From mxm@iris80.biosym.com Mon Aug 30 14:15:12 1993 Received: from bioc1.biosym.com for mxm@iris80.biosym.com by oscsunb.ccl.net (5.65c+KVa/930601.1506) id AA16631; Tue, 31 Aug 1993 00:15:19 -0400 Received: from iris80.biosym.com by bioc1.biosym.com (5.64/0.0) id AA23085; Mon, 30 Aug 93 21:15:14 -0700 Received: by iris80.biosym.com (920330.SGI/920502.SGI) for @bioc1.biosym.com:CHEMISTRY@ccl.net id AA03140; Mon, 30 Aug 93 21:15:12 -0700 Date: Mon, 30 Aug 93 21:15:12 -0700 From: mxm@biosym.com (Max Muir ) Message-Id: <9308310415.AA03140@iris80.biosym.com> To: CHEMISTRY@ccl.net Subject: Responses to 'finding transition states with MOPAC6.0' Dear CyberChemists, thanks for your help. >using MOPAC6.0 I have been attempting to correlate calculated >heats of formation of some transition states with experimental >activation energies for the following reaction > > H R1 R1 > . \ / ./ > tBu + C = C -------> tBu - CH2 - C > / \ \ > H R2 R2 > > I am getting some credible looking structures for the transition > states. However, I cannot seem to get close to the saddle point, > where the gradient normal is zero. I set SCFCRT=10^-12 and > GNORM=0.0001, and the calculation exits normally thus- > > CYCLE: 9 TIME: 195.67 TIME LEFT: 356495.2 GRAD.: 0.000 HEAT: 4.288334 > > But when I do a FORCE calcn to verify the single -ve ROOT, MOPAC reports that > GRADIENT NORM = 0.12229, which is not really good enough for publication is > it? I have one and one only negative root. What's the problem? What's the (Hysterical questions deleted). I fixed up WRITE.f to write out gradient norm as the calculation finishes (like AMPAC). Thus . . CYCLE: 6 TIME: 240.34 TIME LEFT: 357099.6 GRAD.: 0.000 HEAT: 4.288334 HESSIAN CALCULATED NUMERICALLY CYCLE: 7 TIME: 240.05 TIME LEFT: 356618.8 GRAD.: 0.000 HEAT: 4.288334 ------------------------------------------------------------------------------- GRAPH UHF AM1 NODIIS ITRY=500 MMOK DMAX=0.20 TS SCFCRT=0.000000000001 + GNORM=0.0002 LET NOINTER RECALC=1 INSIGHT generated AMPAC/MOPAC input file DATE: Tue Aug 24 18:44:09 1993 GEOMETRY OPTIMISED USING EIGENVECTOR FOLLOWING (EF). SCF FIELD WAS ACHIEVED AM1 CALCULATION VERSION 6.00 30-Aug-93 FINAL HEAT OF FORMATION = 4.28833 KCAL TOTAL ENERGY = -1257.77074 EV ELECTRONIC ENERGY = -6795.64588 EV CORE-CORE REPULSION = 5537.87514 EV mxm GRADIENT NORM = 0.0001815 <-------<< Yippee!! IONIZATION POTENTIAL = 7.96377 NO. OF ALPHA ELECTRONS = 25 NO. OF BETA ELECTRONS = 24 MOLECULAR WEIGHT = 113.222 SCF CALCULATIONS = 491 COMPUTATION TIME = 28 MINUTES AND 15.740 SECONDS However, it looks like there is no easy way to get the refined structure into MOPAC for the force calcn without altering the file readers/writers. And in any case it does not seem to matter. I here append the responses. _______________________________________________________________________ Date: 30 Aug 93 8:08 +0200 From: Frank Jensen Subject: mopac ts's Max, Your "problem" is simply that the geometry as printed in the output or achieve file only contain some 5-6 digits. In the optimization the full accuracy of the geometry is produced and you may obtain very small gnorm's, but the final geometry is only printed with an accuracy that gives you the gnorm of ~0.1 in the force calculation. A force calculation with a gnorm < 1.0 is fine. If you realy need the full accuracy you would have to change the format statement in the code to print out more digits. Frank _______________________________________________________________________ From: jas@medinah.atc.ucarb.com (Jack Smith) Subject: Re: finding transition states using MOPAC6.0 Max: If you're using SADDLE to locate the transition state, then follow it with a gradient minimization (I usually use EF) before doing the FORCE calculation. SADDLE does not appear to refine its final geometry. I'd save the trial saddle point before doing the gradient minimizatin, though - I have had many "SADDLE" points just fall off to one side of the saddle point and have to start all over. I'd also follow