From VERCAU@BNANDP11.bitnet Fri Apr 30 14:11:03 1993 Message-Id: <199304301309.AA13912@oscsunb.ccl.net> Date: Fri, 30 Apr 93 14:10:03 +01 From: "Daniel P. Vercauteren" Subject: AI in chemistry To: chemistry@ccl.net ************************************************************************ * * * Educative Session in Large Scale Computation for Quantum * * Physics and Chemistry * * * * Programme Gouvernemental en Technologie de l'Information * * Calcul de Puissance en Chimie et Physique Quantiques * * * * Facultes Universitaires Notre-Dame de la Paix, Namur, Belgium * * Namur Scientific Computing Facility Center * * J.-M. Andre and J.-P. Vigneron * * * ************************************************************************ 1993 Namur SCF Specialized Lectures THE USE OF ARTIFICIAL INTELLIGENCE IN CHEMISTRY by Prof. D. DOLATA (Univ of Arizona, Tucson, AZ) Auditorium CH1, FUNDP, Dept of Chemistry, 2, rue Grafe, B-5000, Namur, Belgium Monday, May 3, 1993, 16h15 - 18h30 ---------------------------------- Introduction to Artificial Intelligence (AI) AI in Chemistry Tuesday, May 4, 1993, 16h15 - 18h30 ----------------------------------- Expert Systems WIZARD* and Theorem Proving Wednesday, May 5, 1993, 16h15 - 18h30 ------------------------------------- Applications of Wizard in Chemistry Future Directions of AI in Chemistry * Ref. for Wizard: J. Comput. Chem, 11, 680 (1990) For further information, please contact either: - Prof. J.-M. Andre, Facultes Universitaires Notre-Dame de la Paix (FUNDP), Laboratoire de Chimie Theorique Appliquee (CTA), 61, rue de Bruxelles, B-5000 Namur, Belgium Tel.: +32 (81) 724553, Fax: +32 (81) 724530 E-mail: ANDRE at SCF.FUNDP.AC.BE - Prof. J.-P. Vigneron, Facultes Universitaires Notre-Dame de la Paix (FUNDP), Laboratoire de Physique du Solide (LPS), 61, rue de Bruxelles, B-5000 Namur, Belgium Tel.: +32 (81) 724711, Fax: +32 (81) 230391 E-mail: VIGNERON at SCF.FUNDP.AC.BE - Prof. D.P. Vercauteren, Facultes Universitaires Notre-Dame de la Paix (FUNDP), Laboratoire de Physico Chimie Informatique (PCI), 61, rue de Bruxelles, B-5000 Namur, Belgium Tel.: +32 (81) 724534, Fax: +32 (81) 724530 E-mail: VERCAU at SCF.FUNDP.AC.BE Acknowledge-To: From scsupham@reading.ac.uk Fri Apr 30 10:14:09 1993 From: scsupham@reading.ac.uk Date: Fri, 30 Apr 93 14:32:05 BST Message-Id: <9293.9304301332@scsscsc3> To: chemistry@ccl.net Subject: calculating bond orders/Wiberg Indices ? ---------- X-Sun-Data-Type: text X-Sun-Data-Description: text X-Sun-Data-Name: text X-Sun-Content-Lines: 11 Dear All, What information is needed to calculate bond orders/Wiberg indices ? I have a full Mulliken population analysis available: is that enough ? yours hopefully, john upham John Upham, Dept. of Chemistry, University of Reading, Berks., RG6 2AD, UK. Email: scsupham%reading.ac.uk@uk.ac (BITnet), scsupham@uk.ac.reading (Janet) Voice: +44 734 875123 x7441 (day), Fax: +44 734 311610 ---------- X-Sun-Data-Type: default X-Sun-Data-Description: default X-Sun-Data-Name: .signature X-Sun-Content-Lines: 3 John Upham, Dept. of Chemistry, University of Reading, Berks., RG6 2AD, UK. Email: scsupham%reading.ac.uk@uk.ac (BITnet), scsupham@uk.ac.reading (Janet) Voice: +44 734 875123 x7441 (day), Fax: +44 734 311610 From schinke@biochemtech.uni-halle.dbp.de Fri Apr 30 17:40:33 1993 Date: Fri, 30 Apr 1993 15:40:33 +0200 From: schinke@biochemtech.uni-halle.dbp.de Message-Id: <930430154032*/S=schinke/OU=biochemtech/PRMD=UNI-HALLE/ADMD=DBP/C=DE/@MHS> To: chemistry@ccl.net Subject: Multiple Molecule-Systems with Mopac? Dear Subscribers, we are using MOPAC 5.0 (purchased with SYBYL 6.0). Recent we would compute a multi-molecule-system (see the *.dat-file below, generated with