From owner-chemistry@ccl.net Fri Jun 16 00:00:26 1995 Received: from hkpv17.polyu.edu.hk for bcnlma@hkpucc.polyu.edu.hk by www.ccl.net (8.6.10/930601.1506) id XAA01819; Thu, 15 Jun 1995 23:47:17 -0400 From: Received: from [158.132.30.106] ([158.132.30.106]) by hkpv17.polyu.edu.hk with SMTP; Fri, 16 Jun 1995 11:40:40 GMT Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Fri, 16 Jun 1995 11:38:13 +0800 To: CHEMISTRY@ccl.net Subject: Semiemperical freq scaling factor Dear all, I am aware of frequency scaling factor for HF and MP2. Has there been an accepted scaling factor determined for semi-emperical methods like AM1? Thanks. yours sincerely, Ida N. L. Ma Dr. Ida N. L. Ma Assistant Professor, GH621, Dept. of Applied Biology and Chemical Technology Hong Kong Polytechnic University Hung Hom, Hong Kong Tel: 852-27665616 FAX: 852-23649932 From owner-chemistry@ccl.net Fri Jun 16 00:15:24 1995 Received: from hkpv17.polyu.edu.hk for bcnlma@hkpucc.polyu.edu.hk by www.ccl.net (8.6.10/930601.1506) id AAA01944; Fri, 16 Jun 1995 00:03:37 -0400 From: Received: from [158.132.30.106] ([158.132.30.106]) by hkpv17.polyu.edu.hk with SMTP; Fri, 16 Jun 1995 11:42:31 GMT Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Fri, 16 Jun 1995 11:40:04 +0800 To: CHEMISTRY@ccl.net Subject: SUMMARY: 3rd party HD for RS6000 Dear all, Thanks for all those who reply to my quest for 3rd party harddisk. The following is a summary: Summary of response: (1) Dealers: (a) Phoenix Computers Ltd Phoenix House Oxwich Close Brackmills Northampton NN4 7BH Phone (general) +44 (0)1604 769000 Phone (sales) +44 (0)1604 706666 Fax +44 (0)1604 764323 (b) Integration Solution FAX: 616-2977450 (c) Sun microsystem (d) DIRECTTECH SYSTEMS INC. Fax: 612-942-0430, Ph. No. 800-279-5520 (e) Falcon Systems 1417 W. North Market Boulevard Sacramento, CA 95834 USA Phone: (916) 928-9255 FAX: (916) 928-9355 (f) r2 (r-squared) Vanguargd Technology Inc. 11211 East Arapahoe Road Engelwood, CO 80112-9947 USA Phone: (303) 790-6090 FAX: (303) 799-9297 (g) INSIGHT DIRECT, INC. Fax 602-902-1177 and Ph. no 800-805-3122 (2) Others: "open up your workstation and check what brand of HD is used" "ordinary PC-SCSI disks in RS6000, in particular SEAGATE" "We use Western Digital winchesters of their "Caviar" series, they proved to be very reliable + 3 years warranty" yours sincerely, Ida N. L. Ma Dr. Ida N. L. Ma Assistant Professor, GH621, Dept. of Applied Biology and Chemical Technology Hong Kong Polytechnic University Hung Hom, Hong Kong Tel: 852-27665616 FAX: 852-23649932 From owner-chemistry@ccl.net Fri Jun 16 03:15:28 1995 Received: from trefle.saclay.cea.fr for zenoudac@limeil.cea.fr by www.ccl.net (8.6.10/930601.1506) id DAA03657; Fri, 16 Jun 1995 03:01:02 -0400 Received: from oeillet.saclay.cea.fr by trefle.saclay.cea.fr (8.6.10/ CEANET-ROUTER-3.0) with ESMTP id JAA02080 for ; Fri, 16 Jun 1995 09:01:12 +0200 Received: from cerbere.limeil.cea.fr by oeillet.saclay.cea.fr (8.6.10/ CEANET-ROUTER-3.0) with SMTP id JAA07496 for ; Fri, 16 Jun 1995 09:03:19 +0200 Received: by cerbere.limeil.cea.fr (5.x/CEANET-1.1+) id AA11515; Fri, 16 Jun 1995 08:46:24 +0200 Received: from degaulle.limeil.cea.fr(132.165.3.1) by cerbere via smap id sma011513; Fri Jun 16 08:46:14 1995 Received: from limeil.cea.fr (napoleon) by mailhost.limeil.cea.fr (4.1/CEANET-1.1+) id AA14521; Fri, 16 Jun 95 08:58:08 +0200 Received: by limeil.cea.fr (4.1/SMI-4.1) id AA05300; Fri, 16 Jun 95 09:03:49 +0200 From: zenoudac@limeil.cea.fr (zenoudac) Date: Fri, 16 Jun 95 09:03:44 +0200 Message-Id: <9506160703.AA05295@limeil.cea.fr> To: chemistry@ccl.net Subject: Help for IR Spectra ! Hi everybody !! I try to explain better my problem ; I work on my Ph.D. thesis and I do use a German Program called Molpro92, which allows to get spectroscopic parameters with a quite good accuracy, also dipole and transition dipole moments. NOW I have another program in which I input these results (moments and spectr. parameters) and it outputs a file with 2 columns, featuring frequencies and inte nsities. I'm very pleased with Molpro, but I'm not quite sure the other one does really w ork properly ! So I'd like to check it, using another program of the same kind a nd that's what I'm looking for ! To sum it up, I'm looking for a little code, where you can input spectroscopic parameters such as omegaexe, Re, De, Be, etc... and dipole moments, and then get the IR spectra from it ! Hope I've been a little clearier... All the best Cyril Z. From owner-chemistry@ccl.net Fri Jun 16 05:47:27 1995 Received: from niva.tau.ac.il for yinona@niva.tau.ac.il by www.ccl.net (8.6.10/930601.1506) id FAA05323; Fri, 16 Jun 1995 05:47:27 -0400 Date: Fri, 16 Jun 1995 12:47:03 +0300 (IDT) From: yinon ashkenasy To: chemistry@ccl.net Subject: software to view MD Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi all, I'm doing molecular dynamics calc. with large crystals , and looking into purchasing a good graphics software +hardware that will enable me to: a. see the MD b. animate c. ouput to video I'll be grateful for any help regarding: the platform and the package i should buy. i understand sgi indigo2 with r8000 is a good choice but i'll appreciate any advice (as long as it's less then 50,000$) best regards, yinon -------------------------------------------------------------------------- ------- Yinon Ashkenazy ------- ------- Tel-Aviv University ------- ------- School of Physics and Astronomy ------- ------- Faculty of Exact Sciences ------- ------- Ramat Aviv 69978 ------- ------- Israel ------- -------------------------------------------------------------------------- From owner-chemistry@ccl.net Fri Jun 16 10:32:56 1995 Received: from beavis.chemse.gatech.edu for sahmed@beavis.chemse.gatech.edu by www.ccl.net (8.6.10/930601.1506) id KAA08751; Fri, 16 Jun 1995 10:23:25 -0400 Received: by beavis.chemse.gatech.edu (940816.SGI.8.6.9/940406.SGI) for chemistry@ccl.net id KAA15807; Fri, 16 Jun 1995 10:23:40 -0400 From: "Savant Ahmed" Message-Id: <9506161023.ZM15805@beavis.chemse.gatech.edu> Date: Fri, 16 Jun 1995 