the FORCE calculation with IRC calculations along both directions of the negative root to confirm that the transition state indeed connects the desired reactants to desired products. According to the MOPAC documentation, the PRECISE keyword should generate publication quality results (as far as SCF convergence and Gradient Norms are concerned). _______________________________________________________________________ From: NEELY@DUCVAX.AUBURN.EDU Subject: Re: finding transition states using MOPAC6.0 I've had problems with a second step in MOPAC 6 'claiming' a larger gradient norm than the previous step did. I've not gotten a satis- factory answer to this question. In your case, you need to re- member that nothing is really 0 with floating point arithmetic on a computer--it's all roundoff error. I'd be quite satisfied with a gradient norm of about 0.1 for publication, & I suspect most people would, especially for a transition state.. Irene Newhouse _______________________________________________________________________ From vkitzing@sunny.mpimf-heidelberg.mpg.de Tue Aug 31 11:26:17 1993 Received: from mpimfhd.mpimf-heidelberg.mpg.de (gate.mpimf-heidelberg.mpg.de) for vkitzing@sunny.mpimf-heidelberg.mpg.de by oscsunb.ccl.net (5.65c+KVa/930601.1506) id AA18936; Tue, 31 Aug 1993 03:27:08 -0400 Received: from sunny.mpimf-heidelberg.mpg.de by mpimfhd.mpimf-heidelberg.mpg.de (5.65+/1.34) id AA00838; Tue, 31 Aug 93 09:23:21 +0200 Received: by sunny.mpimf-Heidelberg.mpg.de (4.1/SMI-4.1) id AA06801; Tue, 31 Aug 93 09:26:17 +0200 From: vkitzing@sunny.mpimf-heidelberg.mpg.de (Eberhard von Kitzing) Message-Id: <9308310726.AA06801@sunny.mpimf-Heidelberg.mpg.de> Subject: Re: query regarding AMBER energy minimization To: mbu!neel@vigyan.ernet.in, CHEMISTRY@ccl.net (Computational Chemistry List) Date: Tue, 31 Aug 1993 09:26:17 +0200 (MET DST) In-Reply-To: <9308302202.AA11960@iisc.ernet.in> from "neel@vigyan.ernet.in" at Aug 30, 93 05:02:57 pm X-Mailer: ELM [version 2.4 PL20] Content-Type: text Content-Length: 1501 > > Hello everybody, when i do energy minimization using AMBER forcefield > i frequently get "linmin failure'. Can anybody tell me what is this > linmin & how to avoid it and what it is? Where from i can get to > know minimization algorithms used in AMBER ?Thank you , Neel > Most optimization procedures work in two step. First they try to estimate a good direction in which the energy is expected to lower considerably and second it follows this direction and tries to find the minimum of the energy function along this line (terminus technicus: line search). Subroutines doing this task are traditionally called "linmin". If you use the single precision version of AMBER, you can probably avoid this problems by using the double precision version. If not, you may have located a difficult area with a low gradient. In this situation truncation errors start to become a severe problem. If this is a low energy area you may have found your goal. In the other case you may use a short dynamics run to leave this area. For more detail please see my articles: E. v.Kitzing, Meth. Enzym. (1992) 211, 449-466 E. v.Kitzing, Prog. Nucl. Acid Res. Mol. Biol. (1992) 43, 89-110 ------------------------------------------------------------------------- Eberhard von Kitzing Max-Planck-Institut fuer Medizische Forschung Jahnstr. 29, D69120 Heidelberg, FRG 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 From jas@medinah.atc.ucarb.com Tue Aug 31 04:43:52 1993 Received: from medinah.atc.ucarb.com for jas@medinah.atc.ucarb.com by oscsunb.ccl.net (5.65c+KVa/930601.1506) id AA24034; Tue, 31 Aug 1993 09:43:50 -0400 Received: from jack.csc.ucarb.com by medinah.atc.ucarb.com (AIX 3.2/UCB 5.64/4.03) id AA23900; Tue, 31 Aug 1993 09:43:16 -0400 Message-Id: <9308311343.AA23900@medinah.atc.ucarb.com> Date: Tue, 31 Aug 1993 09:43:52 -0500 To: chemistry@ccl.net From: jas@medinah.atc.ucarb.com (Jack Smith) Subject: 4-coord angles Given five of the six central angles in a general