From msrag@csv.warwick.ac.uk Wed Oct 28 09:48:37 1992 Date: Wed, 28 Oct 1992 09:48:37 GMT From: Dr D Buttar To: chemistry@ccl.net Subject: d orbitals in semiempirical calculations. I would like to perform some semiempirical calculations on chlorine containing compounds, but want to include d orbitals. Could anyone inform me which semiempirical programs allow the inclusion of parameters for d orbitals. Many Thanks, David Buttar University of Warwick From schinke@biochemtech.uni-halle.dbp.de Wed Oct 28 14:49:15 1992 Date: Wed, 28 Oct 1992 13:49:15 +0100 From: schinke@biochemtech.uni-halle.dbp.de To: chemistry@oscsunb.ccl.net Subject: Quest to NMR related topics Dear Subscribers Who can help me? Which computer system and software can I use for a connection between a Bruker-NMR-spectrometer(AM series) and a workstation (UNIX-based). Which software could we use to do this job. Especially we are interested in processing 1D, 2D and 3D NMR-spectras. Thanks for your help in advance. Steffen Thomas (Please direct any notes and letters to the address on the bottom of this letter, Im not a subscriber of the list) =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= =-= Heiko Schinke =-= =-= Martin-Luther-University, Dept. of Biochemistry/Biotechnology =-= =-= P. O. Box 8, D-4020 Halle/Saale, Germany =-= =-= =-= =-= Phone Number: (0345) 617-242 FAX Number: (0345) 647-616 =-= =-= =-= =-= E-Mail: schinke@biochemtech.uni-halle.dbp.de =-= =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From friedman@tammy.harvard.edu Wed Oct 28 05:22:57 1992 Date: Wed, 28 Oct 92 10:22:57 -0500 From: friedman@tammy.harvard.edu (Dawn Friedman) To: chemistry@ccl.net Subject: QCPE Bulletin Does QCPE provide an online index of programs, or must I write for a subscription to the Bulletin? Can someone tell me how to reach whichever alternative is feasible? Thanks, Dawn Friedman From gene@eastrg2.cray.com Wed Oct 28 07:29:38 1992 Date: Wed, 28 Oct 92 12:29:38 EST From: gene@eastrg2.cray.com (Eugene Fleischmann) To: chemistry@ccl.net Subject: RE: Transition Metal Calculations > From chemistry-request@ccl.net Wed Oct 21 16:33:19 1992 > To: CHEMISTRY@oscsunb.ccl.net > Subject: Transition Metal Calculations > Sender: chemistry-request@ccl.net > > Hi, > Having recently joined this list I would like to ask about available > programs that perform geometry optimisation on systems including > 2nd row transition metals. I realise an ab initio packake would > handle this but the systems are large and would require too > much cpu time. I suppose I'm looking at semi-empirical programs ? > > Thanks for any help. > > john upham > > John Upham, School of Chemistry, University of Reading, Berks., RG6 2AD, UK. > Email: scsupham%susssys1.rdg.ac.uk@uk.ac (BITnet), scsupham@rdg.susssys1 (Janet)Voice: +44 734 875123 x7441 (day), Fax: +44 734 311610 > > --- > Administrivia: This message is automatically appended by the mail exploder: > CHEMISTRY@ccl.net --- everyone CHEMISTRY-REQUEST@ccl.net --- coordinator > OSCPOST@ccl.net send help from chemistry Anon. ftp www.ccl.net > --- > > One program that allows calculations on systems with 2nd row transition metal atoms is DGauss, a density functional theory based package from Cray Research. There are other DFT codes available from other sources as well, employing various implementations of the DFT method. DGauss uses gaussian functions and has basis sets available for all elements through Xenon (AN=54). One can also perform ab initio HF calculations on systems containing transition metals using effective core potentials (ECP). ++++++++++++++++++++++++++++++++++++++++ Eugene D. Fleischmann, Ph.D. Senior Sales Analyst Cray Research, Inc. (301)595-2695 gene@eastrg2.cray.com ++++++++++++++++++++++++++++++++++++++++ From jan@si.fi.ameslab.gov Wed Oct 28 05:25:49 1992 From: jan@si.fi.ameslab.gov (Jan Jensen) Subject: Reponses to: "Large Semiempirical Calculations" To: chemistry@ccl.net Date: Wed, 28 Oct 92 11:25:49 CST Fellow Netters, A few people have requested