From GLASSER@AURUM.CHEM.WITS.AC.ZA Fri Mar 17 03:13:14 1995 Received: from caesar for GLASSER@AURUM.CHEM.WITS.AC.ZA by www.ccl.net (8.6.10/930601.1506) id DAA07088; Fri, 17 Mar 1995 03:07:26 -0500 Received: from aurum.chem.wits.ac.za ([146.141.74.18]) by caesar (5.0/SMI-SVR4) id AA26360; Fri, 17 Mar 1995 10:03:13 +0200 Received: from CHEMISTRY/SpoolDir by aurum.chem.wits.ac.za (Mercury 1.12); Fri, 17 Mar 95 10:04:59 GMT +2:00 Received: from SpoolDir by CHEMISTRY (Mercury 1.12); Fri, 17 Mar 95 10:04:28 GMT +2:00 From: "Leslie Glasser" Organization: CHEMISTRY - WITS UNIVERSITY To: chemistry@ccl.net Date: Fri, 17 Mar 1995 10:04:20 GMT + 2:00 Subject: Point Group Determination Priority: normal X-Mailer: Pegasus Mail v3.1 (R1a) Message-Id: <14B436811BC@aurum.chem.wits.ac.za> content-length: 1091 Dear All: I am attempting to find a program to determine point groups (to be used for points on the surface of a sphere, with 100 or more points). The ideal program would be SYMAPPS (Nedwed, et al., Comp. Chem., 18(4), 371-6 (1994)). Unfortunately, this is available only in a demo version at present. There is a module within MOPAC which may do the job - but I am loath to have to install the whole program for a small portion, 'using a steamroller to crack a walnut'. I have searched CCL archives and find a brief reference to a program Turbomol (of which I know nothing). Can anyone offer a suggestion or a program for my use? With thanks Leslie ============================================================== (Prof.) Leslie Glasser Dept. of Chemistry E-mail: glasser@aurum.chem.wits.ac.za Univ. of Witwatersrand Tel: Intl + 27 11 716-2070 P. O. WITS 2050 Fax: Intl + 27 11 339-7967 South Africa ====================================================================== From kreidler@hp817s.rz.uni-duesseldorf.de Fri Mar 17 05:13:05 1995 Received: from hp817s.rz.uni-duesseldorf.de for kreidler@hp817s.rz.uni-duesseldorf.de by www.ccl.net (8.6.10/930601.1506) id EAA07806; Fri, 17 Mar 1995 04:15:20 -0500 Message-Id: <199503170915.EAA07806@www.ccl.net> Received: by hp817s.rz.uni-duesseldorf.de (1.37.109.15/16.2) id AA114961700; Fri, 17 Mar 1995 10:15:00 +0100 From: Kay Kreidler Subject: rotamers in n.m.r. experiment To: chemistry@ccl.net (Theochem Liste) Date: Fri, 17 Mar 95 10:14:59 MEZ Mailer: Elm [revision: 70.85.2.1] Dear netters! I am investigating conformational equilibria of chemical compounds containing Ethane rotors, for example derivatives of succinic acid. I try to calculate the amount of each canonical rotamer due to the time axis of an n.m.r. experiment in aqueous solution. The programs I use are force field programs like MM+ (Hyperchem) and Quanta/CHARMm, semiempirical programs like MOPAC93, VAMP 4.4 and the ab-initio program Gaussian92. Aside of the question of the reliability of the results of anionic structures I am searching for a model substance, in which the rotation is slowly enough to show the individual rotamers as *seperate* signals in the n.m.r. experiment. Does any one of you remember such a case? I will summarize to the mailing list. Thanks a lot Kay Kreidler From S.R.Kilvington@soton.ac.uk Fri Mar 17 05:21:53 1995 Received: from beech.soton.ac.uk for S.R.Kilvington@soton.ac.uk by www.ccl.net (8.6.10/930601.1506) id EAA07929; Fri, 17 Mar 1995 04:22:00 -0500 Received: from vision.soton.ac.uk (vision.soton.ac.uk [152.78.128.74]) by beech.soton.ac.uk (8.6.10/hub-8.5) with ESMTP id JAA06094 for ; Fri, 17 Mar 1995 09:21:56 GMT Received: (from srk@localhost) by vision.soton.ac.uk (8.6.10/client-8.6) id JAA00975 for