10:23:39 -0400 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@ccl.net Subject: Solvation effects in G92 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi all, Could someone tell me how to take solvation effects into account in Gaussian92, at the HF level. Savant -- Savant Ahmed From owner-chemistry@ccl.net Fri Jun 16 11:15:37 1995 Received: from sangam.ncst.ernet.in for bioinfo.ernet.in!deva@bioinfo.ernet.in by www.ccl.net (8.6.10/930601.1506) id LAA09971; Fri, 16 Jun 1995 11:11:13 -0400 Received: from bioinfo.UUCP (uucp@localhost) by sangam.ncst.ernet.in (8.6.12/8.6.6) with UUCP id UAA21753 for chemistry@ccl.net; Fri, 16 Jun 1995 20:41:15 +0530 Received: from bioinfo.UUCP by iucaa (4.1/SMI-4.1) id AA19967; Fri, 16 Jun 95 20:11:04+050 Received: by bioinfo.bioinfo.ernet.in (5.x/SMI-SVR4) id AA00995; Fri, 16 Jun 1995 20:05:52 -0500 Date: Fri, 16 Jun 1995 20:05:52 -0500 From: deva@bioinfo.ernet.in (Deva ) Message-Id: <9506170105.AA00995@bioinfo.bioinfo.ernet.in> To: chemistry@ccl.net Subject: Molec. Mech. In torsion angles Dear Netters, In response to my query on on molecular mechanics in torsion angle space I received a number of interesting and helpful responses. Grateful thanks to all those who responded. I enclose a summary of the responses I got so far. QUESTION >Is there any public domain software to molecular mechanics calculations, >using only torsion angles as variables? If not can anyone give me references >where such calculations were carried out? REPLIES. 1)From Dr. Walter E. Reiher III Perhaps ECEPP/2 might be useful to you. It's available from QCPE. I've never used it, so I don't know if it can be used for any molecules other than peptides; I also can't vouch for the results. The primary authors are Frank Momany and Harold Scheraga. The info page from the QCPE telnet server is attached. >(1) 286. ECEPP: Empirical Conformational Energy Programs > for Peptides > >(2) 286. ECEPP: Empirical Conformational Energy Program > for Peptides > >(3) 454. ECEPP: Empirical Conformational Energy Program > for Peptides > >(4) 558. ECEPP/2: Empirical Conformational Energy Program > for Peptides (IBM 3090 Version) > > > > Input line number for abstract: 3 >454. ECEPP: Empirical Conformational Energy Program > for Peptides > > by M. Jean Browman, Lucy M. Carruthers, Karen L. > Kashuba, Frank A. Momany, Marcia S. Pottle, Susan P. > Rosen, and Shirley M. Rumsey. Write-up by Gerard F. > Endres. Resubmitted by Harold A. Scheraga, Cornell > University, Ithaca, New York 14853. > > The empirical potential energy functions, energy > parameters and geometry parameters used in this program > are described in the literature (F. A. Momany, R. F. > McGuire, A. W. Burgess and H. A. Scheraga, J. Phys. > Chem., 79, 2361 (1975) and G. Nemethy, M. S. Pottle and > H. A. Scheraga, J. Phys. Chem., submitted). The > program treats linear polypeptides and those containing > one or more intramolecular disulfide linkages (cystine >> residues) but not polypeptides with cyclic peptide > backbones. It reads as initial input a data set > containing standard residue information to be used in > the subsequent generation of atomic coordinates and > computation of relative potential energy. The Standard > Residue Data supplied with the program consists of a > basic data set for 26 amino acid residues and 20 end > groups and a supplementary set of 10 amino acid > residues. The data set includes all of the amino acid > residues commonly found in proteins and many end groups > present in synthetic polypeptides. If any residues or > end groups are not needed in a particular application, > an abbreviated set can be used. Any properly formatted > residue data can be substituted for the supplied data, > e.g., if the user does not wish to use the supplied > standard geometry. >> > The user supplies additional data specifying: > > (1) the number of conformations to be treated, > the desired amino acid sequence (including end > groups), and the designation of the > stereochemistry (D or L) of each amino acid > residue > (2) the pairing of half-cystine residues in > intramolecular disulfide bonds > (3) the initial conformation (by supplying values > of all dihedral angles) > (4) which dihedral angles will be treated as > variable, i.e., will differ in subsequent > conformations > (5) new values of these variables for each > subsequent conformation > > The program calls a set of subroutines to generate the > atomic coordinates for each conformation using bond > lengths and bond angles defined in the standard data > set and the dihedral angles specified by the user. > Another set of subroutines is called to compute the > total conformational energy (ETOT) using empirical > potential energy functions. ETOT is computed as the > sum of the following component energies: electrostatic > (EES), nonbonded plus hydrogen bonded (ENB), general > torsional (ETOR), cystine bridge torsional (ECYSTR), > and a loop-closing potential for S-S bonds (ELOOP). > The repulsive part of the nonbonded interaction energy > is reduced by a factor of 0.5 if a particular > interaction is "1-4", i.e., between a pair of atoms > separated by only one bond whose rotation affects their > interatomic distance. A group of subroutines is used > to specify which interactions are 1-4 type for a given > polypeptide sequence. > > The output of the program includes the atomic > coordinates, the total conformational energy, and its > five components for each conformation. The sample main > program can be modified to carry out grid searches, > compute conformational energy maps (f - y plots), or > (in combination with a function-minimizing subroutine) > find conformations corresponding to local energy >> FORTRAN IV (ANSI) > Lines of Code: 4500 ************************************************************************ Walter E. Reiher III, Ph.D. WallyR@netcom.com Consultant in Computational Chemistry P.O. Box 61056 voice 408-720-0240 Sunnyvale, CA 94088 fax 408-720-0378 ************************************************************************ Dr. Klaus. J.W. May wrote: There is software. It is called SCULPT and is from Interactive Simulations. It was developped in close cooperation with Dave and Jane Richardson. It does REALTIME minimizations of torsions, vdw, and electrostatics. It minimizes torsions, but describes Coordinates not in torsional space. It works in cartesian space. It needs so far a silicon graphics machine. It is not public domain, but 1st: the academic price is US$ 700.