From mbu!neel@vigyan.ernet.in Mon Aug 30 12:02:57 1993 Received: from relay1.UU.NET for mbu!neel@vigyan.ernet.in by oscsunb.ccl.net (5.65c+KVa/930601.1506) id AA01988; Mon, 30 Aug 1993 07:40:04 -0400 Received: from spool.uu.net (via LOCALHOST) by relay1.UU.NET with SMTP (5.61/UUNET-internet-primary) id AA25598; Mon, 30 Aug 93 07:40:03 -0400 Received: from sangam.UUCP by uucp5.uu.net with UUCP/RMAIL (queueing-rmail) id 073858.10750; Mon, 30 Aug 1993 07:38:58 EDT Received: from vigyan!mbu.UUCP by sangam.ncst.ernet.in (4.1/SMI-4.2-ERNET-relay) with UUCP id AA09017; Mon, 30 Aug 93 17:03:27+0530 From: mbu!neel@vigyan.ernet.in Received: by iisc.ernet.in (ERNET-IISc/AT&T UNIX SYS V.3.2) id AA11960; Mon, 30 Aug 93 17:02:57 EST Date: Mon, 30 Aug 93 17:02:57 EST Message-Id: <9308302202.AA11960@iisc.ernet.in> Received: by vigyan.iisc.ernet.in (smail2.3) id AA10487; 30 Aug 93 16:55:34 EST (Mon) To: vigyan!chemistry@ccl.net Subject: query regarding AMBER energy minimization 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 From marshall@mcs.anl.gov Mon Aug 30 04:02:18 1993 Received: from antares.mcs.anl.gov (antares9.mcs.anl.gov) for marshall@mcs.anl.gov by oscsunb.ccl.net (5.65c+KVa/930601.1506) id AA04294; Mon, 30 Aug 1993 10:02:21 -0400 Received: from nephron.mcs.anl.gov by antares.mcs.anl.gov with SMTP id AA27606 (5.65c/IDA-1.4.4 for ); Mon, 30 Aug 1993 09:02:20 -0500 Received: by nephron.mcs.anl.gov (NX5.67c/GCF-5.2) id AA01011; Mon, 30 Aug 93 09:02:18 -0500 Date: Mon, 30 Aug 93 09:02:18 -0500 From: marshall@mcs.anl.gov Message-Id: <9308301402.AA01011@nephron.mcs.anl.gov> Received: by NeXT.Mailer (1.87.1) Received: by NeXT Mailer (1.87.1) To: CHEMISTRY@ccl.net (Computational Chemistry User Group) Subject: Parameters for Dinucleotide Linkage Netters: I am working on the MM simulation of NAD and substrates with various proteins and substrates using Charmm 2.2. I have all the parameters that I need for the NAD with the exception of the diphosphate linkage (P-0-P) which links the sugar of the nicatinamide group to the sugar of the adenine group. Does anyone out there have any Charmm (or other MM) energy parameters (bonds, angles, torsions, and impropers) that they could share with me? Thanks. Chris ############################################################# Christopher L. Marshall | e-mail: marshall@mcs.anl.gov Computational Biology Group | Phone: 708/252-3884 Argonne National Laboratory | Fax: 708/252-6126 Building 202; Room Q-104 | 9700 South Cass Avenue | Argonne, IL 60439 | ############################################################# From gjt@nitrogen.lanl.gov Mon Aug 30 05:38:41 1993 Received: from mailhost.lanl.gov for gjt@nitrogen.lanl.gov by oscsunb.ccl.net (5.65c+KVa/930601.1506) id AA07661; Mon, 30 Aug 1993 13:38:41 -0400 Received: from nitrogen.lanl.gov by mailhost.lanl.gov (5.65/1.14) id AA15517; Mon, 30 Aug 93 11:38:31 -0600 Received: by nitrogen.lanl.gov (4.1/5.17) id AA01052; Mon, 30 Aug 93 11:38:41 MDT Date: Mon, 30 Aug 93 11:38:41 MDT From: gjt@nitrogen.LANL.GOV (Gregory J. Tawa (T-12)) Message-Id: <9308301738.AA01052@nitrogen.lanl.gov> To: CHEMISTRY@ccl.net Subject: Quantum Chemistry Codes for Solvation To who