chemistry@ccl.net; Fri, 17 Mar 1995 09:23:18 GMT Message-Id: <199503170923.JAA00975@vision.soton.ac.uk> Subject: RE:malloc etc. on DEC Alpha To: chemistry@ccl.net Date: Fri, 17 Mar 1995 09:23:17 +0000 (GMT) From: "Simon Kilvington" X-Mailer: ELM [version 2.4 PL23] Content-Type: text Content-Length: 2398 >Unfortunately, many programmers (especially among scientists) still >think that it is sufficient to run a few test cases to validate their >programs. What one should do, and what many people in other fields are >already doing, is to think about debugging from the beginning of the >design process. Whenever your start to write a piece of code, your >first thought should be "How can I check whether I have made a >mistake?" Every program unit should be able to test the validity of >to remove the tests from production code. Choose variable and function >names that are sufficiently different from one another that typos can >be caught by the compiler. Use all available tools for checking your >code (ftncheck for Fortran, lint for C), and make use of all compiler >options that help in debugging (i.e. -C with f77). I could extend this >list, but all this has been published before. Whoever really wants >to write reliable code can do so with little effort. > >For some reasons that I cannot follow, scientists seem to ignore the >considerable progress that has been made in software engineering >during the last decades. Even big and much-used packages are in such a >bad shape that they seem to have been written by first-year students >as a programming exercise. I have heard excuses such as "I don't have >time to learn about programming techniques", but the people saying >that seem to have enough time to waste it on endless debugging and >on running programs whose results cannot be trusted. >I have been working in commercial software development (non- >scientific) for more than a decade, and I am sure my >company would have been out of business long out if it had >this "scientific" attitude towards software development. > you should all read a book called "Code Complete" by Steve McConnell, published by the Microsoft Press. to quote from the preface: The research and programming experience collected in this handbook will help you to create higher-quality software and to do your work more quickly and with fewer problems. This book will give you insight into why you've had problems in the past and will show you how to avoid them in the future. The programming practices described here will help you keep big projects under control and help you maintain and modify software successfully as the demands of your projects change. Si. --- Simon Kilvington, srk@soton.ac.uk From thep@risc1.lrm.fi.cnr.it Fri Mar 17 06:13:07 1995 Received: from risc1.lrm.fi.cnr.it for thep@risc1.lrm.fi.cnr.it by www.ccl.net (8.6.10/930601.1506) id FAA08103; Fri, 17 Mar 1995 05:13:52 -0500 Received: by risc1.lrm.fi.cnr.it (AIX 3.2/UCB 5.64/4.03) id AA18725; Fri, 17 Mar 1995 11:02:38 +0100 From: thep@risc1.lrm.fi.cnr.it (Pornthep Sompornpisut) Message-Id: <9503171002.AA18725@risc1.lrm.fi.cnr.it> Subject: the solvent accessibility to proteins To: chemistry@ccl.net Date: Fri, 17 Mar 1995 11:02:35 +0100 (NFT) X-Mailer: ELM [version 2.4 PL23] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 222 Dear Colleagues Could anybody suggest me the references about the accessibility of solvents (especially H2O) to the proteins? Any comments (i.e. theory, aims, programs) will be appreciated . Your sincerely, Pornthep From IB13LVIB@HUEARN.SZTAKI.HU Fri Mar 17 08:13:07 1995 