From h.rzepa@ic.ac.uk Fri Jan 14 04:49:55 1994 Received: from punch.ic.ac.uk for h.rzepa@ic.ac.uk by www.ccl.net (8.6.4/930601.1506) id DAA28946; Fri, 14 Jan 1994 03:54:20 -0500 Received: from sg1.cc.ic.ac.uk by punch.ic.ac.uk with SMTP (PP) id <15953-0@punch.ic.ac.uk>; Fri, 14 Jan 1994 08:51:14 +0000 Received: from macb.ch by cscmgb.cc.ic.ac.uk (920330.SGI/4.0) id AA25316; Fri, 14 Jan 94 08:52:58 GMT Message-Id: <9401140852.AA25316@cscmgb.cc.ic.ac.uk> X-Sender: rzepa@sg1.cc.ic.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Fri, 14 Jan 1994 08:54:04 +0000 To: CHEMISTRY@ccl.net From: h.rzepa@ic.ac.uk (Henry Rzepa) (Henry Rzepa) Subject: Re: semiempirical methods for hypervalent sulfur Perhaps the papers pubished by Walter Thiel on MNDO-d should be consulted. JOURNAL OF COMPUTATIONAL CHEMISTRY 1993 VOL.14 NO.7 PP.775-789 JOURNAL OF COMPUTATIONAL CHEMISTRY 1993 VOL.14 NO.1 PP.37-44 TI: EXTENSION OF MNDO TO D-ORBITALS - PARAMETERS AND RESULTS FOR THE HALOGENS AU: THIEL_W, VOITYUK_AA JN: INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 1992 VOL.44 NO.5 PP.807-829 EXTENSION OF THE MNDO FORMALISM TO D-ORBITALS - INTEGRAL APPROXIMATIONS AND PRELIMINARY NUMERICAL RESULTS AU: THIEL_W, VOITYUK_AA JN: THEORETICA CHIMICA ACTA 1992 VOL.81 NO.6 PP.391-404 I gather most of the problems regarding geometry etc are solved! Dr Henry Rzepa, Dept. Chemistry, Imperial College, LONDON SW7 2AY; rzepa@ic.ac.uk via Eudora 2.01, Tel:+44 71 225 8339, Fax:+44 71 589 3869. >From April '94: (44) 171 584 5774, Fax: (44) 171 584 5804 http://www.ch.ic.ac.uk/rzepa.html From Patrick.Bultinck@rug.ac.be Fri Jan 14 05:49:59 1994 Received: from mserv.rug.ac.be for Patrick.Bultinck@rug.ac.be by www.ccl.net (8.6.4/930601.1506) id EAA29248; Fri, 14 Jan 1994 04:59:50 -0500 Received: from allserv.rug.ac.be by mserv.rug.ac.be with SMTP id AA03530 (5.65c/IDA-1.4.4 for ); Fri, 14 Jan 1994 10:59:18 +0100 Received: by allserv.rug.ac.be (5.0/SMI-SVR4) id AA11028; Fri, 14 Jan 94 10:56:52 +0100 Date: Fri, 14 Jan 1994 10:56:51 +0100 (MET) From: Patrick Bultinck Subject: What and where : CHARMM To: CHEMISTRY@ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 434 Dear Netters, Can anybody provide me some info on what the CHARMM package (program) is, where to get it, what the cost is, in what journal one can find info...? The reason for interest is that CHARMM could be used to handle point charges with GAMESS. thanks for answering !!!! Patrick Bultinck University of Ghent, Belgium E_mail : Patrick.Bultinck@rug.ac.be *** BUT COME ON HEISENBERG, YOU MUST BE SURE ABOUT SOMETHING *** From dodik@yfaat.ch.huji.ac.il Fri Jan 14 05:56:39 1994 Received: from shum.cc.huji.ac.il for dodik@yfaat.ch.huji.ac.il by www.ccl.net (8.6.4/930601.1506) id FAA29394; Fri, 14 Jan 1994 05:16:15 -0500 Received: from yfaat.ch.huji.ac.il by shum.cc.huji.ac.il with SMTP id AA05859 (5.65cHU/IDA-1.4.4 for ); Fri, 14 Jan 1994 12:16:05 +0200 Received: by yfaat.ch.huji.ac.il (AIX 3.2/UCB 5.64/4.03) id AA31972; Fri, 14 Jan 1994 12:14:49 +0200 Date: Fri, 14 Jan 1994 12:14:49 +0200 From: dodik@yfaat.ch.huji.ac.il (David Danovich) Message-Id: <9401141014.AA31972@yfaat.ch.huji.ac.il> To: chemistry@ccl.net Subject: Parallel Gaussian Dear Netters, We are thinking to purchase a parralel system of IBM RS 6000/590's (or anything comperable) to run Gaussian, and we need some good advice. So I have the following questions: 1. where can we purchase the parallel Gaussian? 2. what computers is used for the parallel Gaussian. How many processors and can we used compute claster? 3. What are the specifications like operation memory per processor? 4. what kind of software is used for the parallelization? 