- and 2nd: You can have a free copy via internet. This demoversion has only some minor restrictions. URL is http://www.intsim.com/~isigen CU Klaus Klaus J.W. May e-mail: kmay@trans.net May & Partner SciTech Consult Phone/Fax: xx49-(89) 333 569 Mandlstr. 15 Mobile national: 0172-620 38 38 international: xx49-172-620 30 38 D - 80802 Munich GERMANY ************************************************************************* Dr. Neil Hoare wrote : Dear Devapriya, It might be possible to perform dynamics using using torsional terms in something like CHARMm by using the SKIPE command to exclude terms from the energy evaluation. Hope this is of use, Neil Neil Hoare hoaren@cv.port.ac.uk Research Associate Centre for Molecular Design University of Portsmouth U.K. ********************************************************************** Dr. Thomas Simonson wrote : From: simonson@zinfandel.u-strasbg.fr (Thomas Simonson) To: deva@bioinfo.ernet.in Subject: Re: CCL:Molec.Mechanics in torsion angle space. Content-Type: text Content-Length: 469 Dear Devapriya, The program Xplor now has a very powerful facility for doing molecular mechanics using any arbitrary combination of internal coordinates, cartesian coordinates, or rigid body constraints (see Rice & Brunger, Proteins, 19:277, 1994). While this facility is not part of the current release, it shouldn't be difficult to get a prerelease of the upcoming version 4.0 which does have this facility. Contact Axel Brunger at Yale. Sincerely, Tom Simonson ************************************************************************** >From Dr. Konstantin Momot Try Cerius2; it allows you to include/exclude potential energy terms (bonds, angles, etc.) from consideration. I did carry out a similar thing once, it works fine. Another option would be using Macromodel; it allows to modify force field very easily, so you can remove every term except torsional ones. Konstantin *********************************************************************** >From Dr. Konrad Hinsen I can send you a preprint of an article by myself and G. Kneller, in which we present a simulation method suitable for a large range of constrained systems. As an example we compare several constraint models for a simple alpha-helix, among them one with only torsional angles (i.e. phi/psi-angles). Another work on simulations in these variables is L.M. Rice and A.T. Br\"unger, Proteins {\bf 19}, 277~(1994) ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsenk@ere.umontreal.ca Departement de chimie | Tel.: +1-514-343-6111 ext. 3953 Universite de Montreal | Fax: +1-514-343-7586 C.P. 6128, succ. A | Deutsch/Esperanto/English/Nederlands/ Montreal (QC) H3C 3J7 | Francais (phase experimentale) ------------------------------------------------------------------------------- *************************************************************************** >From Dr. Max Vasquez Look at the work of Scheraga and colleagues (e.g., J Comp. Chem. 12, 594 [1991]) and their program ECEPP/3; an older version ECEPP/2 is available in QCPE. There is also the program FANTOM by W. Braun (see e.g. J Comp Chem 12, 1065 [1991]) based on similar principles; I believe Dr. Braun will make his software available to academic researchers at little or no cost; he used to be at ETH in Zurich but he may have moved recently (to UT - Galveston maybe??). There is also software by Abagyan called ICM (see J. Comp. Chem. 15, 488-506 [1994]); Abagyan is now at New York University, I do not know if he is making his software available. All of the above is primarily restricted or at least optimized to treat peptide systems. Also, most of these codes are not concerned with "true" dynamics, a difficult task in torsion space - see the papers cited by Hinsen in a public reply to your query. Hope this is good to get you started, Max ************************************************ Max Vasquez, PhD Protein Design Labs, Inc. 2375 Garcia Ave. Mountain View, CA 94043 (415) 903-3744 (415) 903-3730 (FAX) Internet: maxv@pdl.com micifos@ix.netcom.com ************************************************* >From Dr. S. Kandadai >From iucaa!minnie.nic.kingston.ibm.com!swamy Sat Jun 10 22:45 GMT 1995 >Received: by iucaa (4.1/SMI-4.1) id AA01099; Sat, 10 Jun 95 22:39:00+050 Date: Fri, 9 Jun 1995 09:26:42 -0400 From: swamy@kgn.ibm.com (Swamy Kandadai) To: deva@bioinfo.ernet.in Subject: Public Domain MM software Content-Type: text Content-Length: 177 You may want to obtain MM2 from QCPE and also ECEPP and ECEPP2 from QCPE. MM2 is bit old and MM3 is being distributed by Tripos and by Norm Allinger. Good luck Swamy Kandadai *************************************************************** >From Dr. K.Ramnarayan Hello: Regarding your question to the net regarding molecular mechanics calculations using only torsion angles as variables the solution to closer to home! Prof. C. Ramakrishnan of Molecular Biophysics Unit, Indian Institute of Science is well known for such calculations. You can contact him to see if you can collaborate with him. Good luck. ..K.Ramnarayan, Ph.D. ImmunoPharmaceutics, Inc. San Diego, CA, U.S.A. ********************************************************************* >From Dr. D.Severance Hi, It depends if you want a graphical interface. Prof. William Jorgensen has a program named "BOSS" which has been used for a large number of simulations. It works in internal coordinate space, so it is trivial to fix all of the bonds and angles and only allow torsional movements (in fact, >from 1984-1992 only torsional moves were possible, but now bonds and angles may also be sampled). It does not have a