SYBYL). After some computation-time MOPAC stopped (during the computation for the first reaction coordinate) and print in his output-file (see below): THREE ATOMS BEING USED TO DEFINE THE COORDINATES OF A FOURTH ATOM, WHOSE BOND-ANGLE IS NOT ZERO OR 180 DEGREEES, ARE IN AN ALMOST STRAIGHT LINE. THERE IS A HIGH PROBABILITY THAT THE COORDINATES OF THE ATOM WILL BE INCORRECT. and at the end: ATOMS 65, 63, AND 54 ARE WITHIN 0.0059 ANGSTROMS OF A STRAIGHT LINE The bond-angle between theese 3 atoms, which are not connected, is 0 degrees. A second attempt, using cartesian coordinates, showed the same results. Can anybody give us hints for the handling of such multi-molecule-systems with MOAPC? Thank You for Your help. With best regards, H. Schinke ############## Input (DAT)-File for the run ############################## PM3 T=360000 NOINTER CHARGE-1 aceto_rxn.dat isopropylchlorid + NH2 in acetonitril 0006 0.0000 0 0.0000 0 0.0000 0 0000 0000 0000 0006 1.5500 1 0.0000 0 0.0000 0 0001 0000 0000 0006 1.5514 1 111.1064 1 0.0000 0 0002 0001 0000 0017 1.7710 1 109.5989 1 -121.0562 1 0002 0001 0003 0007 3.5578 -1 80.7763 1 93.7999 1 0002 0001 0003 0001 1.1011 1 110.5590 1 -60.5032 1 0001 0002 0003 0001 1.0989 1 109.9108 1 -179.0905 1 0001 0002 0003 0001 1.1028 1 110.4057 1 60.9707 1 0001 0002 0003 0001 1.1043 1 109.7158 1 120.9287 1 0002 0001 0003 0001 1.1033 1 109.8467 1 179.2252 1 0003 0002 0001 0001 1.1019 1 110.1398 1 58.7459 1 0003 0002 0001 0001 1.1015 1 110.2444 1 -60.5427 1 0003 0002 0001 0001 1.0822 1 74.1199 1 -87.4158 1 0005 0002 0001 0001 1.0820 1 126.5937 1 15.1313 1 0005 0002 0001 0006 4.7255 1 94.3647 1 128.2758 1 0005 0002 0001 0007 1.1581 1 150.8418 1 -91.2513 1 0015 0005 0002 0006 1.4591 1 29.0551 1 88.8644 1 0015 0005 0002 0001 1.1001 1 109.3496 1 85.7222 1 0017 0015 0005 0001 1.1004 1 109.2794 1 -34.0471 1 0017 0015 0005 0001 1.1008 1 109.6514 1 -154.1209 1 0017 0015 0005 0006 3.5996 1 153.6728 1 -96.5280 1 0014 0005 0002 0007 1.1578 1 13.9165 1 146.8929 1 0021 0014 0005 0006 1.4574 1 166.0703 1 -32.8884 1 0021 0014 0005 0001 1.0985 1 109.5225 1 -46.5050 1 0023 0021 0014 0001 1.0990 1 109.5135 1 -166.5502 1 0023 0021 0014 0001 1.0988 1 109.5336 1 73.3020 1 0023 0021 0014 0006 3.1821 1 135.8468 1 -33.5144 1 0026 0023 0021 0007 1.1575 1 58.8166 1 -86.8753 1 0027 0026 0023 0006 1.4569 1 121.2665 1 93.3518 1 0027 0026 0023 0001 1.0995 1 109.1838 1 157.7614 1 0029 0027 0026 0001 1.0990 1 109.1728 1 38.1084 1 0029 0027 0026 0001 1.1001 1 109.6732 1 -81.9072 1 0029 0027 0026 0006 3.0767 1 103.4743 1 -51.4763 1 0025 0023 0021 0007 1.1575 1 76.3789 1 166.4251 1 0033 0025 0023 0006 1.4574 1 103.6952 1 -13.7778 1 0033 0025 0023 0001 1.0987 1 109.0487 1 -147.5827 1 0035 0033 0025 0001 1.1000 1 109.7437 1 92.3169 1 0035 0033 0025 0001 1.0985 1 109.6728 1 -27.9951 1 0035 0033 0025 0006 3.4510 1 108.8603 1 -165.3810 1 0031 0029 0027 0007 1.1576 1 46.9670 1 131.3490 1 0039 0031 0029 0006 1.4572 1 132.9267 1 -48.6902 1 0039 0031 0029 0001 1.0997 1 109.3387 1 93.5222 1 0041 0039 0031 0001 1.0980 1 109.2758 1 -26.5337 1 0041 0039 0031 0001 1.0987 1 109.8151 1 -146.1868 1 0041 0039 0031 0006 2.9482 1 112.4182 1 -121.6753 1 0011 0003 0002 0007 1.1579 1 90.4906 1 91.2241 1 0045 0011 0003 0006 1.4577 1 89.4953 1 -88.6234 1 0045 0011 0003 0001 1.0995 1 109.7035 1 149.5640 1 0047 0045 0011 0001 1.0982 1 109.2759 1 29.6008 1 0047 0045 0011 0001 1.0990 1 109.6324 1 -90.1483 1 0047 0045 0011 0006 4.5317 1 139.9017 1 -69.9744 1 0012 0003 0002 0007 1.1573 1 145.3014 1 -130.1153 1 0051 0012 0003 0006 1.4565 1 34.8458 1 49.8356 1 0051 0012 0003 0001 1.0993 1 108.9200 1 -157.5288 1 0053 0051 0012 0001 1.0994 1 110.0562 1 82.4921 1 0053 0051 0012 0001 1.0994 1 