Received: from phem3 for IB13LVIB@HUEARN.SZTAKI.HU by www.ccl.net (8.6.10/930601.1506) id HAA09559; Fri, 17 Mar 1995 07:48:56 -0500 Received: from HUEARN.SZTAKI.HU (MAILER@HUEARN) by phem3.acs.ohio-state.edu (PMDF V4.2-13 #5888) id <01HO8GZ9DQE898EPO8@phem3.acs.ohio-state.edu>; Fri, 17 Mar 1995 07:48:39 EST Received: from HUEARN (NJE origin IB13LVIB@HUEARN) by HUEARN.SZTAKI.HU (LMail V1.2a/1.8a) with BSMTP id 0485; Fri, 17 Mar 1995 13:47:50 +0100 Date: Fri, 17 Mar 1995 13:47:49 +0100 (MET) From: Istvan Mayer Subject: BSSE To: chemistry Message-id: <01HO8GZCPRDY98EPO8@phem3.acs.ohio-state.edu> Content-transfer-encoding: 7BIT X-Acknowledge-To: Let me make some comments on the BSSE problem, first about the Boys-Bernardi scheme, then about an alternative (and perhaps more accurate) method, called CHA. 1. J-R. Hill correctly summarizes the origin of BSSE and most aspects of the Boys-Bernardi counterpoise correction. It seems however worth to quote the working fomula of this method as it is usually applied: E(int.,corrected) = E(AB) - E(A*) - E(B*) where E(AB) is the actual supermolecule energy, E(A*) and E(B*) are the monomer energies calculated by using the whole supermolecule basis. This way of calculation mislead a number of people who have assumed that "this method is exact because all the quantities are calculated in the same basis set". This is, however, not the case; it is an (ingenious and often accurate, but no ways exact ot mathematically rigorous) A POSTERIORI correction scheme. Its real meaning is just in the correction formula quoted by Hill, that is E(int.,corrected) = E(int.,uncorr.) + BSSE(correction) where E(int, uncorr.) is the interaction energy which one obtains from a "straightforward" calculation: E(int.,uncorr.)=E(AB)-E(A)-E(B) E(A), E(B) being the free monomer energies calculated in their own basis, and BSSE(correction) = (E(A) - E(A*)) + (E(B) - E(B*)) (For a related discussion see e.g., P. Valiron, A. Vibok and I. Mayer, J. Comp. Chem. 14, 401, 1993; and also: I. Mayer and L. Turi, J. Mol.Struct.(THEOCHEM) 227, 43, 1991.) It is important to call the attention that the Boys-Bernardi's Counterpoise method becomes ambiguous not only if there are more than two molecules but also if the geometry optimization is considered. If the change of the internal monomer geometries ("monomer relaxation") is also admitted, then the only way to avoid the use of mathematically ill-defined quantities is to calculate monomer relaxation in pure monomer basis sets [I.Mayer and P.R.Surjan, Chem. Phys. Lett. 191, 497 (1992)]. Looking from other side, this means that one has to use the correction formula also quoted in Hill's mail for the RELAXED monomer geometries, which means that each point on the energy hypersurface can be obtained by using as much as 7 different energy values. In fact, the uncorrected interaction energy is E(int.,uncorr)=E(AB)-E(A0)-E(B0) where E(AB) is the supermolecule energy with the actual intra- and intermolecular geometrical parameters, E(A0) and E(B0) are the energies of the FREE monomers in their own optimized geometries, respectively. Then the BSSE correction to this is, similarly to that quoted above (and in Hill's mail) BSSE(correction) = ( E(Ar)- E(Ar*)) + (E(Br) - E(Br*)) where "r' indicates the actual relaxed geometry and "*" the use of the whole supermolecule basis in the monomer calculations. Then the resulting corrected interaction energy is E(int.,corrected) = E(int.,uncorr) + BSSE(correction) The geometry optimization would require simultaneous calculation of 5 (!) gradient values (the energies E(A0) and E(B0) do not depend on the actual coordinates in the supermolecule). The same result quoted above can be presented as the actual BSSE-corrected interaction energy of the relaxed monomers: E(int, BSSE-corr.,neglecting relax.) = E(AB) - E(Ar*) - E(Br*) which is then corrected also for the monomer relaxation calculated in the monomer basis sets: E(int., corrected) = E(int, BSSE-corr., neglecting relax) + E(relax, A) + E(relax(B) where E(relax, A) = E(Ar)-E(A0) and E(relax, B) = E(Br)-E(B0) . 