graphical interface at this time (although there is a partial interface built into SYBYL from Tripos). You can contact Bill directly for more information: bill@adrik.chem.yale.edu Good luck! Dan -- Dr. Daniel L. Severance dan@sage.syntex.com Staff Researcher Work phone: (415) 354-7509 Syntex Discovery Research Home phone: (415) 969-5818 R6W-002 Fax (Work): (415) 354-7363 3401 Hillview Ave Palo Alto, CA 94303 ******************************************************************** >From Dr. A.D.Allen Devapriya Choudhury It's not Public Domain but SCULPT from International simmulations provide SCULPT, which uses a REAL time grab and minimise utility, using only torsion angle parameters. email intsim-sales@intsim.com for more details -- ############################################################################## Structural and Computation Chemistry Group________chp1aa@uk.ac.surrey - JANET. Department of Chemistry___________________________phone_______+44-1483-259591. University of Surrey______________________________fax_________+44-1483-259514 Guildford,________________________________________ftp___________131.227.110.69 Surrey, GU2 5XH, UK_________________WWW http://www.chem.surrey.ac.uk/~chp1aa/ ############################################################################## ****************************************************************** Again let me thank all those who replied. This will be a great help in my research. Devapriya Dr. Devapriya Choudhury Research associate Bioinformatics Centre University 0f Poona Pune, Maharashtra 411 007 INDIA e-mail deva@bioinfo.ernet.in From owner-chemistry@ccl.net Fri Jun 16 14:00:36 1995 Received: from volvo.wavefun.com for hcj@mazda.wavefun.com by www.ccl.net (8.6.10/930601.1506) id NAA13203; Fri, 16 Jun 1995 13:53:46 -0400 Received: by volvo.wavefun.com (931110.SGI/930416.SGI) for chemistry@ccl.net id AA14762; Fri, 16 Jun 95 10:53:38 -0700 Received: from mazda.wavefun.com(198.147.95.6) by volvo via smap (V1.3) id sma014760; Fri Jun 16 10:53:31 1995 Received: by mazda.wavefun.com (931110.SGI/930416.SGI) for @volvo.wavefun.com:chemistry@ccl.net id AA20297; Fri, 16 Jun 95 10:53:29 -0700 Date: Fri, 16 Jun 95 10:53:29 -0700 From: hcj@mazda.wavefun.com (Harry C. Johnson) Message-Id: <9506161753.AA20297@mazda.wavefun.com> To: deva@bioinfo.ernet.in Cc: chemistry@ccl.net In-Reply-To: <9506170105.AA00995@bioinfo.bioinfo.ernet.in> (deva@bioinfo.ernet.in) Subject: Re: CCL:Molec. Mech. In torsion angles Reply-To: hcj@wavefun.com >>>>> "Deva" == Deva writes: Deva> Dear Netters, In response to my query on on molecular Deva> mechanics in torsion angle space I received a number of Deva> interesting and helpful responses. Grateful thanks to all Deva> those who responded. I enclose a summary of the responses I Deva> got so far. Deva> QUESTION >> Is there any public domain software to molecular mechanics >> calculations, using only torsion angles as variables? If not >> can anyone give me references where such calculations were >> carried out? Just to add one more. Spartan from Wavefunction Inc. is not public domain, but one of the new features of version 4.0 is the ability to do torsion only optimizations from within mechanics as opposed to semi-empirical, dft, or ab initio. For more info check out the web page at http://wavefun.com. -Harry +-----------------------+------------------+-------------------------+ |Harry C. Johnson IV | ______________ | E-Mail: hcj@wavefun.com | |Computational Chemist | \ _________ / | Phone: (714)955-2120 | |Wavefunction Inc. | \ \\\\\\\\/ | Fax: (714)955-2118 | |18401 Von Karman | \ \\\\\/ | | |Suite 370 | \ \\/ | "Seems to me its all | |Irvine, CA 92715 | \/ | just chemistry" - RUSH | +-----------------------+------------------+-------------------------+ From owner-chemistry@ccl.net Fri Jun 16 14:45:40 1995 Received: from post-ofc01.srv.cis.pitt.edu for jochen+@pitt.edu by www.ccl.net (8.6.10/930601.1506) id OAA14524; Fri, 16 Jun 1995 14:41:51 -0400 Received: from unixs1.cis.pitt.edu (jochen@unixs1.cis.pitt.edu [136.142.185.20]) by post-ofc01.srv.cis.pitt.edu with SMTP (8.6.10/cispo-2.0) ID for ; Fri, 16 Jun 1995 14:38:28 -0400 Date: Fri, 16 Jun 1995 14:38:28 -0400 (EDT) From: Jochen Kupper Subject: SUM: calculations on methyl-indoles To: Computational Chemistry List Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Some days ago I asked for calculations about methylsubstituded indoles. I want to thank all people which replied. These are the messages I got: From CHMORA@sn01.sncc.lsu.edu Fri Jun 16 14:32:02 1995 Date: Tue, 06 Jun 1995 20:08:57 -0600 (CST) From: CHMORA@sn01.sncc.lsu.edu To: jochen+@pitt.edu Subject: Re: CCL:1-, 3- and 5-Methyl-indole - any structural data Dear Jochen: Indole compounds is my area and I happened to have some nice papers related to your question. Try: 1) Pure and Appl. Chem. 1980, Vol. 53, pp 1525-1540 Title: Aromatic Stability of Polycyclic Compounds 2) J. Chem. Soc. Perkins Trans 2 1990, pp 1881-1884 Title: AM1 Study of a beta-Carboline Set. Part II: Pyrrole-N-Deproto- nated Species 3) J. CHem. Soc. Perkin Trabs 2 1990, pp 65-71 Title: AM1 Study of a beta-Carboline Set: Structural Properties and Potential Reactivity 4) J. Heterocyclic Chem. 1984, Vol. 21, pp 273-282 Title: Aromaticity in Bridge Heteroannulenes Hope this helps. Good luck. Sincerely, Guillermo. ------------------------------------------------------------------------------ Internet: chmora@sn01.sncc.lsu.edu From SATYAM@vms.cis.pitt.edu Fri Jun 16 14:32:12 1995 Date: Wed, 07 Jun 1995 09:03:17 -0400 (EDT) From: SATYAM@vms.cis.pitt.edu To: jochen+@pitt.edu Subject: Re: CCL:1-, 3- and 5-Methyl-indole - any structural data Please check the cummulative index in J. Mol. Struct. (Theo. Chem.) A complete list of molecules studied using ab initio theory is given there.. Thanks Satyam ------------------------------------------------------------------------------ From dave@terminus.chem.yale.edu Fri Jun 16 14:32:22 1995 Date: Tue, 13 Jun 95 18:39:42 EDT From: David Maxwell To: Jochen Kupper Subject: Re: CCL:1-, 3- and 