5. Has anybody experienced with parallel Gaussian? Thank you in advance David Danovich +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Dr. David Danovich The Fritz Haber Research Center for Molecular Dynamics The Hebrew University of Jerusalem, Givat-Ram Campus, 91904 Jerusalem, Israel ------------------------------------------------------------------------------- Office phone: (972)-2-586934 Internet Addr: dodik@yfaat.ch.huji.ac.il Home phone: (972)-2-789544 FAX number: (972)-2-585345 +=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+ From Patrick.Bultinck@rug.ac.be Fri Jan 14 06:02:52 1994 Received: from mserv.rug.ac.be for Patrick.Bultinck@rug.ac.be by www.ccl.net (8.6.4/930601.1506) id EAA29213; Fri, 14 Jan 1994 04:53:31 -0500 Received: from allserv.rug.ac.be by mserv.rug.ac.be with SMTP id AA03500 (5.65c/IDA-1.4.4 for ); Fri, 14 Jan 1994 10:53:13 +0100 Received: by allserv.rug.ac.be (5.0/SMI-SVR4) id AA10782; Fri, 14 Jan 94 10:50:47 +0100 Date: Fri, 14 Jan 1994 10:50:46 +0100 (MET) From: Patrick Bultinck Subject: Re: Optimizing Linear Structure in GAMESS To: CHEMISTRY@ccl.net In-Reply-To: <01H7K07H84R68WZPUN@MSUVX1.MEMST.EDU> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 1475 On Tue, 11 Jan 1994 CHENS@memstvx1.memst.edu wrote: > Dear Netters, > I've been trying to optimize the geometry of two C2H2 molecules > situated along a straight line with a certain fixed distance separating > the two molecules (ie. H-C-C-H H-C-C-H) using GAMESS program. The intent > is to hold the four carbon atoms in a straight line with a fixed distance > between the two central carbon atoms and allow all the other parameters > to be fully optimized. I tried using linear bends in the ZMAT group but > the job terminated with a message "roundoff error in bends". Does anyone > have any idea what the problem could be? Any comments will be appreciated. > > S. Chen Dear, I use GAMESS quite often, and would like to help you with your optimization. When I have to do something like that, I do not use linear bonds. Instead, I give in a Z-matrix, without any constraint... I let the job take off for about 3 minutes, then I stop it. I then have a look at the .log file. In there you will find some lines with an encoded Z-matrix, you will see that coord. 1 equals this or that lenghth, angle or whatever. Then I return to the input file, where I insert some IFREEZ groups in the $STATPT group, so I type IFREEZ(number of the coord. in the enc. Z-matrix that you want to keep unchanged)=1 Then you let the job do the job you consider as the job the job has to do. Sincerely, Bultinck Patrick University of Ghent, Belgium E-mail : Patrick.Bultinck@rug.ac.be From mvoue@cc.fundp.ac.be Fri Jan 14 07:50:01 1994 Received: from quick for mvoue@cc.fundp.ac.be by www.ccl.net (8.6.4/930601.1506) id HAA00191; Fri, 14 Jan 1994 07:13:18 -0500 Received: by cc.fundp.ac.be (MX V3.1A) id 12269; Fri, 14 Jan 1994 13:13:31 EST Sender: mvoue@cc.fundp.ac.be Date: Fri, 14 Jan 1994 13:13:25 EST From: mvoue@ccl.net To: chemistry@ccl.net CC: mvoue@ccl.net Message-ID: <00978867.9B6055E0.12269@cc.fundp.ac.be> Subject: TN3270 Dear netters, Does a version of the communication program TN3270 exist for VAX-VMS ? Thanks ... Michel Voue University of NAMUR (Belgium) E-Mail : mvoue@cc.fundp.ac.be From vberckm@schs.uia.ac.be Fri Jan 14 08:49:57 1994 Received: from schs.uia.ac.be for vberckm@schs.uia.ac.be by www.ccl.net (8.6.4/930601.1506) id IAA00733; Fri, 14 Jan 1994 08:43:58 -0500 Received: from localhost by schs.uia.ac.be (8.6.4/Ultrix3.0-C) id OAA13371; Fri, 14 Jan 1994 14:42:50 +0100 Date: Fri, 14 Jan 1994 14:42:49 +0100 (MET) From: Filip Verberckmoes Subject: Compiling Rasmol on an IBM RS6000 ? To: CHEMISTRY@ccl.net Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters, We have downloaded RasMol2 for XWINDOWS, but we are having some problems compiling it for an IBM RS6000, running AIX 3.2.5. These problems probably arise from the fact that no one of us is familiar with compiling C-programs. Is there someone, more experienced than we are, who has compiled Rasmol for an IBM RS6000, that could provide us with a Makefile for this system. Ilse Wolfs Department of Chemistry University of Antwerp (RUCA) Groenenborgerlaan 171 2020 Antwerpen Belgium e-mail:iwolfs@banruc60.bitnet From loh@akocoa.enet.dec.com Thu Jan 13 15:38:18 1994 Received: from inet-gw-2.pa.dec.com for