four-coordinate arrangment (2 special cases, of course, being a tetrahedron and a square plane), what is the forumula for the sixth (and redundant) angle in terms of the other five? Is there a simple invariant (sum rule?) for this system that I'm missing? I thought I'd see if anyone already knew the answer before I went through the trig myself. -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= JACK A. SMITH || Union Carbide Corp. || Phone: (304) 747-5797 Catalyst Skill Center || FAX: (304) 747-5571 P.O. Box 8361 || S. Charleston, WV 25303 || Internet: jas@medinah.atc.ucarb.com -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From mercie@cumc.cornell.edu Tue Aug 31 09:27:40 1993 Received: from cumc.cornell.edu (PATHMAC.MED.CORNELL.EDU) for mercie@cumc.cornell.edu by oscsunb.ccl.net (5.65c+KVa/930601.1506) id AA27290; Tue, 31 Aug 1993 13:36:35 -0400 Received: by cumc.cornell.edu (5.64/ECH1.13) id AA22843; Tue, 31 Aug 93 13:36:04 EDT Posted-Date: Tue, 31 Aug 1993 13:27:40 -0400 (EDT) Date: Tue, 31 Aug 1993 13:27:40 -0400 (EDT) From: Gustavo Mercier Subject: Re: Theoretical Calculations of Lanthanide Organic Complexes To: Nivan Bezerra <21NBCJ@npd1.ufpe.br> Cc: chemistry@ccl.net In-Reply-To: <01H2D2JRF26U8Y503Q@NPD1.UFPE.BR> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On 30 Aug 1993, Nivan Bezerra wrote: > Dear Netters, > > I am interested in theoretical methods for the calculations of > organic complexes of lanthanides, especially Eu(III). > Does anyone know any packages for this type of calculation using > MO, extended Huckel, Xalpha, Density Functional Theory, INDO, AMPAC, > MOPAC, etc? > Thank you very much. You may try several things: 1) Standard packages like G92, Hondo, GAMESS etc using effective core potentials that include relativistic effects in an "average" fashion. See below for references regarding ecp's for lanthanides and other atoms. 2) You may try DFT computations. A package like ADF from Baerends group includes a "basis set" for Eu and you can include relativistic effects. You may contact them to obtain the program (1500 DG fro academic users)- adf@chem.vu.nl or tevelde@chem.vu.nl Regarding semiempirical methods I am unfamiliar with programs that have parameterized the Lanthanides. Anybody aware of such program? Good Luck! Gus Mercier mercie@cumc.cornell.edu *** cut here* The following references should provide you with very recent ECP's for most of the periodic table. The comments I have heard from those who have used them are rather favorable (comments limited to energetics and geometries): Stevens et. al. J. Chem.Phys. 81 (12), Pt. II, 1984 First and Second Row atoms Stevens et. al. Can. J. Chem. 70, 612, (1992) Third through Fifth row atoms. Some typos are known: Table 2: In RECP for second Vp-f component: -129.87594 should read -129.78594 Table 4: Basis for Fe Cp term for 1sp should be -0.007940, not -0.07940 asp term for 4sp should be 0.0410, not 0.410 Table 7: Result for Be Eval with core a should read -1.01214, not -0.01214 Cundari and Stevens J. Chem. Phys. 98 (7) 1993 Lanthanides I hope this is useful. These papers also discuss the variety of methods available to generate ECP's, relativistic effects and references to ECP's for DFT computations. Good Luck gus mercier mercie@cumc.cornell.edu From pathology@a1.mscf.upenn.edu Tue Aug 31 16:44:01 1993 Received: from NOC4.DCCS.UPENN.EDU for pathology@a1.mscf.upenn.edu by oscsunb.ccl.net (5.65c+KVa/930601.1506) id AA29293; Tue, 31 Aug 1993 16:03:42 -0400 Return-Path: Received: by noc4.dccs.upenn.edu id AA16360; Tue, 31 Aug 93 16:03:37 -0400 Received: from in by noc4.dccs.upenn.edu via MR/RELAY with conversational-MRIF; Tue, 31 Aug 93 16:03:37 -0400 Posted: Tue, 31 Aug 93 20:53:01 -0400 Date: Tue, 31 Aug 93 20:44:01 -0400 Sender: pathology@a1.mscf.upenn.edu From: "PATHOLOGY & LAB. MEDICINE" Message-Id: <44106113803991/49243@MSCF> To: "stephen urquhart" , chemistry@ccl.net Subject: RE: Educational PC based kinetics programs search. Msg-Class: !AS