals' Potential and Crystal Data for Aliphatic and Aromatic Hydrocarbons %J Journal of the American Chemical Society %V 111 %P 8576-8582 %K molecular mechanics, emperical force field, MM3, vibrational frequencies, hydrocarbons, aromatic atoms. %0 Journal Article %A Marchese, Francis T. %A Mehrotra, P. K. %A Beveridge, David %D 1981 %T A revised potential function for the water dimer in the EPEN/2 form %J The Journal of Chemical Physics %V 85 %N 1 %P 1-3 %K force field, water, radial distribution function, %0 Journal Article %A Marple, J. R. %A Dinur, U. %A Hagler, A. T. %D 1988 %T Derivation of force fields for molecular mechanics and dynamics from ab inito energy surfaces %J Proceedings of the National Academy of Sciences of the USA %V 85 %P 5350 %K force field parameter, ab initio calculation %0 Book %A McCammon, J.A. %A Harvey, Stephen %D 1987 %T Dynamics of Proteins and Nucleic Acids %I Cambridge University Press %C Cambridge %K molecular mechanics, introduction, water structure, hydration, force field %0 Journal Article %A Orozco, M. %A Aleman, C. %A Luque, F.J. %D 1993 %T Force-field parametrization from quantum-mechanical data %J Acta Chimica Hungarica-Models in Chemistry %V 130 %N N5 %P 695-717 %K molecular electrostatic potentials/nucleic-acid bases/conformational-analysis/atomic charges/free-energy/semiempirical calculations/partition-coefficients/dynamics simulation/aqueous-solution/wave-functions %X %O FORCE FIELD; %0 Journal Article %A Rappe, A. K. %A Casewit, C. J. %A Colwell, K. S. %A III, W. A. Goddard %A Skiff, W. M. %D 1992 %T UFF, a Full periodic tabel Force Field for molecular mechanics and molecular dynamics simulation %J Journal of the American Chemical Society %V 114 %P 10024-10035 %K molecular mechanics, force field, potential function, parameter, general %0 Journal Article %A Rappe, A.K. %A Colwell, K.S. %A Casewit, C.J. %D 1993 %T Application of a universal force-field to metal-complexes %J Inorganic Chemistry %V 32 %N 16 %P 3438-3450 %K molecular mechanics calculations/nuclear-charge model/ray crystal-structure/conformational-analysis/coordination-compounds/copper(ii) coordination/electron-transfer/dynamics simulations/polyatomic-molecules/potential function %O FORCE FIELD; %0 Journal Article %A Roterman, I. K. %A Lambert, M. H. %A Gibson, K. D. %A Scheraga, H. A. %D 1989 %T A Comparison of the CHARMM, AMBER and ECEPP Potentials for Peptides. (2) f-y Maps for N-Acetyl Alanine N'-Methyl Amide: Comparisons, Contrasts and Simple Experimental Tests. %J Journal of Biomolecular Structure & Dynamics %V 7 %N 3 %P 421-453 %K helical conformation, force field comparison %0 Journal Article %A Sippl, M.J. %D 1993 %T Boltzmann principle, knowledge-based mean fields and protein-folding - an approach to the computational determination of protein structures %J Journal of Computer-Aided Molecular Design %V 7 %N N4 %P 473-501 %K protein folding/protein modeling/knowledge-based prediction/molecular force field/statistical mechanics/immunogenic peptide-fragments/amino-acid-sequence/3-dimensional structure/globular-proteins/computer-simulation/molecular-dynamics/water solution/models/identification/conformations %X %O PROTEIN; FOLD; %0 Journal Article %A Sordo, J. A. %A Probst, M. %A Corongiu, G. %A Chin, S. %A Clementi, E. %D 1987 %T Ab Initio Pair Potentials for the Interactions between Aliphatic Amino Acids %J Journal of the American Chemical Society %V 109 %P 1702-1708 %K force field, amino acid, force parameter, nonbonded interactions %0 Journal Article %A Stone, A. J. %A Price, S. L. %D 1988 %T Some New Ideas in the Theory of Intermolecular Forces: Anisotropic Atom-Atom Potentials %J Journal of Physical Chemistry %V 92 %P 3325-3335 %K force field, anisotropic atom potentials, contributions to pair-potentials, long-range interactions, electrostatic energy, polarization, despersion, short-range interaction, exchange-repulsion, charge