loh@akocoa.enet.dec.com by www.ccl.net (8.6.4/930601.1506) id PAA23092; Thu, 13 Jan 1994 15:38:16 -0500 Received: from us1rmc.bb.dec.com by inet-gw-2.pa.dec.com (5.65/13Jan94) id AA06497; Thu, 13 Jan 94 12:30:28 -0800 Received: by us1rmc.bb.dec.com; id AA19224; Thu, 13 Jan 94 15:27:58 -0500 Message-Id: <9401132027.AA19224@us1rmc.bb.dec.com> Received: from akocoa.enet; by us1rmc.enet; Thu, 13 Jan 94 15:30:14 EST From: Date: Thu, 13 Jan 94 15:30:14 EST To: chemistry@ccl.net Subject: Grant Program for ACS Satellite Seminar on Modeling for Drug Design Digital Is Sponsoring Grants for ACS Satellite Seminar on "Molecular Modeling: The Small Molecule Approach", 1:00PM to 4:00PM EST, March 29, 1994 ------------------------------------------------------------------------- Digital is offering 20 grants to universities and colleges to reduce the ACS viewing site fee to $500. (a savings of $600.; U.S. Price) for this satellite seminar on drug design modeling. Contact Cyrelle Gerson (202)872-8728 [e-mail: ckg97@acs.org] or Carol Valverde (202) 872-6124 at ACS for more information on the grant program. The three-hour satellite seminar will feature leading research experts who are developing new modeling techniques and are successfully putting them to work solving practical problems in drug design research. Organized by Dr. J. Phillip Bowen of the University of Georgia, the seminar will include the following presentations: - Conceptual Framework for Drug Design, by Garland R. Marshall, Director of the Center for Molecular Design and Professor of Molecular Biology and Pharmacology, Washington University - Molecular Modeling in the Design of Potent and Selective D1 Agonists, by Yvonne C. Martin, Senior Project Leader, Computer- Assisted Molecular Design, Abbott Laboratories - Use of Pharmacophore Models in the Design of N-Methyl-D-Aspartate, by Daniel F. Ortwine, Research Associate, Parke-Davis Pharmaceutical Research Division, Warner-Lambert Company. This seminar will also feature two panel discussions--a unique and exciting opportunity to speak directly to the guest panelists and to pose any questions you may have about pharmacophore modeling. From shaoweng@helix.nih.gov Fri Jan 14 11:50:06 1994 Received: from helix.nih.gov for shaoweng@helix.nih.gov by www.ccl.net (8.6.4/930601.1506) id LAA02566; Fri, 14 Jan 1994 11:05:58 -0500 Received: from localhost by helix.nih.gov (8.6.4/1.35(helix-1.0)) id LAA23702; Fri, 14 Jan 1994 11:05:55 -0500 Date: Fri, 14 Jan 1994 11:05:55 -0500 From: shaoweng@helix.nih.gov (Shaomeng Wang) Message-Id: <199401141605.LAA23702@helix.nih.gov> To: chemistry@ccl.net Subject: Seeking help on AVS Cc: shaoweng@helix.nih.gov Dear Netters, We are doing some gaussian calculations and we like to plot the charge density maps and orbitals using the AVS program running on the CONVEX machine. I will appreciate if you can provide me some information on how do to so, especially on the KEYWORDS we should use in GAUSSIAN and MOPAC calculations to generate the right files to be ead by the AVS program. Thank you very much for you help. -Shaomeng Wang From ryszard@MSI.COM Fri Jan 14 11:51:11 1994 Received: from schizoid.msi.com for ryszard@MSI.COM by www.ccl.net (8.6.4/930601.1506) id LAA02849; Fri, 14 Jan 1994 11:37:16 -0500 Received: from hogan.MSI.COM by schizoid.msi.com (4.1/SMI-4.1) id AA11398; Fri, 14 Jan 94 11:36:13 EST Received: by hogan.MSI.COM (AIX 3.2/UCB 5.64/4.03) id AA12177; Fri, 14 Jan 1994 11:36:27 -0500 Date: Fri, 14 Jan 1994 11:36:27 -0500 From: ryszard@MSI.COM (Ryszard Czerminski X 285) Message-Id: <9401141636.AA12177@hogan.MSI.COM> To: CHEMISTRY@ccl.net, Patrick.Bultinck@rug.ac.be Subject: Re: What and where : CHARMM CHARMM ( = Chemistry at HARvard Macromolecular Mechanics ) The main reference is: "CHARMM: A Program for Macromolecular Energy, Minimization, and Dynamics Calculations." J. Comp. Chem., Vol. 4, p187 (1983) Since 1983 there have been numerous studies done using CHARMM package and numerous papers published. CHARMM is actively develped by numerous academic