it may concern, I am interested in ab initio and semiempirical quantum chemistry codes that calculate the properties of solutes in solvents. I am just starting research in this area and I would like to know where to begin! For example, where should I first go for reading, review articles books, and so on. What codes exist to do this kind of work and where can I get them? I appreciate the help! Gregory J. Tawa K723 Theoretical Chemistry and Physics Group (T-12) Phone : 505-667-0324 Los Alamos National Laboratory E-mail : gjt@nitrogen.lanl.gov Los Alamos, N.M. 87545 From m10!trucks@uunet.UU.NET Mon Aug 30 08:22:13 1993 Received: from relay1.UU.NET for m10!trucks@uunet.UU.NET by oscsunb.ccl.net (5.65c+KVa/930601.1506) id AA07968; Mon, 30 Aug 1993 13:58:08 -0400 Received: from spool.uu.net (via LOCALHOST) by relay1.UU.NET with SMTP (5.61/UUNET-internet-primary) id AA26879; Mon, 30 Aug 93 13:58:04 -0400 Message-Id: <9308301758.AA26879@relay1.UU.NET> Received: from m10.UUCP by uucp1.uu.net with UUCP/RMAIL (queueing-rmail) id 135658.3808; Mon, 30 Aug 1993 13:56:58 EDT Received: by m10.gaussian.com; Mon, 30 Aug 93 12:22:13 EDT Date: Mon, 30 Aug 93 12:22:13 EDT From: m10!trucks@uunet.uu.net (Gary Trucks) To: chemistry@ccl.net Subject: Linear Structure Notation Can anyone direct me to documentation or specification of the SMILES linear structure notation? (SMILES = Simplified Molecular Input Line Entry System). In addition, is this considered the "standard", or are there new improved, public domain notation systems more widely accepted? -Bill Ellis P.S. I am posting this for another person in our organization. I will forward all responses to him. Thanks, Gary Trucks Lorentzian, Inc. trucks@lorentzian.com From rsjuds@california.sandia.gov Mon Aug 30 04:09:16 1993 Received: from california.sandia.gov ([146.246.250.1]) for rsjuds@california.sandia.gov by oscsunb.ccl.net (5.65c+KVa/930601.1506) id AA08135; Mon, 30 Aug 1993 14:09:22 -0400 Received: by california.sandia.gov (5.65/1.15) id AA11221; Mon, 30 Aug 93 11:09:16 -0700 Date: Mon, 30 Aug 93 11:09:16 -0700 From: rsjuds@ca.sandia.gov (judson richard s) Message-Id: <9308301809.AA11221@california.sandia.gov> To: chemistry@ccl.net Subject: Genetic Algorithms in Chemistry: bibliography Peter Jurs writes asking about information on the use of Genetic Algorithms in chemistry. This is my current list of papers published using GAs in chemistry for conformation searching, protein folding, homology based protein structure determination, NMR peak assignment and laser pulse design. Richard Judson, rsjuds@ca.sandia.gov ----------------------------------------------------------------------- GA bibliography 8/30/93 ----------------------------------------------------------------------- P. Tuffery, et al., J.Biomol. Struct. and Dyn., vol. 8, 1267 (1991). "A new approach to the rapid determination of protein side chain conformations" C.B. Lucasius, et al., p. 251 in "Handbook of Genetic Algorithms", Ed.: Lawrence Davis (Van Nostrand, NY, 1991) . "A Genetic Algorithm for Conformational Analysis of DNA" M.J.J. Blommers, et al., Biopolymers, vol.32 45 (1992). "Conformational analysis of a dinucleotide