transfer, penetration and damping. %0 Journal Article %A Vedani, A. %A Huhta, D. W. %D 1991 %T A new force field for modeling metalloproteins %J Journal of the American Chemical Society %V 113 %P 5860-5862 %K Hydrogen bonds %0 Journal Article %A Williams, D.E. %A Stouch, T.R. %D 1993 %T Characterization of force-fields for lipid molecules - applications to crystal-structures %J Journal of Computational Chemistry %V 14 %N N9 %P 1066-1076 %K dynamics simulation/representation/conformation/monolayers/parameters/membrane/charge s/packing/model %X %O FORCE FIELD; ------------------------------------------------------------------------- Eberhard von Kitzing Max-Planck-Institut fuer Medizische Forschung Jahnstr. 29, D69120 Heidelberg, FRG Carl-Zuckmayer Str. 17, D69126 Heidelberg (privat) FAX : +49-6221-486 459 (work) Tel.: +49-6221-486 467 (work) Tel.: +49-6221-385 129 (home) internet: vkitzing@sunny.MPImF-Heidelberg.mpg.de Ferenc Molnar --------------------------------------------------------------------------- Institut fuer Physikalische und Theoretische Chemie - Lehrstuhl Prof. Dick - Tel.: (+49) 941 943-4466 /-4486 Universitaet Regensburg Fax.: (+49) 941 943-4488 Universitaetsstrasse 31 D-93053 Regensburg Deutschland / Germany --------------------------------------------------------------------------- EMail (SMTP): Ferenc.Molnar@chemie.uni-regensburg.de --------------------------------------------------------------------------- :-) I wish to have no connection with any ship that does not sail fast, for I intend to go in harm's way. -- John Paul Jones, USN 1747-1792 ;-) --------------------------------------------------------------------------- From wei@tammy.harvard.edu Wed Apr 20 12:30:03 1994 Received: from tammy.harvard.edu for wei@tammy.harvard.edu by www.ccl.net (8.6.4/930601.1506) id MAA19493; Wed, 20 Apr 1994 12:27:52 -0400 Received: by tammy.harvard.edu (5.64/10.0) id AA21345; Wed, 20 Apr 94 12:28:38 -0400 Date: Wed, 20 Apr 94 12:28:38 -0400 From: wei@tammy.harvard.edu (Tai-Guang "Teddy" Wei) Message-Id: <9404201628.AA21345@tammy.harvard.edu> To: Chemistry@ccl.net Subject: Force constants beteen Fe and Glutamic acid Cc: d@tammy.harvard.edu Dear all, I need the force constants between an iron atom(Fe) and a glutamic acid. More specifically, I need the potential constants between the Fe atoms and the carboxy oxygen atoms in the Glutamic acid in a non-haem iron protein. If you have any information about such force constants, please let me know. Thank you very much for your help in advance, Teddy From btluke@VNET.IBM.COM Wed Apr 20 14:31:25 1994 Received: from VNET.IBM.COM for btluke@VNET.IBM.COM by www.ccl.net (8.6.4/930601.1506) id NAA20601; Wed, 20 Apr 1994 13:54:07 -0400 From: Message-Id: <199404201754.NAA20601@www.ccl.net> Received: from KGNVMT by VNET.IBM.COM (IBM VM SMTP V2R2) with BSMTP id 6284; Wed, 20 Apr 94 13:52:40 EDT Date: Wed, 20 Apr 94 13:52:11 EDT To: chemistry@ccl.net, watoc@ic.ac.uk Subject: Symposuim Announcement Call for Papers Symposium on the Application of Genetic/Evolutionary Algorithms in Computer-Aided Chemsitry to be held at the National American Chemical Society Meeting Anaheim, CA April 2-6, 1995 Sponsored by the Division of Computers in Chemistry Focus: This symposium is open to any "flavor" of Genetic/Evolutionary Algorithms that can be applied to any area of Computer-Aided Chemistry. This includes Evolutionary Programming; Extended Genetic Searches; and Standard, Messy, Parallel, Adaptive-Parallel, or Meta Genetic Algorithms. The emphasis should be on how these algorithms can be applied to a given problem. Papers dealing mainly with the results obtained from these algorithms to a particular problem (e.g. QSAR, substructure searches, conformational searches, or training neural nets) should be presented in a symposium focusing on that problem. For additional information, contact