5-Methyl-indole - any structural data > > > Does anybody know about about structural data of 1-, 3- or 5-Methylindole > from ab initio calculations or other sources? > (Will make a summary) > > Regards, > Jochen > > > This world is your home - care about it ! > > Jochen Kuepper > University of Pittsburgh (412) 624-8638 > Department of Chemistry (412) 624-8665 > 603 Chevron Science Center jochen+@pitt.edu > Pittsburgh, PA 15260 > > Please send X-mas greetings to kuepperj@uni-duesseldorf.de ! > Nothing funny about this - it`s the truth ! > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: jochen+@pitt.edu > -- Original Sender From: Address: jochen+@pitt.edu > CHEMISTRY@ccl.net -- everyone | CHEMISTRY-REQUEST@ccl.net -- coordinator > MAILSERV@ccl.net: HELP CHEMISTRY | Gopher: www.ccl.net 73 > Anon. ftp www.ccl.net | CHEMISTRY-SEARCH@ccl.net -- archive search > http://www.ccl.net/chemistry.html | for info send: HELP SEARCH to MAILSERV > > I performed torsional energy calculations on 3-methyindole and 5-ethylindole at the RHF/6-31G* level. The results should appear in J. Comp. Chem. in the next few months along with numerous other torsional energy calculations. Since you are looking for the structural data, I probably could be convinced to look up the coordinates for you. -Dave Maxwell Jochen From owner-chemistry@ccl.net Fri Jun 16 15:45:37 1995 Received: from SIUCVMB.SIU.EDU for TAPASKAR@SIUCVMB.SIU.EDU by www.ccl.net (8.6.10/930601.1506) id PAA15636; Fri, 16 Jun 1995 15:33:53 -0400 Message-Id: <199506161933.PAA15636@www.ccl.net> Received: from SIUCVMB.SIU.EDU by SIUCVMB.SIU.EDU (IBM VM SMTP V2R2) with BSMTP id 9530; Fri, 16 Jun 95 14:31:44 CST Date: Fri, 16 Jun 95 14:14:45 CST From: "Tapas Kar" To: chemistry@ccl.net Subject: Name of the ion Dear Netters: What should be the name of the following ion? O--H O- / \ HC CH \\ // HC--CH Tapas tapaskar@siucvmb.siu.edu From owner-chemistry@ccl.net Fri Jun 16 16:30:37 1995 Received: from sprintf.merit.edu for Karl.F.Moschner@urlus.sprint.com by www.ccl.net (8.6.10/930601.1506) id QAA16659; Fri, 16 Jun 1995 16:30:22 -0400 From: X400-Received: by /PRMD=LANGATE/ADMD=TELEMAIL/C=GB/; Relayed; Fri, 16 Jun 1995 16:23:00 -0400 X400-Received: by /PRMD=LANGATE/ADMD=TELEMAIL/C=GB/; Relayed; Fri, 16 Jun 1995 16:23:00 -0400 X400-Received: by /PRMD=LANGATE/ADMD=TELEMAIL/C=GB/; Relayed; Fri, 16 Jun 1995 16:23:00 -0400 X400-Received: by /PRMD=LANGATE/ADMD=TELEMAIL/C=GB/; Relayed; Fri, 16 Jun 1995 16:23:00 -0400 Date: Fri, 16 Jun 1995 16:23:00 -0400 X400-Originator: Karl.F.Moschner@urlus.sprint.com X400-Recipients: non-disclosure:; X400-MTS-Identifier: [/PRMD=LANGATE/ADMD=TELEMAIL/C=GB/;Fri Jun 16 16:23:26 199501] X400-Content-Type: P2-1984 (2) Content-Identifier: Solvation in G92 Message-ID: <"Fri Jun 16 16:23:26 199501*/I=F/G=Karl/S=Moschner/OU=4267EDUR/O=TMUS.URL/PRMD=LANGATE/ADMD=TELEMAIL/C=GB/"@MHS> To: chemistry@ccl.net Subject: Solvation in G92 - Try G94 MIME-version: 1.0 Content-type: multipart/mixed; boundary="Z7YK1rQcdKE6dqYnS9vj3PnkcAuCJatA" --Z7YK1rQcdKE6dqYnS9vj3PnkcAuCJatA Content-type: text/plain; charset="us-ascii" > Could someone tell me how to take solvation effects into account in > Gaussian92, at the HF level. I haven't carried out self-consistent reaction field calculations in G92 but I am carrying out a series of calculations using "SCRF=SCIPCM" option in G94 and this may be a good reason to upgrade. Optimizations, frequencies, etc. are avilable for all HF and DFT methods. Only single point energies are avialable for MP2 calaulations. To date, I have had no difficulty with ground-state geometries but have run into some difficulties with transition-state calculations which I have communicated to Gaussian Inc. In principal, SCRF=SCIPCM only requires an additional blank line plus a line with the dilectric constant to be used, in floating point format, after your geometry data, i.e., for water D=78.3: # 'Gaussian options' SCRF=SCIPCM (blank) Title (blank) 'Charge' and 'multiplicity' 'Geometry' (blank) 78.3 Additonal parametres may also be entered on the same line as the dielectric value but only the dielectric need be specified. The default parameters are probably best. I was informed by Mike Frisch via Doug Fox, Gaussian Inc., that the additional parameters specify the isodensity contour value (0.0004 is recommended), the number of points for the Lebedev grid (default is 302), and various options which control how the linear equations are solved plus other details. Mike also suggested: "You can certainly set down the number of integration points in SCIPCM... if you like. Try 78.3 0.0004 194 0 to use a 194 point Lebedev grid on each atom. Using a single integration origin: 78.3 0.0004 302 0 2 This speeds up the calculation but is only correct for convex cavities. (the default for the fifth parameter is 3, meaning a separate integration grid around each atom). You can also force inversion of the matrix instead of iterative solution of the linear equations: 78.3 0.004 302 0 3 T This is faster for small-medium systems but very memory intensive and slower for big systems." My thanks to Mike Frsich and Doug Fox. _______________________________________________________________________ / \ | Comments are those of the author and not Unilever Research U. S. | | | | Karl F. Moschner, Ph. D. | | | | Unilever Research U. S. e-mail: Karl.F.Moschner@urlus.sprint.com | | 45 River Road Phone: (201) 943-7100 x2629 | | Edgewater, NJ 07020 FAX: (201) 943-5653 | \_______________________________________________________________________/ --Z7YK1rQcdKE6dqYnS9vj3PnkcAuCJatA Content-type: text/plain; charset="us-ascii" --Z7YK1rQcdKE6dqYnS9vj3PnkcAuCJatA-- From owner-chemistry@ccl.net Fri Jun 16 16:45:38 1995 Received: from SIUCVMB.SIU.EDU for TAPASKAR@SIUCVMB.SIU.EDU by www.ccl.net (8.6.10/930601.1506) id QAA16668; Fri, 16 Jun 1995 16:30:39 -0400 Message-Id: <199506162030.QAA16668@www.ccl.net> Received: from SIUCVMB.SIU.EDU by SIUCVMB.SIU.EDU (IBM VM SMTP V2R2) with BSMTP id 9846; Fri, 16 Jun 95 15:28:30 CST Date: Fri, 16 Jun 95 15:19:54 CST