photodimer with the aid of the genetic algorithm" R.W. Smith, Comput.Phys.Comm. (around 1992). "Energy minimization in binary alloy models via genetic algorithms" R.S. Judson and H. Rabitz, Phys.Rev.Lett. Vol. 68, 1500 (1992). "Teaching Lasers to Control Molecules" R.S. Judson, et al. Intl.J.Quant.Chem. vol 44, 277 (1992). "Do intelligent configuration search techniques outperform random search for large molecules?" R.S. Judson, J.Phys.Chem., vol 96, 10102 (1992). "Teaching polymers to fold" T. Dandekar and P. Argos, Protein Enging., vol. 5, 637 (1992). "Potential of genetic algorithms in protein folding and protein engineering simulations" S. LeGrand and K. Merz, J.Global Opt., Vol. 3, 49 (1993). "The application of the Genetic Algorithm to the minimization of potential energy functions" R. Unger and J.Moult, J.Mol.Bio. Vol. 231, 75 (1993). "Genetic algorithms for protein folding simulations" S. Sun, Protein Sci. Vol. 2, 762 (1993). "Reduced representation model of protein structure prediction: statistical potential and geentic algorithms" A.W.R. Payne and R.C. Glen, J.Mol.Graphics, Vol. 11, 74 (1993). "Molecular Recognition using a binary genetic search algorithm" C.B. Lucasius and G. Kateman, Chemomet.&Intell.Lab.Systems, Vol. 19, 1 (1993). "Understanding and using genetic algorithms, Part 1. Concepts, properties and context" R. Wehrens, et al., J.Chem.Inf.Comput.Sci, Vol. 33, 245 (1993). "Sequential Assignment of 2D-NMR Spectra of Proteins using genetic algorithms" D.B. McGarrah and R.S. Judson, J.Comp.Chem. Vol. 14, p??? (1993). "An analysis of the genetic algorithm method of molecular conformation determination" R.S. Judson, E. Jaeger, A. Treasurywala, J.Comp.Chem. Vol. 14, p??? (1993). "Conformation searching methods for small molecules II: A Genetic algorithm approach" From chemdcl3@emrycc.cc.emory.edu Fri Aug 30 10:44:00 1993 Received: from emoryu1.cc.emory.edu for chemdcl3@emrycc.cc.emory.edu by oscsunb.ccl.net (5.65c+KVa/930601.1506) id AA09763; Mon, 30 Aug 1993 15:43:54 -0400 Received: from emrycc.cc.emory.edu by emoryu1.cc.emory.edu (5.65/Emory_cc.3.4.6) via SMTP id AA22124 ; Mon, 30 Aug 93 15:43:51 -0400 Return-Path: chemdcl3@emrycc.cc.emory.edu Message-Id: <9308301943.AA22124@emoryu1.cc.emory.edu> Date: 30 Aug 93 15:44:00 EST From: "DR. LIOTTA" Subject: MOPAC 6.0 Transition States To: "chemistry" Dear tx (and netters) In reply to your message on obtaining transition states using MOPAC6.0 , try using "NLLSQ CYCLES=100" and "GRADIENTS" in your keywords, and not stipulating "GNORM=0.0001". You will most likely have to repeat the calculation many times until the g-norm (displayed in the "sta" output file) is below 3.0. Once you have reached this g-norm the "NLLSQ CYCLES=100" can be relaced with "SIGMA" to obtain the saddle point in one calculation. Keep "GRADIENTS" in the keywords so that the true g-norm is shown in the "sta" output file. What is the purpose of writing "SCFCRT=10^-12" in the keywords? Veronica From R1JJH@VM1.CC.UAKRON.EDU Mon Aug 30 12:19:18 1993 Received: from phem3 (phem3.acs.ohio-state.edu) for R1JJH@VM1.CC.UAKRON.EDU by oscsunb.ccl.net (5.65c+KVa/930601.1506) id AA10378; Mon, 30 Aug 1993 16:29:07 -0400 Received: from VM1.CC.UAKRON.EDU (MAILER@AKRONVM) by phem3.acs.ohio-state.edu (PMDF V4.2-13 #3557) id <01H2D2SNSY3K8WVYPU@phem3.acs.ohio-state.edu>; Mon, 30 Aug 1993 16:28:58 EDT Received: from AKRONVM (NJE origin R1JJH@AKRONVM) by VM1.CC.UAKRON.EDU (LMail V1.1d/1.7f) with BSMTP id 8431; Mon, 30 Aug 1993 16:22:56 -0400 Date: Mon, 30 Aug 1993 16:19:18 -0400 (EDT) From: Jack Houser Subject: Units of hyperfine coupling constants To: Supercomputer bulletin board Message-Id: <01H2D2SNT7QQ8WVYPU@phem3.acs.ohio-state.edu> Content-Transfer-Encoding: 7BIT Dear Netters: Can anyone tell me what the units are for the hyperfine coupling constants calculated by the INDO program (QCMP 001)? Are they Hz, Gauss, mT or something else? I've checked the manual and can't find any discussion of it. Thanks. Jack Houser Department of Chemistry The University of Akron Akron OH 44325-3601 From 21NBCJ@npd1.ufpe.br Fri Aug 30 13:27:25 1993 Received: from itep.itep.br for 21NBCJ@npd1.ufpe.br by oscsunb.ccl.net (5.65c+KVa/930601.1506) id AA12576; Mon, 30 Aug 1993 18:31:21 -0400 Received: from npd1.ufpe.br by itep.itep.br (PMDF #12039) id <01H2D2RNFD1C000054@itep.itep.br>; Mon, 30 Aug 1993 16:28 -0300 Received: from NPD1.UFPE.BR by NPD1.UFPE.BR (PMDF #3818 ) id <01H2D2JRF26S8Y503Q@NPD1.UFPE.BR>; Mon, 30 Aug 1993 16:27:25 -0300 Date: 30 Aug 1993 16:27:25 -0300 From: Nivan Bezerra <21NBCJ@npd1.ufpe.br> Subject: Theoretical Calculations of Lanthanide Organic Complexes To: chemistry@ccl.net Message-Id: <01H2D2JRF26U8Y503Q@NPD1.UFPE.BR> X-Envelope-To: chemistry@ccl.net X-Vms-To: IN%"chemistry@ccl.net" Content-Transfer-Encoding: 7BIT Mime-Version: 1.0 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. ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Nivan Bezerra da Costa Junior Fone: (081) 271-8440 Universidade Federal de Pernambuco Fax: (081) 271-8442 Centro de Ciencias Exatas e da natureza Departamento de Quimica Fundamental E-mail: Cidade Universitaria HEPNET: NPD1(47909)::21nbcj 50739 - Recife - PE INTERNET: nivan@vaxdqf.ufpe.br 21nbcj@npd1.ufpe.br ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From urquhart@mcmail.cis.mcmaster.ca Mon Aug 30 19:21:52 1993 Received: from mcmail.CIS.McMaster.CA for urquhart@mcmail.cis.mcmaster.ca by oscsunb.ccl.net (5.65c+KVa/930601.1506) id AA16000; Mon, 30 Aug 1993 23:21:34 -0400 Received: by mcmail.cis.mcmaster.ca id AA13371 (5.65c/IDA-1.4.4 for chemistry@ccl.net); Mon, 30 Aug 1993 23:22:24 -0400 Date: Mon, 30 Aug 1993 23:21:52 -0400 (EDT) From: stephen urquhart Subject: Educational PC based kinetics programs search. To: chemistry@ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Fellow Computational Chemists: I am searching for a PC based kinetics program for use in a third year level undergraduate kinetics course. I would prefer something rigorous - i.e. "student proof," to solve numerical solutions to rate law problems. I hope to find freeware, but am also interested in recommendations to commercial packages. Thanks! Stephen ___________________________________________________ Stephen Urquhart urquhart@mcmail.cis.mcmaster.ca Department of Chemistry Phone: (905) 525-9140 x4864 Fax: (905) 521-2773