2. In the last years we have started to develop an A PRIORI scheme of excluding BSSE, in which the Hamiltonian (or Fockian) has been subjected to special analysis, and the terms responsible for BSSE are identified and then omitted from the actual calculations. This is called "Chemical Hamiltonian Approach" (CHA): - Its development is essentially completed at the SCF level (two slightly different variants, see e.g. I. Mayer and P.R.Surjan Int. J. Quantum Chem. 36, 225 (1989); I. Mayer and A. Vibok, Int. J. Quantum Chem. 40, 139 (1991) and 43, 801 (1992) and - especially - the paper Valiron et al. quoted above; for the case of more than two molecules a preprint of a fresh manuscript is available). - It has been adopted to the LCAO-DFT theory (M. Kieninger, S. Suhai and I. Mayer, Chem. Phys. Lett. 230, 485 (1994); - Its application to correlated wave functions is underway; for pivot calculations at the full CI level see I. Mayer et al. Chem. Phys. Lett. 224, 166 (1994) For CHA geometry optimization does not represent any CONCEPTUAL difficulty: only one gradient is needeeed. (Its calculation is, however, is not so trivial, as the "chemical Hamiltonian" in not Hermitean - BSSE does not represent a physical observable, a Hermitean operator could be assigned to which.) One can observe by comparing CHA and Boys Bernardi results, that they converge to each other with the increasing basis sets much faster than BSSE diapperas from the uncorrected interaction energy, so these a priori and a posteriori methods corroborate other to a great extent. I would call the attention to the recent special issue of Chem. Rev., devoted to the intermolecular interactions. Finally it should be noted that BSSE may occur within a single molecule as well - but this is a different story (cf. I.M. IJQC 23, 341, 1983) With best regards to all CCL, Istvan Mayer Central Research Institute for Chemistry of the Hungarian Academy of Sciences E-mail: IB13lVIB@HUBPSZ12.sztaki.hu (or IB13lVIB@HUEARN.bitnet) (Reserve path: H1376May@ella.hu or H1376May@HUELLA.bitnet) From S.R.Kilvington@soton.ac.uk Fri Mar 17 09:13:10 1995 Received: from beech.soton.ac.uk for S.R.Kilvington@soton.ac.uk by www.ccl.net (8.6.10/930601.1506) id IAA10200; Fri, 17 Mar 1995 08:39:19 -0500 Received: from vision.soton.ac.uk (vision.soton.ac.uk [152.78.128.74]) by beech.soton.ac.uk (8.6.10/hub-8.5) with ESMTP id NAA07960 for ; Fri, 17 Mar 1995 13:38:52 GMT Received: (from srk@localhost) by vision.soton.ac.uk (8.6.10/client-8.6) id NAA06025 for chemistry@ccl.net; Fri, 17 Mar 1995 13:40:13 GMT Message-Id: <199503171340.NAA06025@vision.soton.ac.uk> Subject: Code Complete To: chemistry@ccl.net Date: Fri, 17 Mar 1995 13:40:12 +0000 (GMT) From: "Simon Kilvington" X-Mailer: ELM [version 2.4 PL23] Content-Type: text Content-Length: 258 Hi, I had several request for the ISBN for "Code Complete". So here is the full info. Title: Code Complete Author: Steven C McConnell Publisher: Microsoft Press, 1993 ISBN: 1-55615-484-4 cheerio, Si. --- Simon Kilvington, srk@soton.ac.uk