groups. Please contact Molecular Simulations, Inc. (MSI) or Prof. Martin Karplus at Harvard for information about distribution. MSI (USA): phone (617)229-9800; quanta-l@msi.com (mailing list) There is also independent charmm-bbs: send message to charmm-bbs-request@emperor.harvard.edu for subscription. Ryszard Czerminski, MSI From gene@jersey.cray.com Fri Jan 14 11:51:58 1994 Received: from cray.com for gene@jersey.cray.com by www.ccl.net (8.6.4/930601.1506) id KAA02380; Fri, 14 Jan 1994 10:55:59 -0500 Received: from jersey.cray.com by cray.com (Bob mailer 1.2) id AA24563; Fri, 14 Jan 94 09:55:56 CST Received: by jersey.cray.com id AA15015; 5.0/CRI-5.6; Fri, 14 Jan 94 10:55:47 EST Date: Fri, 14 Jan 94 10:55:47 EST From: gene@jersey.cray.com (Eugene Fleischmann) Message-Id: <9401141555.AA15015@jersey.cray.com> To: chemistry@ccl.net Cc: gene@jersey.cray.com Subject: Re: Optimizing Linear Structure in GAMESS Content-Length: 1813 > Dear Netters, > I've been trying to optimize the geometry of two C2H2 molecules > situated along a straight line with a certain fixed distance separating > the two molecules (ie. H-C-C-H H-C-C-H) using GAMESS program. The intent > is to hold the four carbon atoms in a straight line with a fixed distance > between the two central carbon atoms and allow all the other parameters > to be fully optimized. I tried using linear bends in the ZMAT group but > the job terminated with a message "roundoff error in bends". Does anyone > have any idea what the problem could be? Any comments will be appreciated. > > S. Chen For the following geometry, H3-C1-C2-H4 . . . H7-C5-C6-H8 Try the following Z-matrix, which worked just fine in MNDO93, 6 0.00000 0 0.00000 0 0.00000 0 0 0 0 / 6 1.20600 1 0.00000 0 0.00000 0 1 0 0 / 1 0.97300 1 180.00000 0 0.00000 0 1 2 0 / 6 6.53567 1 0.00000 0 0.00000 0 3 1 2 / 6 1.20600 1 180.00000 0 0.00000 0 4 3 1 / 1 0.97300 1 180.00000 0 90.00000 0 5 4 3 / 1 0.97300 1 180.00000 0 90.00000 0 4 5 6 / 1 0.97300 1 180.00000 0 0.00000 0 2 1 3 / Notice that optimization is activated only for the bond stretches. Good luck, Gene ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Eugene D. Fleischmann, Ph.D. Computational Chemist Cray Research, Inc. (609) 252-1250 121 Commons Way gene@calv2.cray.com Princeton, NJ 08540 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From sam@ncsa.uiuc.edu Fri Jan 14 14:50:02 1994 Received: from newton.ncsa.uiuc.edu for sam@ncsa.uiuc.edu by www.ccl.net (8.6.4/930601.1506) id NAA04858; Fri, 14 Jan 1994 13:53:31 -0500 Received: from landrew.ncsa.uiuc.edu by newton.ncsa.uiuc.edu with SMTP id AA26054 (5.65a/IDA-1.4.2 for chemistry@ccl.net); Fri, 14 Jan 94 12:53:30 -0600 Received: by landrew.ncsa.uiuc.edu (4.1/NCSA-4.1) id AA02944; Fri, 14 Jan 94 12:53:28 CST Date: Fri, 14 Jan 94 12:53:28 CST From: sam@ncsa.uiuc.edu (Sam Milosevich) Message-Id: <9401141853.AA02944@landrew.ncsa.uiuc.edu> To: chemistry@ccl.net Subject: Re: TN3270 Cc: mvoue@ccl.net > From chemistry-request@ccl.net Fri Jan 14 07:37:59 1994 > Date: Fri, 14 Jan 1994 13:13:25 EST > From: mvoue@ccl.net > To: chemistry@ccl.net > > Does a version of the communication program TN3270 exist for > VAX-VMS ? FYI -- TGV MULTINET will do it. $ help multinet telnet /tn3270 MULTINET TELNET /TN3270 /TN3270=tn3270-negotiation-mode /NOTN3270 The /TN3270 qualifier allows the negotiation of IBM 3270 emulation mode. The default, /TN3270=AUTOMATIC, causes TELNET to automatically negotiate IBM 3270 emulation mode with the foreign host. If the foreign host supports IBM 3270 mode then TELNET automatically enters IBM 3270 emulation mode. /TN3270=FORCE forces TELNET into IBM 3270 emulation mode when communicating with a machine that supports IBM 3270 mode, but which does not negotiate this mode in such a way that TELNET can automatically determine that IBM 3270 emulation mode is possible. In particular, IBM 370 systems running the ACCESS/MVS TCP package seem to have this problem (requiring the use of /TN3270=FORCE). The /NOTN3270 switch can be used to entirely disable