From: "Tapas Kar" To: chemistry@ccl.net Subject: B-N chemistry Dear Netters: We are in the beginning stages of a project concerning the replacement of C-C units in organic compounds with B-N units and predicting differences between these compounds using ab initio calculations. One part of this research will be examining these replacements in fused ring systems--replacing C-C units in such molecules as naphthalene with 1, 2, 3 etc. B-C units. We were wondering if anyone could suggest any sources where these fused ring compounds were previously studied either theoretically or experimentally. We have had trouble finding sources for the geometries, syntheses, and electron structures for these compounds--we don't even know names for them! Some of the structures are: H H H B B B / \ / \ / \ HN N NH HN N--BH | O | O | | | || HB B BH HB B--NH \ / \ / \ / N N N H H H and other similar compounds of two 6 member and a 6 and 4 member fused ring systems (with C-C units replacing successive B-N units). Any suggestions for souces concerning these compounds woudl be very appreciated. Also, any information like the names for this series of compounds would be very helpful. Thanks for your time! Sincerely, Tapas Kar From owner-chemistry@ccl.net Fri Jun 16 19:00:39 1995 Received: from pnl.gov for d3e129@cagle.pnl.gov by www.ccl.net (8.6.10/930601.1506) id SAA18487; Fri, 16 Jun 1995 18:47:21 -0400 Received: from cagle.pnl.gov by pnl.gov (PMDF V4.3-13 #6012) id <01HRS286LEGW94JOW3@pnl.gov>; Fri, 16 Jun 1995 15:47:17 -0700 (PDT) Received: by cagle.pnl.gov (4.1/SMI-4.1) id AA11768; Fri, 16 Jun 95 15:47:16 PDT Date: Fri, 16 Jun 1995 15:47:16 -0700 (PDT) From: d3e129@cagle.pnl.gov (Ricky A. Kendall) Subject: workshop To: chemistry@ccl.net Message-id: <9506162247.AA11768@cagle.pnl.gov> Content-transfer-encoding: 7BIT High Performance Computational Chemistry Workshop August 13-16, 1995 Pleasanton Hilton 7050 Johnson Drive Pleasanton, CA 94588 Pacific Northwest Laboratory, The National Institutes of Health, and the National Energy Research Supercomputer Center are sponsoring a High Performance Computational Chemistry Workshop in early August 1995. The workshop will be a forum for computational chemistry researchers to present and discuss their current research efforts, algorithms and scientific applications that target high performance parallel supercomputers. The goals of the workshop are to present state-of-the-art developments and applications on parallel supercomputers and to stimulate research efforts and funding in this area. Each of the workshop sessions will comprise invited and contributed talks. Session topics include: HF, DFT, ab initio correlated methods, numerical methods, MD, etc. Speakers that have accepted this invitation include, Prof. E. Clementi, Prof. W. Goddard, Prof. R. Kalia, and Dr. M. F. Guest. A more detailed speaker list will be provided prior to the meeting. Sponsors: Environmental Molecular Sciences Laboratory Pacific Northwest Laboratory Richland, Washington Laboratory of Structural Biology Division of Computer Research and Technology (DCRT) National Institutes of Health Bethesda, Maryland National Energy Research Supercomputer Center Lawrence Livermore National Laboratory Livermore, California Contact Persons: Dr. Ricky A. Kendall MSIN K1-90 Environmental Molecular Sciences Laboratory Pacific Northwest Laboratory Richland, WA 99352-0999 FAX: 509-375-6631 Phone: 509-375-2602 Email: ra_kendall@pnl.gov Dr. Robert J. Harrison MSIN K1-90 Environmental Molecular Sciences Laboratory Pacific Northwest Laboratory Richland, WA 99352-0999 FAX: 509-375-6631 Phone: 509-375-2037 Email: rj_harrison@pnl.gov Dr. Jeffrey A. Nichols MSIN K1-96 Environmental Molecular Sciences Laboratory Pacific Northwest Laboratory Richland, WA 99352-0999 FAX: 509-375-6631 Phone: 509-372-4569 Email: ja_nichols@pnl.gov Dr. Bernard R. Brooks NIH/DCRT, LSB Bldg. 12A, Rm 2007 9000 Rockville Pike Bethesda, MD 20892 email: brbrooks@helix.nih.gov Ms. Tammy S. Welcome L-561 National Energy Research Supercomputer Center Lawrence Livermore National Laboratory Livermore, CA 94550 Email: tsw@nersc.gov Conference Administrator: Rebecca R. Wattenburger MSIN K1-96 Environmental Molecular Sciences Laboratory Pacific Northwest Laboratory Richland, WA 99352-0999 FAX: 509-375-6631 Phone: 509-372-4681 Email: rr_wattenburger@pnl.gov Organizing Committee: Advisory Committee: Bernard R. Brooks, NIH Thom H. Dunning, Jr. Robert A. Eades, PNL Ray A. Bair Robert J. Harrison, PNL David A. Dixon Ricky A. Kendall, PNL Michel Dupuis Jeffrey A. Nichols, PNL Bruce C. Garrett C. William McCurdy, NERSC Martyn F. Guest Rebecca R. Wattenburger, PNL -------------------------------------------------------------------------------- HPCC Workshop Registration Form & Payment Due by July 15, 1995 Please print or type: Full Name: _____________________ __________ ___________________ First Middle Last Business Address:_______________________________________________________________ ________________________________________________________________________________ City:___________________________________ State:______________ Zip:_____________ Country:________________________________ Daytime Phone: ( )_________________ FAX: ( )___________________________ Email Address:__________________________________________________________________ REGISTRATION FEE: $100.00 (Please make checks payable to PNL) After July 1 and space available: $200.00 Making Presentation: (Yes/No) _________ Title of Poster Presentation:___________________________________________________ ________________________________________________________________________________ ________________________________________________________________________________ Arrival Date: _________________ Departure Date: _________________ By July 15 please complete this form and mail, email, or Fax to: HPCC Workshop R. R. Wattenburger Environmental Molecular Sciences Laboratory Pacific Northwest Laboratory PO Box 999 MSIN K1-96 Richland, WA 99352-0999 Fax: 509-375-6631 Phone: 509-372-4681 Email: rr_wattenburger@pnl.gov Abstracts: Camera Ready Abstracts are due July 7th, 1995 at the above address. The abstracts should be one or two pages that clearly describe the presentation and the presenting author's name should be underlined. ----------------------------------------------------------------------------------------- Hotel Reservation Form: Due by July 15, 1995 High Performance Computational Chemistry Workshop August 13-16, 1995 Pleasanton Hilton 7050 Johnson Drive Pleasanton, CA 94588 Phone: (510) 463-8000 Fax: (510) 463-3801 Room reservations must be made directly with the Tutorial Hotel. The Hotel is approximately 7 miles from LLNL. Please submit this form when making your room reservations. To receive the special rate of $74.52 (including local taxes) reservations must be made by July 15, 1995. Reservations made after this date will be based upon availability only. This rate includes complimentary guest parking and access to the Health Club. The rate is for single or double occupancy. Shuttle service from airport to hotel is available for a fee by calling San Ramon Valley Airporter Express at (510) 484-4044 OR Executive Class Transportation at (510) 866-6611. Check in time is 3:00PM Check out is 12:00 Noon Reservations must be accompanied by a check for one nights deposit or credit card number. Type of card: Visa ______ MC ______ Am Ex ______ Exp Date: ____________________ Number: ___________________________________________ Name on card: ________________________________________ Arrival Date: ________________________________________ Departure Date: ________________________________________ Special Requirements: __________________________________________________________ ________________________________________________________________________________ ________________________________________________________________________________ ________________________________________________________________________________ Smoking: __________ Non: __________ Other:__________________________________________________________________________ ________________________________________________________________________________ ________________________________________________________________________________ ________________________________________________________________________________ From owner-chemistry@ccl.net Fri Jun 16 19:07:16 1995 Received: from pnl.gov for d3e129@cagle.pnl.gov by www.ccl.net (8.6.10/930601.1506) id SAA18488; Fri, 16 Jun 1995 18:47:21 -0400 Received: from cagle.pnl.gov by pnl.gov (PMDF V4.3-13 #6012) id <01HRS2877YC094LKNE@pnl.gov>; Fri, 16 Jun 1995 15:47:18 -0700 (PDT) Received: by cagle.pnl.gov (4.1/SMI-4.1) id AA11770; Fri, 16 Jun 95 15:47:17 PDT Date: Fri, 16 Jun 1995 15:47:17 -0700 (PDT) From: d3e129@cagle.pnl.gov (Ricky A. Kendall) Subject: tutorial To: chemistry@ccl.net Message-id: <9506162247.AA11770@cagle.pnl.gov> Content-transfer-encoding: 7BIT Parallel Computational Chemistry Tutorial August 7-11, 1995 National Energy Research Supercomputer Center Lawrence Livermore National Laboratory Livermore, California Pacific Northwest Laboratory, The National Institutes of Health, and the National Energy Research Supercomputer Center (NERSC) are sponsoring a parallel computing tutorial in early August 1995. The tutorial is primarily for graduate students and junior professionals who wish to learn the basics about writing and using parallel applications on massively parallel processing (MPP) systems. The course will cover advanced topics regarding parallel computing and computational chemistry including the use of parallel programming environments such as the Message-Passing Interface (MPI), High Performance Fortran (HPF) and Global Arrays (GA), the design of scalable parallel computational chemistry algorithms, and the execution of standard packages on parallel computers. Ample time for both hands-on experimentation and instruction will be provided by leading researchers from both computer science and computational chemistry. Students will have access to the Cray Research Inc. T3D parallel supercomputer on-site at NERSC and other MPPs on the internet. Space will be limited to 25 participants, to be selected based on the computing experience and research interests of the applicants. Limited funds are available to support students at U.S. educational and research institutions; applicants should indicate if support is requested on the application form. Knowledge of Unix and Fortran or C is assumed. Sponsors: Environmental Molecular Sciences Laboratory Pacific Northwest Laboratory Richland, Washington Laboratory of Structural Biology Division of Computer Research and Technology (DCRT) National Institutes of Health Bethesda, Maryland National Energy Research Supercomputer Center Lawrence Livermore National Laboratory Livermore, California Contact Persons: Dr. Robert J. Harrison MSIN K1-90 Environmental Molecular Sciences Laboratory Pacific Northwest Laboratory Richland, WA 99352-0999 FAX: 509-375-6631 Phone: 509-375-2037 Email: rj_harrison@pnl.gov Dr. Jeffrey A. Nichols MSIN K1-96 Environmental Molecular Sciences Laboratory Pacific Northwest Laboratory Richland, WA 99352-0999 FAX: 509-375-6631 Phone: 509-372-4569 Email: ja_nichols@pnl.gov Dr. Ricky A. Kendall MSIN K1-90 Environmental Molecular Sciences Laboratory Pacific Northwest Laboratory Richland, WA 99352-0999 FAX: 509-375-6631 Phone: 509-375-2602 Email: ra_kendall@pnl.gov Dr. Bernard R. Brooks NIH/DCRT, LSB Bldg. 12A, Rm 2007 9000 Rockville Pike Bethesda, MD 20892 email: brbrooks@helix.nih.gov Ms. Tammy S. Welcome L-561 National Energy Research Supercomputer Center Lawrence Livermore National Laboratory Livermore, CA 94550 Email: tsw@nersc.gov Tutorial Administrator: Rebecca R. Wattenburger MSIN K1-96 Environmental Molecular Sciences Laboratory Pacific Northwest Laboratory Richland, WA 99352-0999 FAX: 509-375-6631 Phone: 509-372-4681 Email: rr_wattenburger@pnl.gov -------------------------------------------------------------------------------- PCC Tutorial Registration Form: Form and Payment Due by July 