Brian T. Luke IBM, MLM/078 Neighborhood Rd. Kingston, NY 12401 email btluke@vnet.ibm.com Please include your email address in the body of any correspondence. Thanks. From matt@mercury.aichem.arizona.edu Wed Apr 20 14:37:50 1994 Received: from mercury.aichem.arizona.edu for matt@mercury.aichem.arizona.edu by www.ccl.net (8.6.4/930601.1506) id NAA20584; Wed, 20 Apr 1994 13:52:01 -0400 Received: by mercury.aichem.arizona.edu (5.57/Ultrix3.0-C) id AA05480; Wed, 20 Apr 94 10:41:16 -0700 Date: Wed, 20 Apr 1994 10:39:14 -0700 (MST) From: Matthew Stahl Subject: MM calc'n of stereoisomers To: chemistry@ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Greetings, Here are the replies to my original post which read: >Netters, > Is it appropriate to apply molecular mechanics to the >determination of the relative stability of two stereoisomers? In other >words, if a single stereocenter is inverted, should I be able to calculate >which one is more stable? Mechanics is normally applied to conformational >isomers, but not configurational isomers. Where do stereoisomers fit into >the picture? I realize now that the post implied comparison of enantiomers. What I was concerned with is the comparison of diasteriomers with mechanics. Can the strain energies of diasteriomers (sterioisomers that are not mirror images) be compared with any validity? Thanks again for all the responses. matt ------------------------------------------------------------------------- From rs0thp@RohmHaas.Com Wed Apr 20 10:20:38 1994 Date: Tue, 19 Apr 1994 16:11:07 +22305458 (EDT) From: "Dr. Tom Pierce" To: Matthew Stahl Subject: Re: CCL:MM calc's of stereoisomers Previously, Matthew Stahl wrote: > Is it appropriate to apply molecular mechanics to the > determination of the relative stability of two stereoisomers? Yes. And the results had better be identical. If they are mirror-images then the energies should be exactly the same. Assuming your minimizer minimizes correctly. > words, if a single stereocenter is inverted, should I be able to calculate > which one is more stable? Potentially a different question. If a sterocenter is inverted, then you do not necessarily have a mirror image. And you may get different energies. Mechanics is normally applied to R and S isomers. > Mechanics is normally applied to conformational > isomers, but not configurational isomers. Where do stereoisomers fit into > the picture? They are the analyzed the same way. Note that small differences in conformational energies are probably not accurate in MM forcefields. (say .5 kcal or less) Fancier calculations (semi-empirical or QM ) without using symmetry might give better answers. -- Sincerely, Thomas Pierce - THPierce@RohmHaas.Com - Computational Chemist "These opinions are those of the writer and not the Rohm and Haas Company." ------------------------------------------------------------------------- From tj@eecs.uic.edu Wed Apr 20 10:20:46 1994 Date: Tue, 19 Apr 1994 15:22:07 -0500 (CDT) From: tj ODonnell To: Matthew Stahl Subject: Re: CCL:MM calc's of stereoisomers There can be no difference in energy between stereoisomers in the molecular mechanics approximation. Think of it like this: all energies depend on pairs of interatomic distances and the inversion of a center does not change (the matrix of) interatomic distances. TJ O'DOnnell tj@bert.eecs.uic.edu ------------------------------------------------------------------------- From dave@terminus.chem.yale.edu Wed Apr 20 10:21:00 1994 Date: Wed, 20 Apr 94 1:02:55 EDT From: David Maxwell To: Matthew Stahl Subject: Re: CCL:MM calc's of stereoisomers Yes, it is appropriate to apply molecular mechanics to the determination of the relative stability of two stereoisomers. However, you will form the entantiomer if there is only one stereocenter and it is inverted. "Enantiomers have identical chemical properties except toward optically active