From scsupham@reading.ac.uk Thu Sep 2 06:29:59 1993 From: scsupham@reading.ac.uk Date: Thu, 2 Sep 93 11:08:29 BST Message-Id: <263.9309021008@scsscsc3> To: chemistry@ccl.net Subject: G92 MP2 geometry optimisation problem ---------- X-Sun-Data-Type: text X-Sun-Data-Description: text X-Sun-Data-Name: text X-Sun-Content-Lines: 39 Hi G92 users, I've been trying to do a geometry optimisation using MP2 and so far the program has done 63 geometry cycles without converging ! I started the structure (thiophene) from the microwave structure. What am I doing wrong ??? Should I used opt rather than fopt ? Help ! Would it be better to use cartesians rather than a Z-matrix ?? john upham cut here--- %CHK=thio_mp2 #p rMP2/3-21G** SCF=DIRECT fopt MP2=stingy thiophene geometry opt using the MP2 level of theory 0 1 S C 1 r2 C 1 r2 2 a3 C 2 r4 1 a4 3 d4 C 3 r4 1 a4 2 d4 H 2 r6 1 a6 3 d6 H 3 r6 1 a6 2 d6 H 4 r8 2 a8 1 d6 H 5 r8 3 a8 1 d6 Variables: r2= 1.7140 a3= 92.09 r4= 1.3690 a4= 111.50 r6= 1.0780 a6= 119.80 r8= 1.0800 a8= 124.25 Constants: d4= 0.00 d6= 180.00 ---------- X-Sun-Data-Type: default X-Sun-Data-Description: default X-Sun-Data-Name: thio.gin X-Sun-Content-Lines: 28 %CHK=thio_mp2 #p rMP2/3-21G** SCF=DIRECT fopt MP2=stingy thiophene geometry opt using the MP2 level of theory 0 1 S C 1 r2 C 1 r2 2 a3 C 2 r4 1 a4 3 d4 C 3 r4 1 a4 2 d4 H 2 r6 1 a6 3 d6 H 3 r6 1 a6 2 d6 H 4 r8 2 a8 1 d6 H 5 r8 3 a8 1 d6 Variables: r2= 1.7140 a3= 92.09 r4= 1.3690 a4= 111.50 r6= 1.0780 a6= 119.80 r8= 1.0800 a8= 124.25 Constants: d4= 0.00 d6= 180.00 From swl26@cas.org Thu Sep 2 03:33:55 1993 Date: Thu, 2 Sep 93 07:33:55 EDT From: swl26@cas.org (Steve Layten x3451) Message-Id: <9309020733.AA22106@cas.org> Subject: Re: acetamide molecule To: gjt@nitrogen.lanl.gov If you have an STN International account, you can download the 3D-coordinates for this molecule (and about 4.8 million of the 12 million in the CAS Registry file). The 3D-coordinates were generated by the CONCORD program (from Tripos). Coordinates can be downloaded in Alchemy or Sybyl file formats (also from Tripos), and distances/angles can be measured in these packages. The service on STN International is NOT free, and a fee is charged for each substance when 3d-coordinates are downloaded. Enough of what sounds like a commercial. For more information, send me a note. -- Steven W. Layten, Senior Engineer Chemical Abstracts Service, PO Box 3012, Columbus, OH 43210 +1 614 447 3600 INET: swl26@cas.org UUCP: osu-cis!chemabs!swl26 # # # Speaking only for myself, and NOT for Chemical Abstracts Service! # # # From Veittes@rrz.Uni-Koeln.DE Thu Sep 2 16:44:39 1993 Date: Thu, 2 Sep 1993 14:44:39 +0200 From: Markus Veittes Message-Id: <199309021244.AA67139@rs1.rrz.Uni-Koeln.DE> To: chemistry@ccl.net Subject: Turbomole mpgrad Does anyone know something about the Turbomole mpgrad program and his author Dr. F. Haase from the Humboldt University of Berlin (Germany) ? Any hints are welcome. Many thanks. Markus Veittes, Regional Computing Center Cologne (Germany) E-mail: veittes@rrz.uni-koeln.de From reinert@VAX.MPIZ-KOELN.mpg.d400.de Thu Sep 2 21:02:34 1993 Date: Thu, 2 Sep 1993 19:02:34 +0200 From: reinert@vax.mpiz-koeln.mpg.d400.de Message-Id: <12*/S=reinert/OU=VAX/O=MPIZ-KOELN/PRMD=MPG/ADMD=dbp/C=de/@MHS> To: chemistry@ccl.net Subject: JUMNA Dear computational Chemists, I am looking for the nucleic acid modeling program JUMNA by Richard Lavery. Though I tried to contact him via e-mail and via snail mail nothing happened. Can someone give me a hint how and where to obtain this software? Many thanks in advance, Peter Peter Reinert (ZWDV), Max-Planck-Institut fuer Zuechtungsforschung, Carl-von-Linne-Weg 10, 50829 Koeln, Germany Phone: ++49/221/5062-539 or -538 or -537, FAX: ++49/221/5062-513 "reinert@vax.mpiz-koeln.mpg.d400.de" From jyk@host11.lctn.u-nancy.fr Thu Sep 2 17:49:21 1993 Date: Thu, 2 Sep 1993 15:49:21 +0200 From: jyk@host11.lctn.u-nancy.fr Message-Id: <9309021349.AA13320@host11.lctn.u-nancy.fr> To: chemistry@ccl.net Subject: electrochemistry simulation Hi netters, The aim of a part of my work is to compute the electrical discharge ( or charge ) curve of the LiV2O5 compound with the help of the simulation. I would like to know , whether it is possible to simulate the experimental electrical discharge ( or charge ) curve. The chemical equation I use is the