109.1379 1 -37.6058 1 0053 0051 0012 0006 3.4721 1 116.7486 1 -176.4873 1 0004 0002 0001 0007 1.1572 1 101.7777 1 86.5285 1 0057 0004 0002 0006 1.4560 1 78.1876 1 -93.6430 1 0057 0004 0002 0001 1.0984 1 109.8789 1 69.2024 1 0059 0057 0004 0001 1.0962 1 108.6552 1 -50.4940 1 0059 0057 0004 0001 1.0984 1 109.8177 1 -170.0241 1 0059 0057 0004 0006 4.4310 1 131.3391 1 -95.8235 1 0054 0053 0051 0007 1.1574 1 168.8801 1 -42.8294 1 0063 0054 0053 0006 1.4566 1 11.3006 1 137.2662 1 0063 0054 0053 0001 1.0997 1 109.2702 1 48.5555 1 0065 0063 0054 0001 1.0992 1 109.5672 1 -71.5576 1 0065 0063 0054 0001 1.0995 1 109.3136 1 168.5094 1 0065 0063 0054 0006 2.8666 1 111.9127 1 114.2402 1 0011 0003 0002 0007 1.1577 1 78.8063 1 126.9038 1 0069 0011 0003 0006 1.4573 1 101.1095 1 -52.9852 1 0069 0011 0003 0001 1.0988 1 109.4665 1 88.1980 1 0071 0069 0011 0001 1.0994 1 109.6016 1 -31.7086 1 0071 0069 0011 0001 1.0989 1 109.3863 1 -151.8561 1 0071 0069 0011 0006 3.1681 1 116.9983 1 65.3880 1 0014 0005 0002 0007 1.1577 1 68.7614 1 18.5956 1 0075 0014 0005 0006 1.4574 1 111.3471 1 -161.5537 1 0075 0014 0005 0001 1.0990 1 110.0250 1 -38.6061 1 0077 0075 0014 0001 1.0988 1 108.9522 1 -158.6613 1 0077 0075 0014 0001 1.0981 1 109.5142 1 81.4778 1 0077 0075 0014 0006 3.0430 1 101.6525 1 178.7693 1 0042 0041 0039 0007 1.1573 1 86.4724 1 -12.0939 1 0081 0042 0041 0006 1.4566 1 93.4012 1 167.6526 1 0081 0042 0041 0001 1.0988 1 110.0533 1 132.2910 1 0083 0081 0042 0001 1.0996 1 109.5192 1 11.8415 1 0083 0081 0042 0001 1.0989 1 108.6354 1 -107.8211 1 0083 0081 0042 0006 2.8961 1 117.9918 1 39.7798 1 0055 0053 0051 0007 1.1572 1 94.4558 1 -21.5512 1 0087 0055 0053 0006 1.4568 1 85.5489 1 158.3391 1 0087 0055 0053 0001 1.0993 1 109.4929 1 75.9636 1 0089 0087 0055 0001 1.0997 1 109.8437 1 -44.3760 1 0089 0087 0055 0001 1.0980 1 108.9221 1 -164.2069 1 0089 0087 0055 4.0 3.8 3.6 3.4 3.2 3.0 2.9 2.8 2.7 2.6 2.5 2.4 2.3 2.2 2.1 2.0 1.9 1.8 1.7 1.6 1.5 ####### end dat-file ########### start out-file ###################### ---------------- stuff deleted --------------------------------- RESTART FILE WRITTEN, TIME LEFT: 336271.4 GRAD.: 70.180 HEAT: 250.6730 CYCLE: 17 TIME:1985.31 TIME LEFT: 334286.1 GRAD.: 86.913 HEAT: 248.3024 CYCLE: 18 TIME: 318.24 TIME LEFT: 333967.8 GRAD.: 88.962 HEAT: 248.1202 RESTART FILE WRITTEN, TIME LEFT: 330634.8 GRAD.: 112.826 HEAT: 244.9363 CALCULATION ABANDONED AT THIS POINT THREE ATOMS BEING USED TO DEFINE THE COORDINATES OF A FOURTH ATOM, WHOSE BOND-ANGLE IS NOT ZERO OR 180 DEGREEES, ARE IN AN ALMOST STRAIGHT LINE. THERE IS A HIGH PROBABILITY THAT THE COORDINATES OF THE ATOM WILL BE INCORRECT. THE FAULTY ATOM IS ATOM NUMBER 66 ---------------- stuff deleted ---------------------------------- 53 C 1.43856 * 27.56940 * 47.24132 * 51 12 3 54 H 1.10289 * 113.07091 * -159.36420 * 53 51 12 55 H 1.10628 * 110.38282 * 82.03550 * 53 51 12 56 H 1.10154 * 110.86405 * -39.47341 * 53 51 12 57 C 4.08353 * 95.06319 * -183.15715 * 4 2 1 58 N 1.15994 * 115.38586 * 98.17581 * 57 4 2 59 C 1.43955 * 64.12061 * -80.79930 * 57 4 2 60 H 1.10829 * 109.67685 * 69.63226 * 59 57 4 61 H 1.10079 * 110.64538 * -49.08832 * 59 57 4 62 H 1.09725 * 110.82013 * -170.03940 * 59 57 4 63 C 4.37425 * 137.62500 * -102.46271 * 54 53 51 64 N 1.16069 * 185.63463 * -39.66892 * 63 54 53 65 C 1.44209 * 0.07684 * 131.59166 * 63 54 53 66 H 1.10339 * 111.26819 * 49.01765 * 65 63 54 ---------------- stuff deleted ---------------------------------- ATOMS 65, 63, AND 54 ARE WITHIN 0.0059 ANGSTROMS OF A STRAIGHT LINE ################### end out-file ################################# =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= =-= Heiko Schinke =-= =-= Martin-Luther-University, Dept. of