Stephen, take a look at the program produced by the lab of Carl Frieden at the Department of Biochemistry and Molecular Biophysics at Washington University School of Medicine. The main program is KINSIM and is described in good detail in C Frieden, "Numerical intergration of rate equations by computer," Trends in Biochemical Science, 18:58-60 (1993). The program runs on VAX, Mac and PC and is available by ftp. It is oriented towards enzyme kinetics, but you may find it useful for other situations, too. Gregg Wells Department of Pathology University of Pennsylvania Philadelphia, PA 19104-4283 email: pathology@a1.mscf.upenn.edu From merkle@parc.xerox.com Tue Aug 31 06:27:28 1993 Received: from alpha.Xerox.COM for merkle@parc.xerox.com by oscsunb.ccl.net (5.65c+KVa/930601.1506) id AA29661; Tue, 31 Aug 1993 16:27:50 -0400 Received: from manarken.parc.xerox.com ([13.2.116.21]) by alpha.xerox.com with SMTP id <12242>; Tue, 31 Aug 1993 13:27:41 -0700 Received: by manarken.parc.xerox.com id <12171>; Tue, 31 Aug 1993 13:27:35 -0700 From: Ralph Merkle To: chemistry@ccl.net, nanotech@cs.rutgers.edu Subject: Molecular Manufacturing and Chemical Design Automation News Message-Id: <93Aug31.132735pdt.12171@manarken.parc.xerox.com> Date: Tue, 31 Aug 1993 13:27:28 -0700 Chemical Design Automation News permanently ceased publication with the August 1993 issue. Unfortunately, I had an invited article on "Molecular Manufacturing: Adding Positional Control to Chemical Synthesis" scheduled for the *September* issue.... C'est la vie. The article is now available in postscript format by anonymous FTP >from "parcftp" in file "/pub/nano/MolecularManufacturing.ps". Ralph C. Merkle Xerox PARC 3333 Coyote Hill Road Palo Alto, CA 94304 merkle@xerox.com From hogue@canada.den.mmc.com Mon Aug 30 19:30:57 1993 Received: from canada.den.mmc.com for hogue@canada.den.mmc.com by oscsunb.ccl.net (5.65c+KVa/930601.1506) id AA13247; Mon, 30 Aug 1993 19:30:53 -0400 Received: by canada.den.mmc.com (4.1/1.34.a) id AA04111; Mon, 30 Aug 93 17:30:43 MDT Date: Mon, 30 Aug 93 17:30:43 MDT From: hogue@canada.den.mmc.com (Pat Hogue 1-2183) Message-Id: <9308302330.AA04111@canada.den.mmc.com> To: chemistry@ccl.net Subject: Uranium Status: RO Does anyone out there have working parameters for uranium? Pat Hogue From NETNEWS@UICVM.CC.UIC.EDU Tue Aug 31 09:36:53 1993 Received: from phem3 (phem3.acs.ohio-state.edu) for NETNEWS@UICVM.CC.UIC.EDU by oscsunb.ccl.net (5.65c+KVa/930601.1506) id AA29787; Tue, 31 Aug 1993 16:34:54 -0400 Received: from UICVM.CC.UIC.EDU (MAILER@UICVM) by phem3.acs.ohio-state.edu (PMDF V4.2-13 #3557) id <01H2EHA71W688WW2PR@phem3.acs.ohio-state.edu>; Tue, 31 Aug 1993 16:34:46 EDT Received: from UICVM.UIC.EDU (NJE origin NETNEWS@UICVM) by UICVM.CC.UIC.EDU (LMail V1.1d/1.7f) with BSMTP id 6413; Tue, 31 Aug 1993 15:31:48 -0500 Date: Tue, 31 Aug 1993 14:36:53 -0500 (CDT) From: Prasad Ravi Subject: Parallel & cluster versions of CHARMm, GAMESS, Discover, MOPAC Sender: NETNEWS@UICVM.UIC.EDU To: CHEMISTRY@ccl.net Message-Id: <93243.143653U21709@uicvm.uic.edu> Organization: University of Illinois at Chicago, ADN Computer Center Content-Transfer-Encoding: 7BIT Distribution: local Path: uicvm.uic.edu!u21709 Newsgroups: bit.listserv.chemistry Lines: 10 Hello Folks, I am wondering if there exist parallel and/or cluster versions of the above packages - I am especially interested in versions that use PVM for message passing. Thanks for any information. Prasad Ravi. pravi@ncsa.uiuc.edu From jas@medinah.atc.ucarb.com Tue Aug 31 12:26:59 1993 Received: from medinah.atc.ucarb.com for jas@medinah.atc.ucarb.com by oscsunb.ccl.net (5.65c+KVa/930601.1506) id AA00773; Tue, 31 Aug 1993 17:27:01 -0400 Received: from jack.csc.ucarb.com by medinah.atc.ucarb.com (AIX 3.2/UCB 5.64/4.03) id AA28639; Tue, 31 Aug 1993 17:26:22 -0400 Message-Id: <9308312126.AA28639@medinah.atc.ucarb.com> Date: Tue, 31 Aug 1993 17:26:59 -0500 To: chemistry@ccl.net From: jas@medinah.atc.ucarb.com (Jack Smith) Subject: Re: 4-coord