a summary of reponses to my posting on large semiempirical calculations, so here it is (preceeded by the original posting). One reponse, from Mark Thompson, got lost in the editing process. If I remember right, it mentioned semiempirical MD studies on 80-100 atom system. (I would be grateful to Mark Thompson if he would summarize the original posting for the net.) Thanks to everybody who responded, it was very educational. It sure looks like many molecular mechanics studies of chemical systems could be checked against (if not entirely replaced by) semiempirical studies. Jan H. Jensen Dept. of Chemistry Iowa State University ORIGINAL POSTING Fellow netters, Here are some questions to all you semiempirical folks. What is the practical size limit on molecules one can do with semiempirical theory (e.g. AM1)? Is there a (un)official record for the largest system? It would seem that as computers get faster and memory and disk cheaper, quantum mechanical calculations should make their way into territory previously dominated by molecular mechanics (e.g. peptides, enzyme active sites, natural products, etc.). How far away are we from 500 or 1000 atom systems? Any tips, success stories, timings, etc. will be appreciated; and summarized for the list if there is sufficient interest. Jan Jensen ------- Dear prof. Jensen, Last winter prof M. Zerner from Florida reported on a wintermeeting in the Netehrlands an excited state calculation on the photosynthetic reaction centre. I do not know how much atom are involved in there, but there certainly are several hundred. See: JACS(1990),112,7828-7830. Best regards, Han Zuilhof ------- Hi, I have done AM1 calculations on 150 atom systems on my Iris 4D/35 with 48Mbytes of RAM workstation. I am sure that with a bigger system, one can push the 500 atom limit. Dzung The DNA fragment in the Gaussian 92 poster is 378 atoms, and a HF/STO-3G single point only takes about 2 days on a workstation (RS/6000-550). So 500 atoms is thinking pretty small for a semiempirical calculation, at least for a single point. I know that people at Cray have done over 500 atoms in MNDO90, but I'm don't think they worked up much of a sweat doing something that size. An optimization is much more difficult, of course, because of the large number of degrees of freedom (to say nothing of the multiple minima problem). Mike Frisch ------- I have just completed a study which required that I describe clusters containing up to 158 atoms (536 valence orbitals). I found that the limiting factor on the maintain I use (a CRAY X-MP) was memory, not cpu. On this machine (at the time of the old operating system which artificially limited the ammount of memory one user could obtain: 10M) I could go no further than 210 atoms. The cpu was really never an issue because even the largest cluster required only about 5 minutes per single point energy. I suspect that people out there have far better resources at there disposal than I, and they very well could be infringing on the molecular mechanics domain (500 atoms) already. Best Wishes Randall C. Boehm ------- I'm using GEOMOS from QCPE (#584). It is limited to 75 atoms, including dummy atoms. Good luck. Pat Hogue ------- Dear Jan: I don't know what the actual record is but I think we're quite far away from 500 atoms. From my own experience, we were able to optimize a small molecule in the acive site of a dehydrogenase. The active site was obtained by cutting off residues within 5A from the molecule. The complex obtained in this way had 132 atoms. The force field for the whole molecule was obtained on a SGI Iris after four days (with nice -19 but the computer wasn't too busy with other applications at the time). I'd be interested in other replies you get. Sincerely, Piotr From milfeld@hermes.chpc.utexas.edu Wed Oct 28 06:37:55 1992 From: milfeld@hermes.chpc.utexas.edu (Kent F. Milfeld) Subject: (AMDM) Austin Molec. Design Meeting Dec. 11 To: chemistry@ccl.net Date: Wed, 28 Oct 92 12:37:55 CST ***************************************************** * * * Austin Molecular Design Meeting * * AMDM * * * * - Seminars in Molecular Design - * * * ***************************************************** Announcement Scientists interested in molecular design are invited to attend a one day program of seminars, posters, and vendor demos at the Univ. of Texas System's Center for High Performance Computing (CHPC) on Friday, December 11, 1992. Both CHPC (UT) and the Institute for Molecular Design (U. of Houston) will co-host the meeting. Registration Fees are $30 before Nov. 18 ($15 students), and $50 after Nov. 18 ($25 students). Registration costs cover abstract book, lunch, refreshments, and finger-foods during poster session. For registration forms and announcement updates send email to amdm@chpc.utexas.edu (Attn: Leslie Bockoven,registration, Dr. Regina Monaco, abstracts; Dr. Kent Milfeld administratia.) Posters are welcome--please send abstract. Registration forms available by anonymous ftp: ftp.chpc.utexas.edu Use full internet address for password (e.g., wrk_stat@willu.a10.edu), cd to pub/doc, then get amdm.regis. The emphasis of this gathering will be a fundamental and basic view of the fields which contribute to molecular design and modeling (Dynamics, NMR, X-ray Crystallography, etc.), and research within these areas relating to modeling and design. Scientific Program: Subject Dynamics, Thermodynamics Brownian Motion Dr. J. Andrew McCammon (U of Houston) Annealing/Structure Dr. B. Montgomery Pettitt (U of Houston) NMR Dr. Angela Gronenborn (NIH) X-ray Dr. Marvin Hackert (U of Texas, Austin) Quantum Simulations Dr. Peter Rossky (U of Texas, Austin) Modeling Force Fields Dr. Clark Landis (U of Colorado) Density Functional Theory Dr. Stefan Estreicher (Texas Tech.) Seminars begin at 8:00 and continue until ~3:45 ; poster session will begin at ~3:45, end at ~6:00; ; demos all day. Talks will vary, 35-50 minutes, depending upon subject and number of speakers. The University of Texas System amdm@chpc.utexas.edu Center for High Performance Computing 1-800-262-2472 phone 10100 Burnet Rd. CMS 1.154 (512) 471-2445 fax Austin TX 78758-4497 \\_____/===\_____// Inst. for o O --0\ /0-- & Molec. /|/ (@) Design o-o _________________________ From smb@smb.chem.niu.edu Wed Oct 28 10:13:05 1992 Date: Wed, 28 Oct 92 16:13:05 -0600 From: smb@smb.chem.niu.edu (Steven Bachrach) To: CHEMISTRY@ccl.net Subject: G90 unable to determine electronic state? Dear Fellow GAUSSIAN users, I have run across a problem for which I am stumped. I am calculating [3]radialene (also known as trimethylenecyclopropane) at HF/6-31G* and I obtain the following note with the printing of the orbital energies: ORBITAL SYMMETRIES. OCCUPIED (?A) (?B) (?B) (?B) (E') (E') (?C) (?D) (?D) (?B) (?E) (?E) (?D) (?F) (?F) (?G) (A2") (?G) (?C) (E") (E") VIRTUAL (A2") (?C) (?H) (E") (E") (?I) (?I) (?H) (?H) (?H) (?H) (?H) (?H) (?H) (?H) (?C) (?H) (?C) (A2") (E") (E") (?C) (?H) (?H) (A2") (E") (E") (?C) (?G) (?H) (?D) (?G) (?E) (?H) (?D) (?D) (?E) (?C) (?B) (?B) (A2") (?C) (?A) (?B) (?B) (E") (E") (?B) (A1") (?A) (E") (E") (?B) (?B) (E") (E") (?C) (?A) (?A) (A2") (?A) (A1") (?A) (?A) (?A) (?B) (?E) (?A) (?A) (?A) (E") (E") (?B) (?A) (?A) (?E) (?D) (?G) (?B) (?A) (?A) Unable to determine electronic state: partially filled degenerate orbitals. Alpha eigenvalues -- -11.25198 -11.25072 -11.25072 -11.23576 -11.23575 Alpha eigenvalues -- -11.23575 -1.18082 -1.00572 -1.00572 -0.93624 Alpha eigenvalues -- -0.70648 -0.70648 -0.65194 -0.61726 -0.61726 Alpha eigenvalues -- -0.58907 -0.51302 -0.44276 -0.44276 -0.33522 Alpha eigenvalues -- -0.33522 0.06562 0.25762 0.27171 0.28584 Alpha eigenvalues -- 0.28584 0.29117 0.29117 0.33139 0.33139 Alpha eigenvalues -- 0.45392 0.45392 0.49633 0.50039 0.54311 Alpha eigenvalues -- 0.54311 0.58055 0.71895 0.71895 0.73146 Alpha eigenvalues -- 0.80615 0.80615 0.87885 0.90105 0.90105 Alpha eigenvalues -- 0.91554 0.97250 0.97250 1.02324 1.03032 Alpha eigenvalues -- 1.11098 1.11098 1.13319 1.20105 1.21262 