IBM 3270 emulation mode negotiation. @MULTINET MULTINET TELNET Subtopic? From liang@chvymw.chem.ncsu.edu Fri Jan 14 14:54:14 1994 Received: from chvymw for liang@chvymw.chem.ncsu.edu by www.ccl.net (8.6.4/930601.1506) id NAA04881; Fri, 14 Jan 1994 13:57:35 -0500 From: Message-Id: <199401141857.NAA04881@www.ccl.net> Date: Fri, 14 Jan 1994 13:56:42 -0500 To: CHEMISTRY@ccl.net Subject: Summary /search for review papers on parameterization of force fields X-VMS-To: SMTP%"CHEMISTRY@ccl.net" Summary /search for review papers on parameterization of force fields Many thanks to those who responded to my query. Here goes the summary. Weigen Liang original posting: From: SMTP%"liang@chmwvy.chem.ncsu.edu" 11-JAN-1994 Subj: search for review papers on parameterization of force fields Dear netters, I'm searching recent literature for REVIEW papers of parameterization of force field in molecular modeling without much success. In some lucky cases I found papers reviewing a particular type of force field, i.e., MM3, DREDING, UFF, etc, but most of the time I just got papers dealing with a small series of molecules, even a single molecule. Does anybody have a good lead to those papers which review (or invent) particular types of force fields, even the whole field of parameterization of force field in molecular modeling? I would appreciate it if you give me a clue, and if there are significant emails, I'll summarize them and post them to the list. Thanks. Weigen Liang Responses from dear netters ff-1 From: SMTP%"jxh@ibm12.biosym.com" 11-JAN-1994 12:37:06.74 Joerg-R. Hill Look at: 1) The Consistent Force Field and Its Quantum Mechanical Extension, A. Warshel in: Semiempirical Methods of Electronic Structure Calculation, Part A: Techniques, (Modern Theoretical Chemistry 7), Ed. Gerald A. Segal, Plenum Press, New York and London, 1977, p. 133 2) Molecular Mechanics Force-Field Parameterization Procedures; A. J. Hopfinger, R. A. Pearlstein, J. Comp. Chem., 5 (1984) 486 - 499 3) Proximity effects on organic reactivity: Development of force fields from quantum chemical calculations, and applications to the study of organic reaction rates; Andrea E. Dorigo, K. N. Houk in: Advances in Molecular Modeling, vol. 1, JAI Press Inc., 1988, p. 135 4) Derivation of force fields for molecular mechanics and dynamics from ab initio energy surfaces; J. R. Maple, U. Dinur, A. T. Hagler, Proc. Natl. Acad. Sci. USA, 85 (1988) 5350 5) J. R. Maple, T. S. Thatcher, U. Dinur, A. T. Hagler; Chemical Design Automation News 5, 9 (1990) 10 ff-2 From: SMTP%"shenkin@still3.chem.columbia.edu" 11-JAN-1994 12:40:18.33 Peter S. Shenkin Well, you could go to the original AMBER, MM2, MM3 or OPLSA papers. Also, there's still good stuff in Burkert & Allinger, "Molecular Mechanics" (ACS Monograph 177), which would be a good place to start. ff-3 From: SMTP%"kim@sfu.ca" 11-JAN-1994 13:37:34.38 Chan-Kyung Kim Prof. Wolfe published series of papers in the Canadian Journal of Chemistry, 66, 2687 - 2750 (1988). In these papers, he developed MMP2 parameters for peptides and penicillins. ff-4 From: SMTP%"wk01189@worldlink.com" 11-JAN-1994 13:46:58.75 Max Vasquez The november 93 issue (No. 7) of Chemical Reviews is dedicated to molecular mechanics and modeling. Unfortunately, Arnie Hagler's contribution did not make it in time for that issue: it was(is) a review of current force field methodology. Still you may find some of the other articles quite useful. Also, there are two recent papers in JACS "inventing" new force fields, and at the same time presenting a brief overview (not really a review) of other force fields (at least the major references are given). These are: (1) Amodeo & Barone JACS 114, 9085-9093 (1992) (2) Halgren JACS 114, 7827-7843 (1992) Attempts to compare force fields seem to run into controversy; see for example the discussion in J.Biomol.Struct.Dynamics 8, 1103-1111 (1991) between Kollman's and Scheraga's groups regarding force fields for biomolecules. I hope this helps. In any case, keep you eyes open for Hagler's