Biochemistry/Biotechnology =-= =-= P. O. Box 8, D-4020 Halle/Saale, Germany =-= =-= =-= =-= Phone: ++49/345/617242 FAX: ++49/345/647161 =-= =-= =-= =-= E-Mail: schinke@biochemtech.uni-halle.dbp.de =-= =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From ZPZCM@jazz.ucc.uno.edu Tue Apr 30 05:16:06 1993 Date: 30 Apr 1993 11:16:06 -0600 (CST) From: "ZORAN P. ZDRAVKOVSKI" Subject: MOPAC: SADDLE calculations To: chemistry@ccl.net Message-Id: <01GXMCB23Z7M8WWVS9@jazz.ucc.uno.edu> We are trying to do some calculations of transition states with MOPAC using the SADDLE keyword option. We would appreciate if anyone has any references to published results so we can check our calculations. Any other suggestions are welcome. Zoran Zdravkovski Univ. Kiril & Metodij UNO, Dept. of Chem. PMF, Institue of Chemistry New Orelans, LA 70148 91000 Skopje U. S. A. Macedonia ZPZCM@UNO.EDU From chris@glycob.ox.ac.uk Fri Apr 30 12:52:48 1993 Date: Fri, 30 Apr 1993 16:52:48 EDT From: chris@glycob.ox.ac.uk To: chemistry@ccl.net Message-Id: <0096BD00.581020A0.3279@glycob.ox.ac.uk> Subject: MDANAL in Amber Dear Netters, Am I the only person attempting to use the MDANAL package within Amber to analyse hydrogen bonding within a trajectory run and, if so, am I the only person to find it a nightmare to use? Can anyone explain to me how to use the package in order to analyse whether a given oxygen atom in my compound is hydrogen bonded to a water molecule or molecules over a finite period of time? An input file example would be most gratefully received. Thank you in advance. *************************************************************** * Dr. Chris. Edge * Tel. +44-865-275-338 * * Glycobiology Institute * Fax. +44-865-275-216 * * Oxford University * e-mail chris@glycob.ox.ac.uk * * South Parks Road * 100117.3646@compuserve.com * * Oxford OX1 3QU U.K. * * *************************************************************** From MMADRID@B.PSC.EDU Fri Apr 30 08:49:33 1993 Date: Fri, 30 Apr 1993 12:49:33 -0400 (EDT) From: MMADRID@B.PSC.EDU To: chemistry@ccl.net Message-Id: <930430124933.20802015@B.PSC.EDU> Subject: Computational NMR workshop being offered at the PSC in July COMPUTATIONAL NUCLEAR MAGNETIC RESONANCE WORKSHOP Pittsburgh Supercomputing Center July 6-9, 1993 Pittsburgh Supercomputing Center (PSC) is offering biomedical researchers a computational Nuclear Magnetic Resonance (NMR) workshop. The objective of this applications workshop is to introduce participants to different techniques for the elucidation of solution structures of proteins and nucleic acids from NMR interproton distance constraints. Topics to be covered include data reduction, simulated annealing, distance geometry, back calculations and refinements. X-PLOR, CORMA and MARDIGRAS will be extensively discussed. Workshop leaders are: Dr. Axel Brunger, Yale University, Dr. Thomas James, University of California, San Francisco, and Dr. Michael Nilges, European Molecular Biology Laboratory, Heidelberg. Hands-on sessions will be emphasized and participants are encouraged to bring relevant problems from their current research. No prior supercomputing experience is necessary. This workshop is funded by a grant from the Biomedical Research Technology Program, National Center for Research Resources, National Institutes of Health. Travel, meals and hotel accommodations for academic participants are supported by this grant. Enrollment is limited to 20. Deadline for applications is: May 14, 1993. Please direct all inquires to: Nancy Blankenstein (412) 268-4960 or send electronic mail to blankens@cpwpsca (bitnet) or blankens@a.psc.edu (internet) From markm@charles.polymer.uakron.edu Fri Apr 30 10:08:02 1993 Date: Fri, 30 Apr 93 14:08:02 -0400 From: markm@charles.polymer.uakron.edu (Mark Alan Matties) Message-Id: <9304301808.AA12780@charles.polymer.uakron.edu> To: chemistry@ccl.net Subject: MM params for Cd++ ???? i want to do some mm on cadmium arachdate. any recommendations or references on Cd ion parameters would be greatly appreciated. i use sybyl, polygraf, and insight/discover. thanks for any help. mark ps - i know the ion problem is tough. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mark alan matties u of akron markm@polymer.uakron.edu dept of polymer science "aoibheann beatha an scola/ire" akron, ohio, usa From markm@charles.polymer.uakron.edu Fri Apr 30 10:08:02 1993 Date: Fri, 30 Apr 93 14:08:02 -0400 From: markm@charles.polymer.uakron.edu (Mark Alan Matties) Message-Id: <9304301808.AA12780@charles.polymer.uakron.edu> To: chemistry@ccl.net Subject: MM params for Cd++ ???? i want to do some mm on cadmium arachdate. any recommendations or references on Cd ion parameters would be greatly appreciated. i use sybyl, polygraf, and insight/discover. thanks for any help. mark ps - i know the ion problem is tough. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mark alan matties u of akron markm@polymer.uakron.edu dept of polymer science "aoibheann beatha an scola/ire" akron, ohio, usa From lowrey@lsm.nrl.navy.mil Fri Apr 30 10:48:51 1993 Date: Fri, 30 Apr 1993 14:48:51 EDT From: AL LOWREY To: CHEMISTRY@ccl.net Message-Id: <0096BCEF.07EBD4E0.16457@lsm.nrl.navy.mil> Subject: Public Domain Fortran Flow Analyzer ? Dear Net Does anyone know of a public domain code analyzer that will help us sort through code from the 1970's ? I understand that somewhere there are systems that will analyze the program flow of Fortran codes; more sophisticated than FLINT. Thanks Al Lowrey lowrey@lsm.nrl.navy.mil From willa@cgl.ucsf.EDU Fri Apr 30 05:34:09 1993 Date: Fri, 30 Apr 93 12:34:09 -0700 Message-Id: <9304301934.AA11493@socrates.ucsf.EDU> From: willa@cgl.ucsf.edu (Willa Crowell ) To: chemistry@ccl.net Subject: A Quantum Biology/Pharmacology Conference International Society of Quantum Biology and Pharmacology 1993 President's Meeting Chemical Reactions and Molecular Recognition in Drug Design Asilomar Conference Center Pacific Grove, California December 12-15, 1993 Meeting Theme: Combining quantum mechanical and molecular mechanical methods to study chemical reactions in solution and in enzymes. Simulations on non-covalent processes of relevance in drug design, protein folding and protein-ligand complexes. Invited Speakers: Bill Jorgensen, Yale Ken Houk, UCLA Jiali Gao, SUNY, Buffalo C. Cramer, Minnesota Ken Merz, Penn State University Alain St-Amant, UCSF Arieh Warshel, USC Nina Sommers, Monsanto Dennis Underwood, Merck Gerry Maggiora, Upjohn Frank Brown, Glaxo M. Pettit, Houston Dave Pearlman, Vertex Dave Case, Scripps Barry Honig, Columbia Toshio Ichiye, Washington State Valerie Daggett, Washington Dave Spellmeyer, Chiron Tentative Schedule: Monday Morning: Chemical Reactions in Solution and Enzymes I Jorgensen, Houk, Gao, Cramer Monday Evening: Chemical Reactions in Solution and Enzymes II Merz, St-Amant, Warshel Tuesday Morning: Protein Modeling and Drug Design Sommers, Underwood, Maggiora, Brown Tuesday Evening: Molecular Simulations in Solution Pettit, Pearlman, Case Wednesday Morning: Molecular Modeling: Peptides and Proteins Honig, Daggett, Ichiye, Spellmeyer For information: Contact Willa Crowell (415-476-1540) e-mail: willa@cgl.ucsf.edu willa@ucsfvm.bitnet Registration and Lodging Cost: $325 (payable to ISQBP) Includes Sunday, Monday & Tuesday lodging, and meals from Sunday night through Wednesday noon. Send check and application to: Willa