Alpha eigenvalues -- 1.21262 1.22136 1.22136 1.28795 1.28795 Alpha eigenvalues -- 1.33390 1.49356 1.51190 1.51190 1.56059 Alpha eigenvalues -- 1.56059 1.68007 1.68007 1.80671 1.89532 Alpha eigenvalues -- 1.95644 1.95852 1.95852 2.15320 2.15320 Alpha eigenvalues -- 2.20278 2.20278 2.33406 2.36663 2.36663 Alpha eigenvalues -- 2.47896 2.48772 2.49248 2.49599 2.56728 Alpha eigenvalues -- 2.56728 2.67192 2.67192 2.99927 3.06840 Alpha eigenvalues -- 3.06840 3.07609 3.07609 3.60270 3.60270 Alpha eigenvalues -- 3.72680 4.45863 4.57687 4.57687 4.66894 Alpha eigenvalues -- 5.27297 5.27297 Note the inability to determine the electronic state. Now i count 42 electrons in this systems, as does the program, which means 21 occupied MOs (this is an RHF calculation). I look at the orbital energies and the first 21 orbitals all have negative energies, are all doubly occupied, and there is no partially filled degenerate sets of orbitals. Orbitals (2,3) (8,9) (11,12) (14,15) (18,19) and (20,21) are doubly degenerate sets and are fully occupied as is the triple degenerate set (4,5,6). The LUMO (MO 22) is nondegenerate. What gives here? Oh, by the way I am running G90. Thanks for the help. Steven Bachrach Department of Chemistry Northern Illinois University DeKalb, Il 60115 smb@smb.chem.niu.edu From d3f012@gator.pnl.gov Wed Oct 28 07:44:43 1992 Date: Wed, 28 Oct 92 15:44:43 PST From: d3f012@gator.pnl.gov Subject: Re: Reponses to: "Large Semiempirical Calculations" To: chemistry@ccl.net, jan@si.fi.ameslab.gov > Fellow Netters, > > A few people have requested a summary of reponses to my posting on > large semiempirical calculations, so here it is (preceeded by the original > posting). One reponse, from Mark Thompson, got lost in the editing process. > If I remember right, it mentioned semiempirical MD studies on 80-100 atom > system. (I would be grateful to Mark Thompson if he would summarize the > original posting for the net.) Thanks to everybody who responded, it was > very educational. It sure looks like many molecular mechanics studies of > chemical systems could be checked against (if not entirely replaced by) > semiempirical studies. > > Jan H. Jensen > Dept. of Chemistry > Iowa State University > > ORIGINAL POSTING > > Fellow netters, > > Here are some questions to all you semiempirical folks. What is the > practical size limit on molecules one can do with semiempirical theory > (e.g. AM1)? Is there a (un)official record for the largest system? > It would seem that as computers get faster and memory and disk cheaper, > quantum mechanical calculations should make their way into territory previously > dominated by molecular mechanics (e.g. peptides, enzyme active sites, > natural products, etc.). How far away are we from 500 or 1000 atom > systems? Any tips, success stories, timings, etc. will be appreciated; > and summarized for the list if there is sufficient interest. > > Jan Jensen ######################################################### Here is my original response with some changes. Mark T. ######################################################### Jan, I published results of semiempirical UV/vis spectroscopic calculations using INDO/s on the chromophores of the photosynthetic reaction center of Rps. viridis. [JACS 113, (1991) p. 8210] These calculations contained: 536 atoms, 1532 electrons,1436 basis functions. The single-excited CI used the lowest 1680 single excited configurations from the ground state. These size calculations are very routine now. At the time, they were done on a Cray YMP. Now, they can be done on IBM 550-strength workstations. (These calculations were all performed with Argus) .... At PNL we are running semi-empirical MD calculations (with forces >from Hartree Fock) on 60-100 atom systems on workstations. Mark Thompson ************************************************************************** Mark A. Thompson 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 **************************************************************************