following , _______________________________________________________________________ | | | Bx | | V2O5 ( solid ) + x * Li ( solid ) -------> LixV2O5 ( solid ) | | | |_______________________________________________________________________| at ambient temperature , and for 0 < x < 1. Is it possible to find programs , which are able to calculate the value Bx ? Perhaps someone has already done such a calculation with the same compound or with another. Can you send me your impression about such a calculation. What are the difficultes ? When the Bx value has been determined for a large number of points, how can we relate this value to the following equation ( Nernst law ) which gives the emf . ______________________ | | | - 1 | | e ( V ) = ---- DG | | nF | |______________________| Jean-Yves KEMPF Universite de Nancy I, Laboratoire de chimie theorique B.P. 239 54506 Vandoeuvre-les-Nancy FRANCE. Here is my e-mail : jyk@host11.lctn.u-nancy.fr Thank you. ----- End of the message ----- From schurko@CC.UManitoba.CA Thu Sep 2 05:38:33 1993 Date: Thu, 2 Sep 1993 10:38:33 -0500 (CDT) From: Robert Schurko Subject: Re: G92 MP2 geometry optimisation problem To: scsupham@reading.ac.uk Message-Id: On Thu, 2 Sep 1993 scsupham@reading.ac.uk wrote: > > Hi G92 users, > I've been trying to do a geometry optimisation using MP2 and so far > the program has done 63 geometry cycles without converging ! I started the > structure (thiophene) from the microwave structure. What am I doing wrong ??? > Should I used opt rather than fopt ? Help ! Would it be better to use > cartesians rather than a Z-matrix ?? > > john upham > > cut here--- > > %CHK=thio_mp2 > #p rMP2/3-21G** SCF=DIRECT fopt MP2=stingy > > thiophene geometry opt using the MP2 level of theory > > 0 1 First, have you attempted optimizing the geometry with a lower basis set using perhaps just HF optimization? The best thing to do is run a preliminary rhf run, with perhaps rhf/sto-3g to optimize the given microwave geometry. Second, using the option opt=readfc run the basis set you are using for MP2's (i.e. run an rhf/6-31g* or whatever basis it is you're using). Then, finally, run the MP2, and be sure to use opt=readfc, and a chkpoint file to take these force constants from (i.e. the chk file from the previous rhf run). I hope this works for you. Rob From stoutepf@chemsci1.es.dupont.com Thu Sep 2 07:36:58 1993 Message-Id: <9309021636.AA09135@chemsci1.es.dupont.com. chemsci1 chemsci1.es.dupont.com> Date: Thu, 2 Sep 1993 12:36:58 -0500 To: CHEMISTRY@ccl.net From: stoutepf@chemsci1.es.dupont.com (Pieter Stouten) Subject: Re: acetamide molecule On Thu, 2 Sep 93 07:33:55 Steve Layten wrote: >If you have an STN International account, you can download the >3D-coordinates for this molecule (and about 4.8 million of the 12 million >in the CAS Registry file). The 3D-coordinates were generated by the >CONCORD program (from Tripos). Coordinates can be downloaded in Alchemy >or Sybyl file formats (also from Tripos), and distances/angles can be >measured in these packages. > I don't think that concord _MODELS_ provide more than a crude description of molecules based on 2D _MODELS_. If one wants to have a model for just one compound virtually any modelling program can do a considerably better job. I assume, however, that experimental data was requested and here STN comes in very handy. I did a quick search for acetamide and words like "structure", "x-ray", "ab initio", "diffraction". I found the following. * Jeffrey, G. A.; Ruble, J. R.; McMullan, R. K.; DeFrees, D. J.; Binkley, J. S. & Pople, J. A., "Neutron diffraction at 23 K and ab initio molecular- orbital studies of the molecular structure of acetamide", Acta Crystallogr., Sect. B, B36 (1980) 2292-2299. * Ottersen, Tor, "Structure of the peptide linkage. Structures of formamide and acetamide at -165.deg. and an ab initio study of formamide, acetamide, and N-methylformamide", Acta Chem. Scand., Ser. A, A29 (1975) 939-944. Hope this proves useful. Cheers, Pieter. Pieter Stouten, Senior Research Scientist || Computer Aided Drug Design Group || The Du Pont Merck Pharmaceutical Company || Adventures get spoiled P.O. Box 80353, Wilmington, DE 19880-0353 || by being reduced to data Phone: +1 (302) 695 3515 || -- Fax: +1 (302) 695 2813 || Poul Anderson ARA/Fax: +1 (302) 695 4324 || E-mail: stoutepf@chemsci1.es.dupont.com || E-mail: stoutepf@lldmpc.dnet.dupont.com || From chp1aa@surrey.ac.uk Thu Sep 2 14:29:28 1993 From: Mr Andrew D Allen Message-Id: <9309021037.AA00436@central.surrey.ac.uk> Subject: Crystal Eyes To: chemistry@ccl.net Date: Thu, 2 Sep 93 11:37:13 BST Just a quicky. Does anyone know how much a set of crystal eyes would cost, for the SG Indigo? And who to order from? Andy. From scheiner@ibm10.biosym.com Thu Sep 2 04:02:05 1993 Date: Thu, 2 Sep 1993 11:02:05 -0700 From: scheiner@ibm10.biosym.com (Andy Scheiner) Message-Id: <9309021802.AA20201@ibm10.biosym.com> To: CHEMISTRY@ccl.net Subject: Turbomole MPGRAD & Dr. F. Haase Markus, you can contact the author directly : his email address is fh@oberon.zipc.wtza-berlin.de there is a publication in the august1993 issue of j.comp.chem. about this ... hope this helps, best regards, Andy Scheiner Biosym Technologies PS the code is being distributed as part of TURBOMOLE by BIOSYM Technologies, Inc. in San Diego, USA. From merkle@parc.xerox.com Thu Sep 2 04:24:49 1993 From: Ralph Merkle To: chemistry@ccl.net, nanotech@cs.rutgers.edu Subject: Chemical Design Automation News Message-Id: <93Sep2.112454pdt.12171@manarken.parc.xerox.com> Date: Thu, 2 Sep 1993 11:24:49 -0700 I talked with the editorial office at Butterworth - Heinemann, and was very pleased to hear that they will be continuing the publication of Chemical Design Automation News. This arrangement was apparently finalized about two weeks ago. My understanding that the August issue would be the last issue was in error and came from a conversation in mid July with the former editor of Chemical Design Automation News: Barbara F. Graham. (Barbara is actively seeking employment in the Boston area and can be reached at 617-899-0376). As a consequence my article, "Molecular Manufacturing: Adding Positional Control to Chemical Synthesis," will not be available for anonymous FTP. I look forwards to seeing it soon in Chemical Design Automation News. Ralph C. Merkle From 72600.1502@CompuServe.COM Mon Sep 2 11:26:46 1993 Date: 02 Sep 93 15:26:46 EDT From: Cindy Diamond <72600.1502@compuserve.com> To: Netters Subject: CASE, Flowcharting Software Message-Id: <930902192645_72600.1502_EHA31-1@CompuServe.COM> I know this is a little offbase, but has anyone out there worked with either CASE or Flowcharting software packages for windows. I'm interested particularly in "Flow Charting 3" and "ABC Flow Charter". Any comments or suggestions would be appreciated. Thanks. From barry@tralee.cray.com Thu Sep 2 10:36:21 1993 From: barry@tralee.cray.com (Barry C. Bolding) Message-Id: <9309022036.AA05086@tralee.cray.com> Subject: fob and pdb files for use with XPLOR To: CHEMISTRY@ccl.net Date: Thu, 2 Sep 93 15:36:21 CDT I am looking for an xray structure factor files (.fob) and associated pdb files for systems with >2000 atoms (the larger the better) for testing refinement with the X-PLOR program. The associated X-PLOR input files, with symmetry operations and lattice constants would also be helpful. Thanks, Barry *** *** *** *** *** *** *** *** *** *** *** *** *** *** *** *** *** *** Dr. Barry Bolding Senior Computational Chemist ___ H H Cray Research, Inc. / \___/ H \ Cray Research Park \___/ \___/ Si-H 655E Lone Oak Drive / \___/ \___/ H Eagan, MN 55121 \___/ \___/ \___/ H \___/ \___/ \___/ Phone: (612)-683-3642 \___/ \___/ \ Internet: barry@cray.com \___/ \___/ *** *** *** *** *** *** *** *** *** *** *** *** *** *** *** *** *** *** From maloneyhuske%phvax.dnet@smithkline.com Thu Sep 2 15:19:12 1993 Date: Thu, 2 Sep 93 19:19:12 -0400 Message-Id: <9309022319.AA19121@smithkline.com> From: maloneyhuske%phvax.dnet@smithkline.com (Keith MaloneyHuss x6083) To: "chemistry@ccl.net"%INET.dnet@smithkline.com Subject: Natural conformation of protein=global minimum? Is it assumed that the natural conformation of all proteins is the free energy global minimum? If so, why? It must be at least a local minimum, but why assume there is no possible lower energy state? It is obviously not easily accessable or it would be the natural configuration. Aren't there chaperones to assist folding that determine the final conformation, and thus select conformation based not upon absolute energy minimum criteria but rather find a good (read very stable) local minimum which is in the required shape for the protein's function? --keith