reagents" -Morrison & Boyd. By definition, they will have the same internal energy. If there are other stereocenters present, then the physical properties can change. Please refer to a chapter on stereochemistry in a suitable chemistry book for more information. -Dave Maxwell (dave@terminus.chem.yale.edu) ------------------------------------------------------------------------- From suter@physik.unizh.ch Wed Apr 20 10:21:15 1994 Date: Wed, 20 Apr 1994 10:07:36 +0200 (MET DST) From: Hans-Ueli Suter To: matt@mercury.aichem.arizona.edu Cc: Hans-Ueli Suter Subject: CCL:MM calc's of stereoisomers (fwd) Dear Sir, Stereoisomers or enentiomers should have the same energy. The symmetry of the hamiltonian of all methods, molecular mechanics, semeimpirical and ab initio is so that they do not distinguish between enantiomers. There is a theory , if you are interested I can give you the reference, which calculates the energy difference of enantiomer. However, this difference is very small, around 10**-40 a.u. for small systems. hope this helps, Hans Ulrich Suter ------------------------------------------------------------------------- From ROOMS@CUNYVM.BITNET Wed Apr 20 10:21:40 1994 Date: Wed, 20 Apr 1994 10:04:54 -0400 (EDT) From: Rami Osman To: Matthew Stahl Subject: Re: CCL:MM calc's of stereoisomers Hi Mathew, Naturally, the answer is NO. You will not be able to distinguish between two stereoisomers, because the energy expression does not depend on the streochem- istry of a single chiral atom. It actually doesn't matter which Hamiltonian you use, i.e., quantum mechanical or molecular mechanics. The only thing that distinguishes btween the steroisomers (I assume they are enantiomers) is their interaction with polarized light, and this is not part of the Hamiltonian. Good Luck with the rest of the calculation, Roman Osman ------------------------------------------------------------------------- From GKING@arserrc.gov Wed Apr 20 10:21:45 1994 Date: Wed, 20 Apr 1994 10:40:05 -0400 (EDT) From: GKING@arserrc.gov To: matt@mercury.aichem.arizona.edu Subject: Re: CCL:MM calc's of stereoisomers Hi Matt, You've probably received a bunch of replies to your question already, but I'll put my 2 cents in anyway. If the isomers in question are true mirror images, then their physical properties (heat of formation, boiling point, etc.) are identical, so the stabilities of the two stereoisomers are the same. This is due to symmetry, and has nothing to do with what computational method you happen to be using. Regards, Greg ==================================================================== Gregory King Internet: gking@arserrc.gov Eastern Reg. Res. Ctr., ARS, USDA Voice: (1) 215 233 6675 600 East Mermaid Lane Fax: (1) 215 233 6559 Philadelphia, PA 19118-2551 ==================================================================== From Jie.Yuan@UC.Edu Wed Apr 20 15:30:05 1994 Received: from ROLL.SAN.UC.EDU for Jie.Yuan@UC.Edu by www.ccl.net (8.6.4/930601.1506) id PAA21609; Wed, 20 Apr 1994 15:20:59 -0400 Received: from UCBEH.SAN.UC.EDU by UCBEH.SAN.UC.EDU (PMDF V4.3-7 #4918) id <01HBEHISOQLS91W163@UCBEH.SAN.UC.EDU>; Wed, 20 Apr 1994 15:03:32 EST Date: Wed, 20 Apr 1994 15:03:32 -0500 (EST) From: "JIE YUAN, CHEMISTRY, U. CINCINNATI" Subject: Mirror Sites of PDB? To: chemistry@ccl.net Message-id: <01HBEHISR5F691W163@UCBEH.SAN.UC.EDU> X-VMS-To: IN%"chemistry@ccl.net" X-VMS-Cc: YUANJ MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Hi CCL! Are there mirror ftp/gopher sites of the PDB (Protein Data Bank)? I tried to access it at pdb.pdb.bnl.gov by either ftp or gopher. The response is terribly poor and transmission very slow. I know that the famous Macintosh software sites, e.g. sumex (Stanford U.) and umich, now have more than a dozen mirror sites to ease access. It should be possible for PDB to establish some mirror sites, isn't it? Cheers! Jie ===== Jie Yuan === Chemistry === U. Cincinnati === Jie.Yuan@UC.EDU ===== PS: We have only the Jan. '93 release on CD. Anyone has the Jan '94 release? From PHYSPLMP@MIZZOU1.missouri.edu Wed Apr 20 17:30:19 1994 Received: from MIZZOU1.missouri.edu for PHYSPLMP@MIZZOU1.missouri.edu by www.ccl.net (8.6.4/930601.1506) id QAA24008; Wed, 20 Apr 1994 16:52:03 -0400 From: Message-Id: <199404202052.QAA24008@www.ccl.net> Received: from MIZZOU1 by MIZZOU1.missouri.edu (IBM VM SMTP V2R2) with BSMTP id 4523; Wed, 20 Apr 94 15:40:13 CDT Received: by MIZZOU1 (Mailer R2.10 ptf000) id 9436; Wed, 20 Apr 94 15:40:12 CDT Date: Wed, 20 Apr 94 15:39:04 CDT To: chemistry@ccl.net Subject: Call for papers, XXVII Midwest Theoretical Chem. Conf. Conference participants may choose to give either an oral or a poster presentat ion. The oral presentations will be limited to 20 min. including questions. If we are unable to accommondate your preference for an oral presentation, you will be notified promptly. Poster presentations will be limited to a 4 ft by 6 ft space. All presenters must submit a one page (8.5 by 11 in) sharp, clear camera-ready abstract. All abstracts should include 1) paper title 2) author( s) names with presenter underlined 3) affiliation(s) of the author(s) 4) abstra ct text. All text and figures should be confined to the inner rectangle of dimension 6 by 9 in. Your preference for poster or oral presentation should be indicated in the lower left-hand corner of this inner rectangle. Abstracts should be sent to: XXVII MTCC Department of Chemistry University of Missouri Columbia, MO 65211 In order for your abstract to be included in the conference program booklet, it must be received no later than Monday, May 2, 1994. A block of rooms has been reserved in student dormitories (The University is no t in session during the week of the conference) The rates, including breakfast Single $23/night, Double $14/night/person. Accommodations include towels a nd bed linens and breakfast. Deadline for making room reservations is Tuesday, May 10. There is only one motel within easy walking distance of the campus, Campus Inn, Stadium Blvd and College Ave. (314-499-2731) however there a many motels in Columbia including Days Inn, Holiday Inn, Bugetel, Comfort Inn, Drury Inn. No off campus rooms have been reserved and you should contact them direct ly. A list with telephone numbers can be mailed to you but most have 800 numbe rs. The pre-conference registration fee will be $50.00 which includes breaks, program book of abstracts and the cost of the Friday banquet and should be received by May 16. Registration on the 19th is $55.00. Registration for hardware and software venders wishing to demonstrate their products is $ 150 and includes one personal registration. Additional banquet tickets are $ 16.00. From vasz@bif.creighton.edu Wed Apr 20 18:30:25 1994 Received: from bif.creighton.edu for vasz@bif.creighton.edu by www.ccl.net (8.6.4/930601.1506) id RAA24605; Wed, 20 Apr 1994 17:36:35 -0400 Received: by bif.creighton.edu (920330.SGI/911001.SGI) for CHEMISTRY@ccl.net id AA20247; Wed, 20 Apr 94 16:37:27 -0500 Date: Wed, 20 Apr 94 16:37:27 -0500 From: vasz@bif.creighton.edu (Sandor Lovas) Message-Id: <9404202137.AA20247@bif.creighton.edu> To: CHEMISTRY@ccl.net Subject: OPLS for CF3CH2OH Hi, I am looking for OPLS parameter set of trifluoro methanol. Does anybody know about it. Thanks in advance. Sandor Lovas Creighton Univ. Omaha, NE, USA e-mail: vasz@bif.creighton.edu From cmartin@rainbow.uchicago.edu Wed Apr 20 18:32:06 1994 Received: from midway.uchicago.edu for cmartin@rainbow.uchicago.edu by www.ccl.net (8.6.4/930601.1506) id RAA24703; Wed, 20 Apr 1994 17:50:45 -0400 Received: from rainbow.uchicago.edu by midway.uchicago.edu for CHEMISTRY@ccl.net Wed, 20 Apr 94 16:50:45 CDT Received: by rainbow.uchicago.edu (920330.SGI/920502.SGI) for @midway.uchicago.edu:CHEMISTRY@ccl.net