1, 1995 Please print or type: Full Name: _____________________ __________ ___________________ First Middle Last Business Address:_______________________________________________________________ ________________________________________________________________________________ City:___________________________________ State:______________ Zip:_____________ Country:________________________________ Daytime Phone: ( )_________________ FAX: ( )___________________________ Email Address:__________________________________________________________________ REGISTRATION FEE: (Please make checks payable to PNL) Student or Postdoctoral: $50.00 ++After July 1 $100.00 Professional: $100.00 ++After July 1 $200.00 Support needed? Yes/No ____________ * Provide brief description of application area (i.e., classical MD, electronic structure of molecules, etc.):__________________________________________________ ________________________________________________________________________________ ________________________________________________________________________________ * Provide brief description of computer equipment used:_________________________ ________________________________________________________________________________ ________________________________________________________________________________ * If grad student or postdoc provide name of supervisor:________________________ ++ If space is available! By July 1 please complete registration form & LLNL Security form and mail, email, or fax to: Parallel Computational Chemistry Tutorial R. R. Wattenburger Environmental Molecular Sciences Laboratory Pacific Northwest Laboratory P.O. Box 999, MSIN K1-96 Richland, WA 99352-0999 Fax: 509-375-6631 Phone: 509-372-4681 Email: rr_wattenburger@pnl.gov SECURITY REQUIREMENTS AT LAWRENCE LIVERMORE NATIONAL LABORATORY (LLNL) REQUIRE THE FOLLOWING ADDITIONAL INFORMATION TO BADGE THE PARTICIPANTS FOR THE TUTORIAL. Full Name: _____________________ __________ ___________________________ First Middle Last Home Address:___________________________________________________________________ ________________________________________________________________________________ City:___________________________________ State:______________ Zip:_____________ Country:________________________________ Complete name of employer or affiliation and their business address: Employer:_______________________________________________________________________ Business Address:_______________________________________________________________ City:___________________________________ State:______________ Zip:_____________ Country:________________________________ Citizenship: US ____ Other __________________________________________________ **** Please indicate your citizenship & countries you have dual citizenship **** Non-US Citizens: Country: ________________________________________ City of Birth: __________________________________ Gender: Male _____ Female _____ Social Security Number: ___________________ Your ID type, number and the state and country that issued it. The ID type may be drivers license, military or DOE laboratory badge, or passport. You must present this same ID at the badging office to gain access to LLNL. ID Type: Drivers License/Passport Number: ______________________________________________ Exp Date: ______________________________________________ Issuing State/Country: _________________________________________________________ By July 1 please complete both forms and mail email or fax to: Parallel Computational Chemistry Tutorial R.R. Wattenburger Environmental Molecular Sciences Laboratory Pacific Northwest Laboratory PO Box 999 MSIN K1-96 Richland, WA 99352-0999 Fax: 509-375-6631 Phone : 509-372-4681 Email: rr_wattenburger@pnl.gov (Applicantions received after this date may NOT be processed as there is a time constraint on preparing the necessary security paperwork for access to LLNL.) -------------------------------------------------------------------------------- Hotel Reservation Form: Due by July 15, 1995 Parallel Computational Chemistry Tutorial August 7-11, 1995 Pleasanton Hilton 7050 Johnson Drive Pleasanton, CA 94588 Phone: (510) 463-8000 Fax: (510) 463-3801 Room reservations must be made directly with the Tutorial Hotel. The Hotel is approximately 7 miles from LLNL. Please submit this form when making your room reservations. To receive the special rate of $74.52 (including local taxes) reservations must be made by July 15, 1995. Reservations made after this date will be based upon availability only. This rate includes complimentary guest parking and access to the Health Club. The rate is for single or double occupancy. Shuttle service from airport to hotel is available for a fee by calling San Ramon Valley Airporter Express at (510) 484-4044 OR Executive Class Transportation at (510) 866-6611. Transportation from the Hotel to NERSC will be provided. Check in time is 3:00PM Check out is 12:00 Noon Reservations must be accompanied by a check for one nights deposit or credit card number. Type of card: Visa ______ MC ______ Am Ex ______ Exp Date: ____________________ Number: ___________________________________________ Name on card: ________________________________________ Arrival Date: ________________________________________ Departure Date: ________________________________________ Special Requirements: __________________________________________________________ ________________________________________________________________________________ ________________________________________________________________________________ ________________________________________________________________________________ Smoking: __________ Non: __________ Willing to share a room: Yes ______ No ______ Other:__________________________________________________________________________ ________________________________________________________________________________ ________________________________________________________________________________ ________________________________________________________________________________