paper in Chem.Rev. to appear sometime soon. ff-5 From: SMTP%"tudor@wucmd.wustl.edu" 11-JAN-1994 15:58:13.71 Tudor-Ionel Oprea one of such paper series, but without comprehensive examples, is generated by JG Vinter and colleagues, concerning the COSMIC force field and molecular modelling package. Three papers i have in mind, all published in JCAMD, Vinter et al, JCAMD 1:31-51 - about COSMIC Abraham, Haworth JCAMD 2:125-135 - about the Morse potential Morley et al, JCAMD 5:475-504 - about COSMIC(90) these papers reflect the evolution of a good force field (as compared to others), that is based on a simple philosophy: keep atom types to a minimum (only 26 at types) compare that with 200 for CHARMm and ilk (bare in mind it is a general organic ff, so metals should be not counted) Enjoy the papers - most of the times you will find that they are well written! ff-6 From: SMTP%"cletner@remcure.bmb.wright.edu" 14-JAN-1994 08:54:35.07 Charles Letner These are the paper on AMDER development, united and all-atom versions. Good for info on the actual parameterization. 1) Weiner & Kollman, J. Comp. Chem., Vol. 7, No. 2 230-252 (1986) 2) Weiner, et al., JACS, Vol 106, No. 3 (1984) These are comparisons of some of the "bio" fields. 1) Hall & Pavitt, J. Comp. Chem., Vol. 5 No. 5, 441-450 (1984) 2) Whitlow & Teeter, JACS, 108, 7163-7172 (1986) 3) Kini & Evans, J. Biomol. Str. & Dyn., Vol. 9, No.3 475-488 (1991) also same authors and journal Vol 10, No. 2 265-279 (1992) Next two are sort of interesting. The first on comes down on AMBER and CHARMM force fields; says that they may lead to totally false results. The second one is a response. Note the authors here. ;) 1) Roterman, Gibson, & Scheraga, J. Biomol. Struct. & Dyn, Vol. 7, No. 3 391-453 (1989). Actually two paper in a series 2) Kollman & Dill, J. Biomol. Struct. & Dyn., Vol 8., No. 5, 1103-1107 (1991) ff-7 From: SMTP%"Jeffrey.Nauss@UC.Edu" 11-JAN-1994 18:05:50.78 Jeff Nauss I am interested in whatever references you may come up with. In the meantime, here are some that might help with the CVFF forcefield used by Biosym: Maple et al. PNAS 85, 5350 (1988) Hagler et al. JACS 101, 5131 (1979) Hagler et al. JACS 101, 5122 (1979) Lifson et al. JACS 101, 5111 (1979) Then there is: Stouch et al. J. Comp Chem 12, 1033 (1991) Williams & Stouch, J. Comp Chem 14, 1066 (1993) ff-8 From: SMTP%"tracy@austin.unimelb.edu.au" 12-JAN-1994 01:16:53.72 Tracy Nero Here are a couple of refs for you. I hope they help. If I come across more (which I know I have at home) I'll mail them to you. COMFA see J. Med. Chem.,1993, vol 36, 70-80 Tripos force field see J. Comp. Chem.,1989, vol 10, 982-1012 Molecular Mechanics , ACS Monograph, 1982, page 177 U. Burkert and N.L.Allinger AMBER force field see J. Am. Chem. Soc., 1984, vol 106, 765- J. Comp. Chem., 1986, vol 7, 230- ff-9 From: SMTP%"mercie@med.cornell.edu" 12-JAN-1994 08:33:43.53 gus mercier In the QCPE bulletin v. 12 no. 1 1992 p.6-11 there is an extensive bibliography of MM2 parameters. mercie@cumc.cornell.edu end of file From jkl@ccl.net Fri Jan 14 15:50:02 1994 Received: from krakow.ccl.net for jkl@ccl.net by www.ccl.net (8.6.4/930601.1506) id OAA05446; Fri, 14 Jan 1994 14:57:17 -0500 From: Jan Labanowski Received: from localhost for jkl@ccl.net by krakow.ccl.net (8.6.4/920428.1525) id OAA24921; Fri, 14 Jan 1994 14:57:17 -0500 Date: Fri, 14 Jan 1994 14:57:17 -0500 Message-Id: <199401141957.OAA24921@krakow.ccl.net> To: chemistry@ccl.net Subject: contents/abstracts of journals available Cc: jkl@ccl.net Dear Netters, Thanks to Springer-Verlag and Wiley, we have the contents of the following premiere journals dealing with computational chemistry: International Journal of Quantum Chemistry (J. Wiley & Sons) (Cont+Abstracts) Journal of Computational Chemistry (J. Wiley & Sons) (Cont+Abstracts) Theoretica Chimica Acta (Springer-Verlag) (Contents only) They are available in the directory /pub/chemistry/periodicals in CCL archives on the www.ccl.net and are updated as new issues are being published. We