id AA22169; Wed, 20 Apr 94 17:26:50 -0500 From: cmartin@rainbow.uchicago.edu (Charles Martin) Message-Id: <9404202226.AA22169@rainbow.uchicago.edu> Subject: Density Functional Models To: CHEMISTRY@ccl.net Date: Wed, 20 Apr 1994 17:26:49 -0600 (CDT) X-Mailer: ELM [version 2.4 PL22] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 1037 Netters, Beased on the recent discussions of semiempirical methods, I am wondering how far the theoretical development of density functional theory (DFT) has come. For example, as with semiempirical model Hamiltonian, it is possible to compute the exact denisty functional operators for a given molecule (with a nonuniform denisty) using ab initio many-body techniques (See, for instance, Karl F. Freed and Mel Levy, JCP 77(1), page 396, 1 July 1992). Has anyone ever tried this? Is anyone working on this or something similar? Are there any recent review articles on DFT? Thanks Chuck ================================================================== Charles H. Martin email: chm6@quads.uchicago.edu US Mail: c/o Freed Group The James Franck Institute and The Department of Chemistry The University of Chicago 5640 South Ellis Avenue Chicago, Illinois 60637 Work: (312) 702-3457 Fax: (312) 702-5863 ================================================================== From AHOLDER@VAX1.UMKC.EDU Wed Apr 20 18:33:09 1994 Received: from VAX1.UMKC.EDU for AHOLDER@VAX1.UMKC.EDU by www.ccl.net (8.6.4/930601.1506) id RAA24624; Wed, 20 Apr 1994 17:38:12 -0400 From: Received: from VAX1.UMKC.EDU by VAX1.UMKC.EDU (PMDF V4.2-11 #4431) id <01HBEL015B7O9S52NP@VAX1.UMKC.EDU>; Wed, 20 Apr 1994 16:37:47 CST Date: Wed, 20 Apr 1994 16:37:47 -0600 (CST) Subject: A fire extinguisher/olive branch. To: CHEMISTRY@ccl.net Message-id: <01HBEL015B7Q9S52NP@VAX1.UMKC.EDU> X-VMS-To: IN%"CHEMISTRY@ccl.net" MIME-version: 1.0 Content-transfer-encoding: 7BIT Netters, Well, I stuck my foot in it again. In trying to illustrate a point, it seems I used a bad illustration. It also seems that some folks got upset about that and took some of my comments a bit out of context and "went to the weeds" as we say where I'm from. I DID NOT say that molecular mech- anics was not "REAL CHEMISTRY". I DID NOT intend to convey any sense of superiority about one model over another. I WAS NOT being superior. I didn't even say I was doing "REAL CHEMISTRY" and other people were not! I DID NOT intend to offend anyone or to denigrate anyone else's work. Let's take a quick look at what I DID say that apparently irritated some people: > The development of a semiempirical quantum mechanical model is indeed >similar to the development of a molecular mechanics force field in that >the objective is to reproduce experimental data. That is about where >the similarity ends. The underlying guts of the models are totally >different! I can safely say that MM has nothing to do with chemistry, >but is more or less a fit to a convenient set of functions. It >does have chemical validity in that it gives us good answers to some >questions. > QM is an entirely different situation, in that the actual arbiters of >chemistry, the electrons, are treated directly by mathematical functions. >The chemistry come OUT of a model that describes the electrons. >This may seem to be a matter of degree to some, but I think that it is an >important distinction, especially as it finally applies to parameterization >of quantum chemical models. Let's also recall the context of my posting, which was semiempirical PARAM- ETERIZATION. I was using this section to set up the idea that parameter- izing for specific properties is not the best choice. My purpose was to contrast and compare SE to MM because so many more people are familiar with MM parameterization. MM is a good chemical model. In fact MM is a WODERFUL model. It does not do electronic properties, however, which is why quite a number of us turn