angles (answer) The original question: > Given five of the six central angles in a general four-coordinate >arrangment (2 special cases, of course, being a tetrahedron and a square >plane), what is the forumula for the sixth (and redundant) angle in terms >of the other five? Is there a simple invariant (sum rule?) for this system >that I'm missing? I thought I'd see if anyone already knew the answer >before I went through the trig myself. The answer appears to be that the sum of the cosines = -2. Try it. Thanks, Christoph, Peter and Phil. -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= JACK A. SMITH || Union Carbide Corp. || Phone: (304) 747-5797 Catalyst Skill Center || FAX: (304) 747-5571 P.O. Box 8361 || S. Charleston, WV 25303 || Internet: jas@medinah.atc.ucarb.com -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From caldwell@utdallas.edu Tue Aug 31 12:46:18 1993 Received: from utdallas.edu for caldwell@utdallas.edu by oscsunb.ccl.net (5.65c+KVa/930601.1506) id AA01771; Tue, 31 Aug 1993 18:46:43 -0400 Received: from hydrogen.utdallas.edu by utdallas.edu (ZMailer 2.1.3 #231) with BLIMP id <74201>; Tue, 31 Aug 1993 17:46:32 -0500 From: "Richard A. Caldwell" To: chemistry@ccl.net Subject: HUckel for Macs Cc: caldwell@utdallas.edu Message-Id: <93Aug31.174632cdt.74201@utdallas.edu> Date: Tue, 31 Aug 1993 17:46:18 -0500 Does anyone have a good public domain Hueckel MO program for Macintoshes? I'd like to make it generally available to our students. Thanks, Dick Caldwell From CUNDARIT@MSUVX1.MEMST.EDU Tue Aug 31 12:50:46 1993 Received: from msuvx1.memst.edu (memstvx1.memst.edu) for CUNDARIT@MSUVX1.MEMST.EDU by oscsunb.ccl.net (5.65c+KVa/930601.1506) id AA02501; Tue, 31 Aug 1993 19:47:40 -0400 Received: from MSUVX1.MEMST.EDU by MSUVX1.MEMST.EDU (PMDF V4.2-11 #3869) id <01H2EM1NPS9C9EDGDP@MSUVX1.MEMST.EDU>; Tue, 31 Aug 1993 18:50:46 CST Date: Tue, 31 Aug 1993 18:50:46 -0600 (CST) From: CUNDARIT@memstvx1.memst.edu Subject: lanthanide chemistry To: chemistry@ccl.net Message-Id: <01H2EM1NRXF69EDGDP@MSUVX1.MEMST.EDU> X-Vms-To: IN%"chemistry@ccl.net" Mime-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Content-Transfer-Encoding: 7BIT Hi, The latest version of GAMESS from Mark Gordon and the Iowa State group has the lanthanide ECPs and valence basis sets developed by myself and Walt Stevens (JCP 1993, 98, 5555) built in. For now, they are limited to single-point energy runs, but work with any wavefunction. Our initial results at Memphis State for predicting the structure of the simplest lanthanide trihalides are excellent (i.e., reproduction of bond lengths to within 1-3%). We run into the usual problem for d- and f-block chemistry with regards to energetics, i.e. there is a limited exptl. data base to compare with, so the jury must remain out on that one for now. It is my understanding that the Ross-Pitzer-Ermler team is in the last phases of developing and testing ECPs and valence basis sets for the lanthanides. Dolg, Preuss and Stoll have developed lanthanide effective core potentials with a variety of core sizes. So there are a few options on the ab-initio side. As far as semi-empirical approaches, the only one I am aware of is the INDO appraoch derived by Mike Zerner, Notker Rosch and co. One application of computational methods to lanthanides that we are very excited about is the use of molecular mechanics. I commend to the attention of anyone interested in such an approach to lanthanide chemistry the paper by Ben Hay (IC, 1991, 30, 2876). We have implemented Ben's paramters into Chem3D+ on a Quadra 800 and in the space of an hour we can optimize the structure of a good sized lanthanide complex, include a dozen or so simulated annealing cycles. The coupling of the Chem 3D+ GUI with the MM2 force field eases the analysis and treatment of high coordination number lanthanide complexes. Tom Cundari Assistant Professor Department of Chemistry Memphis State University Memphis, TN 38152 phone: 901-678-2629 fax: 901-678-3447