should all be very thankful to Springer-Verlag and Wiley publishers for providing this information to us free of charge. If you know any other publishers who would be willing to place such information in our archives let me know and let them know. I am willing to store it !!! You can access CCL archives via e-mail, ftp or gopher. To find out more about the Computational Chemistry Archives send the following message: select chemistry help chemistry help search help quit to the address MAILSERV@ccl.net and the information will be forwarded to your mailbox automatically. There is a small change in the gopher on www.ccl.net if you go to it via default port 70. You need to click on the: Other OSC Gopher Servers and then on OSC Chemistry Gopher Server to get to CCL archives. You can go directly to the CCL archives by using: gopher www.ccl.net 73 Have a good weekend. Jan Labanowski CCL Coordinator jkl@ccl.net From d3f012@pellucidar.pnl.gov Fri Jan 14 18:50:08 1994 Received: from pnlg.pnl.gov for d3f012@pellucidar.pnl.gov by www.ccl.net (8.6.4/930601.1506) id RAA07658; Fri, 14 Jan 1994 17:51:18 -0500 From: Received: from pellucidar.pnl.gov (130.20.182.74) by pnlg.pnl.gov; Fri, 14 Jan 94 14:46 PST Received: by pellucidar.pnl.gov (920330.SGI/920502.SGI) for @pnlg.pnl.gov:chemistry@ccl.net id AA22915; Fri, 14 Jan 94 14:45:54 -0800 Date: Fri, 14 Jan 94 14:45:54 -0800 Subject: Geometry issues for semiempirical methods To: chemistry@ccl.net Cc: d3f012@pellucidar.pnl.gov Message-id: <9401142245.AA22915@pellucidar.pnl.gov> X-Envelope-to: chemistry@ccl.net Semiempirical methods, specifically MNDO/AM1/PM3, do rather poorly on calculated rotational barriers for molecules such as 1,2-Dihaloalkanes, 1,2-Dimethoxyethane, and even ethane itself. Usually the rotational barrier between syn-trans is underestimated by as much as 50%. Has anyone else documented this sort of problem (I presume this problem is fairly well known). Is anyone working on (or published) modified model Hamiltonians that can treat this issue? I wonder how SAM1, Walter Thiel's new MNDO method, or SINDO might treat this...any thoughts? I'd be happy to summarize if you email directly to me. Mark Thompson ps. There is a recent paper on 1,2-Dihaloalkanes by Dave Dixon and coworkers that discusses this issue. (J. Phys. Chem. vol 96, p 10740, 1992). ************************************************************************** Mark A. Thompson Sr. Research Scientist email: d3f012@pnlg.pnl.gov Molecular Science Research Center FAX : 509-375-6631 Pacific Northwest Laboratory voice: 509-375-6734 PO Box 999, Mail Stop K1-90 Richland, WA. 99352 Argus available via anonymous ftp from pnlg.pnl.gov (130.20.64.11) (in the argus directory). Download the README file first. ************************************************************************** From AHOLDER@VAX1.UMKC.EDU Fri Jan 14 18:53:20 1994 Received: from VAX1.UMKC.EDU for AHOLDER@VAX1.UMKC.EDU by www.ccl.net (8.6.4/930601.1506) id SAA07793; Fri, 14 Jan 1994 18:24:03 -0500 From: Received: from VAX1.UMKC.EDU by VAX1.UMKC.EDU (PMDF V4.2-11 #4431) id <01H7OILUQAKG9M24DA@VAX1.UMKC.EDU>; Fri, 14 Jan 1994 17:22:59 CST Date: Fri, 14 Jan 1994 17:22:59 -0600 (CST) Subject: rvgloss@arcriba.edu.ar To: CHEMISTRY@ccl.net Message-id: <01H7OILUSFQA9M24DA@VAX1.UMKC.EDU> X-VMS-To: IN%"CHEMISTRY@ccl.net" MIME-version: 1.0 Content-transfer-encoding: 7BIT Hello Netters. Daniel Glossman asked some interesting questions about hypervalent sulfur species computed by semiempirical methods. It's an excellent question in that none of the "mainline" (i.e. Dewar-style) methods up til the recent advent of SAM1 has included an explicit treatment of d-orbitals. This precluded the old standard sp3d2 hybridization pattern that we all know from Cootn and Wilkinson. It was shown how- ever that successful results could be obtained within this limitation in a method using Gaussian corrections to the core-core replusion term in the approximation (PM3 : J. J. P. Stewart, J. Comput. Chem. 10, 221 (1989); AM1 : M. J. S. Dewar, Y.