Crowell Box 0446 UCSF SF, CA 94143 Attendance is limited to 150 people. Application Form: Name __________________________________ Institution: _________________________ Address: _____________________________ _____________________________ E-mail address: ______________________ From tripos!vela!victor@wupost.wustl.edu Fri Apr 30 11:46:04 1993 Date: Fri, 30 Apr 93 16:46:04 -0500 From: tripos!vela!victor@wupost.wustl.edu (Vic Lewchenko) Message-Id: <9304302146.AA13684@vela.tripos> To: chemistry@ccl.net Subject: RE: Multiple Molecule-Systems with Mopac? In reply to Heiko Schinke's question concerning: >Dear Subscribers, >we are using MOPAC 5.0 (purchased with SYBYL 6.0). Recent we would compute >a multi-molecule-system (see the *.dat-file below, generated with SYBYL). >After some computation-time MOPAC stopped (during the computation for the >first reaction coordinate) and print in his output-file (see below): > > THREE ATOMS BEING USED TO DEFINE THE > COORDINATES OF A FOURTH ATOM, WHOSE BOND-ANGLE IS > NOT ZERO OR 180 DEGREEES, ARE IN AN ALMOST STRAIGHT > LINE. THERE IS A HIGH PROBABILITY THAT THE > COORDINATES OF THE ATOM WILL BE INCORRECT. > > and at the end: > > ATOMS 65, 63, AND 54 ARE WITHIN 0.0059 ANGSTROMS OF A STRAIGHT LINE I would make the following suggestion: When setting up the MOPAC calcualtion in SYBYL, use the SETUP option Z_MATRIX to edit the Z_MATRIX. In SYBYL 6.0, you will have to do the setup from the command line to use this option (it is not yet supported from the dialog box). At the command line enter: SYBYL> QCPE M1 MOPAC SETUP Z_MATRIX you will then see the z matrix listed to the screen. Select row 66 to modify the definition of atom 66. Enter the atom ids for the atoms that will define the distance, angle and torsion internal coordinates. Examine the molecule on the screen and select atoms which do not line up in a straight line. Ideally the atoms you select will be bonded to each other, but this is not always possible. Also the atoms you select must be lower in id number than the atom you are defining (66). I think this is the simplest solution to your problem. Other possible solutions would include renumbering your molecule or adding dummy atoms. If you are still having problems, please e-mail me a mol2 file of your molecule and I will be glad to try to help you further. Regards, Vic Lewchenko Tripos Associates St.Louis, MO USA E-mail: victor@tripos.com From shepard@dirac.tcg.anl.gov Fri Apr 30 13:06:10 1993 Date: Fri, 30 Apr 93 18:06:10 CDT From: shepard@dirac.tcg.anl.gov (Ron Shepard) Message-Id: <9304302306.AA19250@dirac.tcg.anl.gov> To: CHEMISTRY@ccl.net Subject: IP number change for COLUMBUS and TCGMSG codes To all COLUMBUS and TCGMSG users: The IP number for the anonymous ftp server ftp.tcg.anl.gov will change next Wednesday, 05-May-93. The new address will be: 146.137.200.2 This is part of a major change here at Argonne, so if you have problems connecting, please be patient. Ron Shepard shepard@tcg.anl.gov From schinke@biochemtech.uni-halle.dbp.de Fri Apr 30 17:40:33 1993 Date: Fri, 30 Apr 1993 15:40:33 +0200 From: schinke@biochemtech.uni-halle.dbp.de Message-Id: <930430154032*/S=schinke/OU=biochemtech/PRMD=UNI-HALLE/ADMD=DBP/C=DE/@MHS> To: chemistry@ccl.net Subject: Multiple Molecule-Systems with Mopac? Dear Subscribers, we are using MOPAC 5.0 (purchased with SYBYL 6.0). Recent we would compute a multi-molecule-system (see the *.dat-file below, generated with SYBYL). After some computation-time MOPAC stopped (during the computation for the first reaction coordinate) and print in his output-file (see below): THREE ATOMS BEING USED TO DEFINE THE COORDINATES OF A FOURTH ATOM, WHOSE BOND-ANGLE IS NOT ZERO OR 180 