to quantum mechanics. The derivation of a general model such as AM1 requires an extraordinary care so that the method reproduces many properties with acceptable accuracy. This was my point, and my ONLY point. I did not intend to attack MM. It is a useful and valid tool (note how clearly I state this at the end of the first paragraph of the excerpt above). I am not a scientific (or I hope any other type) of elitist. (If you knew where I came from in my early life, you'd know I couldn't afford to be an elitist!) I simply expressed an opinion and was attacked. Oh well, I can take that. I enjoyed reading the comments of others that posted after me (and sent me private mail) with reasoned dis-agreements to my position. I am not married to my view, it is simply an opinion I hold and wanted to take an opportunity to express since some things had been said. A number of people have expressed thanks for some of my previous postings in SE theory, where I have been working for a number of years. It was my impression that the list should primarily function as a forum for discussion and exchange of information, which task I think it adequately performs. In this regard, note that I am a SEMIEMPIRICAL researcher! Some ab initio workers call us "number-twiddlers"! I readily admit that ab initio HF theory will usually give a better and certainly more reliable answer than semiempirical methods if they can be applied to the system. Also, MM usually does better for heats for formation and conformer energetics than semiempirical. See, I'm not an elitist, really, really I fully agree with Dr. Burkhart's assertion about models and science. Science is indeed nothing but the construction of models in which to organize and explain our data. I get to teach General Chemistry I relatively frequently as prt of my duties here at the University of Missouri-Kansas City. I make this point the first day bt telling the students that the "search for ultimate truth begins down the hall in religion class. This is science. We are in the business of building and expanding models to help our limited brains understand a universe that is otherwise far too complex for comprehension." When I was with Michael Dewar, he made a point of convincing all of us that the "religion of models" was doomed to failure, because a better one will always come along. Anyhow, I hope that this clears up that I am NOT an elitist and that I DO think that molecular mechanics is worthwhile. It is quite painful for me to learn these lessons in public, but I will try to be more precise with my wording in the future if I can ever work up the nerve to post to the CC list again. (That last part was a joke.) Finally, I would like to say something about context that probably applies to all forms of electronic communication, where it seems a lot of us spend a substantial amount of time. It is quite easy to MISS THE CONTEXT of someone's statements when looking at an e-mail message because there are no verbal or physical (body-language) clues. It is also easy to READ IN meaning where none was intended. I constantly guard against this, and seemed to have let myself slip by not being as clear as possible with my statements in the original posting. I would like to call for all of us to give one another the benefit of the doubt in future discussions. If you say to yourself "He/she/it COULDN'T mean that!", they probably didn't. Why not check privately with them? Let's allow reason to re-assert itself. Andy Holder =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= DR. ANDREW HOLDER Assistant Professor of Computational/Organic Chemistry Department of Chemistry || University of Missouri - Kansas City || Internet Addr: aholder@vax1.umkc.edu Spencer Chemistry, Room 315 || Phone Number: (816) 235-2293 Kansas City, Missouri 64110 || FAX Number: (816) 235-5502 =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=