-C. Yuan, Inorg. Chem. 29, 3881 (1990)). MNDO's performance was substantially poorer than AM1 or PM3, especially for hypervalent systems. Which brings us to an intertesting question: Is it really sp3d2 hybrid- ization or are the d-orbitlas used as some sort of extra flexibility (polarization?)? This has been bandied about for quite some time. A rel- atively definitive article (A. E. Reed, P. v. R. Schleyer, J. Am. Chem. Soc. 112, 1434 (1990)) seems to suggest that its not d-orbitals, but d- functions. I tend to come down in this camp myself. Anyway, whether or not its "orbital" or "function" it seesm that computationally they are needed for a proper description of these systems. Next: How do sp only semiempirical methods treat these systems? Answer: Badly and non-systematically. It is my belief that the hypervalent systems that AM1 or PM3 might get correct are fortuitous. Basically, I would not trust these results for anything important. To really get these systems, we need d-functions/orbitals in the description. TA DA: SAM1 to the rescue. Michael Dewar has been working over a period of some 8 years I know of on a way to bring d-orbitals into semi- empirical theory. This was accomplished with the new SAM1 method (M. J. S. Dewar, C. Jie, G. Yu, Tetrahedron 23, 5003 (1993); A. J. Holder, R. D. Dennington, C. Jie, Tetrahedron in press, (1994)). Here in Kansas City we have finished up the sulfur param- eterization with SAM1 and the results for hypervalent systems are much better. (All of this will be published shortly. This is not meant to be a stall, as we are still working on some of this. SAM1 with sulfur will be available in AMPAC 5.0 from Semichem to be released in March at the ACS meeting in San Diego.) There is some selected data below to illustrate the point. SF4 --- SAM1 Exptl Heat of Formation -179.5 -182.4 SF(1) 1.53 1.54 SF(2) 1.68 1.65 FSF(1) 128.8 129.2 FSF(2) 96.7 93.4 Ioniz. Pot. 12.55 12.03 General Results for Sulfur with SAM1 ------------------------------------ (The following are unsigned average errors.) SAM1 AM1 PM3 Heat of Formation (76 molecs) 6.45 7.09 9.33 Dipole Moments (45 molecs) 0.40 0.49 0.59 Ioniz. Pot. (67 molecs) 0.39 0.33 0.39 The results for P are even more dramatic, with the average errors in heats of formation being HALVED over PM3 and AM1! As well as hypervalent heavy main group elements, we are working on transition metals and hope to have iron and copper available in the 5.0 release as well. Hope this wasn't too boring. And YES, Doug, I'm always listening. You'll get 5.0 when its ready and you can repeat the study you mentioned with SAM1. Cheerio, Andy Holder =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= DR. ANDREW HOLDER Assistant Professor of Computational/Organic Chemistry Department of Chemistry || BITNET Addr: AHOLDER@UMKCVAX1 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 =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From SHAUN%JASON.DECNET@relay.the.net Fri Jan 14 23:50:07 1994 Received: from nic.the.net for SHAUN%JASON.DECNET@relay.the.net by www.ccl.net (8.6.4/930601.1506) id XAA08929; Fri, 14 Jan 1994 23:29:26 -0500 Received: from decnet-mail (SHAUN@JASON) by nic.the.net (PMDF V4.2-14 #4544) id <01H7OT7OY9SW000187@nic.the.net>; Fri, 14 Jan 1994 22:29:22 CDT Date: Fri, 14 Jan 1994 22:29:22 -0500 (CDT) From: "Shaun D. Black" Subject: Help with TPPI COSY NMR expeiments To: chemistry@ccl.net Message-id: <01H7OT7OYBOI000187@nic.the.net> X-Envelope-to: chemistry@ccl.net X-VMS-To: THENIC::IN%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Is anyone willing to offer a brief description of the TPPI COSY and TPPI Relay COSY NMR experiments. I'm familiar with a variety of NMR techniques, but these are new ones to me. Thanks in advance. Cheers, Shaun =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= = Shaun D. Black, PhD | Internet: shaun%jason.decnet@relay.the.net = = Dept. of Biochemistry | University of Texas Health Center, at Tyler = =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=