DEGREEES, ARE IN AN ALMOST STRAIGHT LINE. THERE IS A HIGH PROBABILITY THAT THE COORDINATES OF THE ATOM WILL BE INCORRECT. and at the end: ATOMS 65, 63, AND 54 ARE WITHIN 0.0059 ANGSTROMS OF A STRAIGHT LINE The bond-angle between theese 3 atoms, which are not connected, is 0 degrees. A second attempt, using cartesian coordinates, showed the same results. Can anybody give us hints for the handling of such multi-molecule-systems with MOAPC? Thank You for Your help. With best regards, H. Schinke ############## Input (DAT)-File for the run ############################## PM3 T=360000 NOINTER CHARGE-1 aceto_rxn.dat isopropylchlorid + NH2 in acetonitril 0006 0.0000 0 0.0000 0 0.0000 0 0000 0000 0000 0006 1.5500 1 0.0000 0 0.0000 0 0001 0000 0000 0006 1.5514 1 111.1064 1 0.0000 0 0002 0001 0000 0017 1.7710 1 109.5989 1 -121.0562 1 0002 0001 0003 0007 3.5578 -1 80.7763 1 93.7999 1 0002 0001 0003 0001 1.1011 1 110.5590 1 -60.5032 1 0001 0002 0003 0001 1.0989 1 109.9108 1 -179.0905 1 0001 0002 0003 0001 1.1028 1 110.4057 1 60.9707 1 0001 0002 0003 0001 1.1043 1 109.7158 1 120.9287 1 0002 0001 0003 0001 1.1033 1 109.8467 1 179.2252 1 0003 0002 0001 0001 1.1019 1 110.1398 1 58.7459 1 0003 0002 0001 0001 1.1015 1 110.2444 1 -60.5427 1 0003 0002 0001 0001 1.0822 1 74.1199 1 -87.4158 1 0005 0002 0001 0001 1.0820 1 126.5937 1 15.1313 1 0005 0002 0001 0006 4.7255 1 94.3647 1 128.2758 1 0005 0002 0001 0007 1.1581 1 150.8418 1 -91.2513 1 0015 0005 0002 0006 1.4591 1 29.0551 1 88.8644 1 0015 0005 0002 0001 1.1001 1 109.3496 1 85.7222 1 0017 0015 0005 0001 1.1004 1 109.2794 1 -34.0471 1 0017 0015 0005 0001 1.1008 1 109.6514 1 -154.1209 1 0017 0015 0005 0006 3.5996 1 153.6728 1 -96.5280 1 0014 0005 0002 0007 1.1578 1 13.9165 1 146.8929 1 0021 0014 0005 0006 1.4574 1 166.0703 1 -32.8884 1 0021 0014 0005 0001 1.0985 1 109.5225 1 -46.5050 1 0023 0021 0014 0001 1.0990 1 109.5135 1 -166.5502 1 0023 0021 0014 0001 1.0988 1 109.5336 1 73.3020 1 0023 0021 0014 0006 3.1821 1 135.8468 1 -33.5144 1 0026 0023 0021 0007 1.1575 1 58.8166 1 -86.8753 1 0027 0026 0023 0006 1.4569 1 121.2665 1 93.3518 1 0027 0026 0023 0001 1.0995 1 109.1838 1 157.7614 1 0029 0027 0026 0001 1.0990 1 109.1728 1 38.1084 1 0029 0027 0026 0001 1.1001 1 109.6732 1 -81.9072 1 0029 0027 0026 0006 3.0767 1 103.4743 1 -51.4763 1 0025 0023 0021 0007 1.1575 1 76.3789 1 166.4251 1 0033 0025 0023 0006 1.4574 1 103.6952 1 -13.7778 1 0033 0025 0023 0001 1.0987 1 109.0487 1 -147.5827 1 0035 0033 0025 0001 1.1000 1 109.7437 1 92.3169 1 0035 0033 0025 0001 1.0985 1 109.6728 1 -27.9951 1 0035 0033 0025 0006 3.4510 1 108.8603 1 -165.3810 1 0031 0029 0027 0007 1.1576 1 46.9670 1 131.3490 1 0039 0031 0029 0006 1.4572 1 132.9267 1 -48.6902 1 0039 0031 0029 0001 1.0997 1 109.3387 1 93.5222 1 0041 0039 0031 0001 1.0980 1 109.2758 1 -26.5337 1 0041 0039 0031 0001 1.0987 1 109.8151 1 -146.1868 1 0041 0039 0031 0006 2.9482 1 112.4182 1 -121.6753 1 0011 0003 0002 0007 1.1579 1 90.4906 1 91.2241 1 0045 0011 0003 0006 1.4577 1 89.4953 1 -88.6234 1 0045 0011 0003 0001 1.0995 1 109.7035 1 149.5640 1 0047 0045 0011 0001 1.0982 1 109.2759 1 29.6008 1 0047 0045 0011 0001 1.0990 1 109.6324 1 -90.1483 1 0047 0045 0011 0006 4.5317 1 139.9017 1 -69.9744 1 0012 0003 0002 0007 1.1573 1 145.3014 1 -130.1153 1 0051 0012 0003 0006 1.4565 1 34.8458 1 49.8356 1 0051 0012 0003 0001 1.0993 1 108.9200 1 -157.5288 1 0053 0051 0012 0001 1.0994 1 110.0562 1 82.4921 1 0053 0051 0012 0001 1.0994 1 109.1379 1 -37.6058 1 0053 0051 0012 0006 3.4721 1 116.7486 1 -176.4873 1 0004 0002 0001 0007 1.1572 1 101.7777 1 86.5285 1 0057 0004 0002 0006 1.4560 1 78.1876 1 -93.6430 1 0057 0004 0002 0001 1.0984 1 109.8789 1 69.2024 1 0059 0057 0004 0001 1.0962 1 108.6552 1 -50.4940 1 0059 0057 0004 0001 1.0984 1 109.8177 1 -170.0241 1 0059 0057 0004 0006 4.4310 1 131.3391 1 -95.8235 1 0054 0053 0051 0007 1.1574 1 168.8801 1 -42.8294 1 0063 0054 0053 0006 1.4566 1 11.3006 1 137.2662 1 0063 0054 0053 0001 1.0997 1 109.2702 1 48.5555 1 0065 0063 0054 0001 1.0992 1 109.5672 1 -71.5576 1 0065 0063 0054 0001 1.0995 1 109.3136 1 168.5094 1 0065 0063 0054 0006 2.8666 1 111.9127 1 114.2402 1 0011 0003 0002 0007 1.1577 1 78.8063 1 126.9038 1 0069 0011 0003 0006 1.4573 1 101.1095 1 -52.9852 1 0069 0011 0003 0001 1.0988 1 109.4665 1 88.1980 1 0071 0069 0011 0001 1.0994 1 109.6016 1 -31.7086 1 0071 0069 0011 0001 1.0989 1 109.3863 1 -151.8561 1 0071 0069 0011 0006 3.1681 1 116.9983 1 65.3880 1 0014 0005 0002 0007 1.1577 1 68.7614 1 18.5956 1 0075 0014 0005 0006 1.4574 1 111.3471 1 -161.5537 1 0075 0014 0005 0001 1.0990 1 110.0250 1 -38.6061 1 0077 0075 0014 0001 1.0988 1 108.9522 1 -158.6613 1 0077 0075 0014 0001 1.0981 1 109.5142 1 81.4778 1 0077 0075 0014 0006 3.0430 1 101.6525 1 178.7693 1 0042 0041 0039 0007 1.1573 1 86.4724 1 -12.0939 1 0081 0042 0041 0006 1.4566 1 93.4012 1 167.6526 1 0081 0042 0041 0001 1.0988 1 110.0533 1 132.2910 1 0083 0081 0042 0001 1.0996 1 109.5192 1 11.8415 1 0083 0081 0042 0001 1.0989 1 108.6354 1 -107.8211 1 0083 0081 0042 0006 2.8961 1 117.9918 1 39.7798 1 0055 0053 0051 0007 1.1572 1 94.4558 1 -21.5512 1 0087 0055 0053 0006 1.4568 1 85.5489 1 158.3391 1 0087 0055 0053 0001 1.0993 1 109.4929 1 75.9636 1 0089 0087 0055 0001 1.0997 1 109.8437 1 -44.3760 1 0089 0087 0055 0001 1.0980 1 108.9221 1 -164.2069 1 0089 0087 0055 4.0 3.8 3.6 3.4 3.2 3.0 2.9 2.8 2.7 2.6 2.5 2.4 2.3 2.2 2.1 2.0 1.9 1.8 1.7 1.6 1.5 ####### end dat-file ########### start out-file ###################### ---------------- stuff deleted --------------------------------- RESTART FILE WRITTEN, TIME LEFT: 336271.4 GRAD.: 70.180 HEAT: 250.6730 CYCLE: 17 TIME:1985.31 TIME LEFT: 334286.1 GRAD.: 86.913 HEAT: 248.3024 CYCLE: 18 TIME: 318.24 TIME LEFT: 333967.8 GRAD.: 88.962 HEAT: 248.1202 RESTART FILE WRITTEN, TIME LEFT: 330634.8 GRAD.: 112.826 HEAT: 244.9363 CALCULATION ABANDONED AT THIS POINT THREE ATOMS BEING USED TO DEFINE THE COORDINATES OF A FOURTH ATOM, WHOSE BOND-ANGLE IS NOT ZERO OR 180 DEGREEES, ARE IN AN ALMOST STRAIGHT LINE. THERE IS A HIGH PROBABILITY THAT THE COORDINATES OF THE ATOM WILL BE INCORRECT. THE FAULTY ATOM IS ATOM NUMBER 66 ---------------- stuff deleted ---------------------------------- 53 C 1.43856 * 27.56940 * 47.24132 * 51 12 3 54 H 1.10289 * 113.07091 * -159.36420 * 53 51 12 55 H 1.10628 * 110.38282 * 82.03550 * 53 51 12 56 H 1.10154 * 110.86405 * -39.47341 * 53 51 12 57 C 4.08353 * 95.06319 * -183.15715 * 4 2 1 58 N 1.15994 * 115.38586 * 98.17581 * 57 4 2 59 C 1.43955 * 64.12061 * -80.79930 * 57 4 2 60 H 1.10829 * 109.67685 * 69.63226 * 59 57 4 61 H 1.10079 * 110.64538 * -49.08832 * 59 57 4 62 H 1.09725 * 110.82013 * -170.03940 * 59 57 4 63 C 4.37425 * 137.62500 * -102.46271 * 54 53 51 64 N 1.16069 * 185.63463 * -39.66892 * 63 54 53 65 C 1.44209 * 0.07684 * 131.59166 * 63 54 53 66 H 1.10339 * 111.26819 * 49.01765 * 65 63 54 ---------------- stuff deleted ---------------------------------- ATOMS 65, 63, AND 54 ARE WITHIN 0.0059 ANGSTROMS OF A STRAIGHT LINE ################### end out-file ################################# =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= =-= Heiko Schinke =-= =-= Martin-Luther-University, Dept. of Biochemistry/Biotechnology =-= =-= P. O. Box 8, D-4020 Halle/Saale, Germany =-= =-= =-= =-= Phone: ++49/345/617242 FAX: ++49/345/647161 =-= =-= =-= =-= E-Mail: schinke@biochemtech.uni-halle.dbp.de =-= =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=