From herbert.homeier@rchs1.chemie.uni-regensburg.de Fri Mar 17 09:19:03 1995 Received: from comsun.rz.uni-regensburg.de for herbert.homeier@rchs1.chemie.uni-regensburg.de by www.ccl.net (8.6.10/930601.1506) id JAA10478; Fri, 17 Mar 1995 09:01:43 -0500 Received: from rchs1.chemie.uni-regensburg.de by comsun.rz.uni-regensburg.de with SMTP id AA24459 (5.65c/IDA-1.4.4 for ); Fri, 17 Mar 1995 15:00:18 +0100 Received: by rchs1.chemie.uni-regensburg.de (4.1/URRZ-sub (1.5)) id AA09979; Fri, 17 Mar 95 15:01:36 +0100 Date: Fri, 17 Mar 95 15:01:36 +0100 From: Herbert Homeier (t4720) Message-Id: <9503171401.AA09979@rchs1.chemie.uni-regensburg.de> To: CHEMISTRY@ccl.net Subject: Summary of chemistry WWW sites Cc: 5GK9SUNJ@vmsa.csd.mu.edu Hi, I am sorry that this answer to the original question is a little late, but I want to point out that many chemistry related servers and resources can be found using the URL http://rchs1.uni-regensburg.de/index.html#links Hopefully this helps. Best regards Herbert -------------------------------------------------------------- Dr. Herbert H. H. Homeier Institut fuer Physikalische und Theoretische Chemie Universitaet Regensburg D-93040 Regensburg, Germany Phone: +49-941-943 4720 FAX : +49-941-943 2305 email: na.hhomeier@na-net.ornl.gov HOMEPAGE --------------------------------------------------------------- > From c5008 Fri Mar 17 11:41:00 1995 > Date: Fri, 17 Mar 95 11:41:00 +0100 > From: Herbert Homeier (t4720) > Subject: Chemistry WWW sites > Content-Type> : > text/plain> > Mime-Version: 1.0 > X-Courtesy-Of: NCSA Mosaic 2.4 on Sun > X-Url: http://rchs1.chemie.uni-regensburg.de/%7Emaillist/data/0968.html > Apparently-To: c5008 > Content-Length: 16989 > X-Lines: 474 > Status: RO > > CCL:Summary of chemistry WWW sites > > JIANGUO SUN, CHEMISTRY DEPT., MARQUETTE U. (5GK9SUNJ@vmsa.csd.mu.edu) > Thu, 16 Mar 1995 19:39:50 -0600 (CST) > > Messages sorted by: [ date ][ thread ][ subject ][ author ] > Previous message: Garrett M. Morris: "CCL:malloc etc. on DEC Alpha" > > Dear netters: > To reponse the requests from many people who are also interested in > Chemistry WWW sites, I summarized the replies here. Thanks for all your helps. > > Jianguo > > ************************************************************************** > My original question was: > > > Could anyone tell me where I can find some WWW webs about chemistry > >resources? I need some samples (any chemistry) to build ours. > > The replies are: > > #1 **************************** > From: IN%"jkl@ccl.net" "Jan Labanowski" 13-MAR-1995 22:27:50.91 > > Did you try: > > http://www.ccl.net/chemistry.html > > and clicked on hypertext in "Other Sites of Interest?" Then you can usually > download the pages and save them as files, and see what other people do. > > Jan > jkl@ccl.net > > #2 *************************** > From: IN%"thys@uia.ua.ac.be" "Gerd Thys" 14-MAR-1995 00:37:40.88 > > Feel free to have a look at my WWW-page... I have collected more than 100 > links to chemistry-related resources. > > You can access my Chemistry-page through > > http://www.uia.ac.be/u/thys/chem.html > > or if you want, you can also look at my root-page, which includes other > (=non-chemistry) interesting stuff: > > http://www.uia.ac.be/u/thys/index.html > > hope this is of any help > > best regards > > Gerd > ---------------------------------------------------------------------------- > Gerd Thys Ph.D. Student > Structural Chemistry Group > University of Antwerp (UIA) > Universiteitsplein 1 E-mail: thys@uia.ua.ac.be > B-2610 wilrijk URL: http://www.uia.ac.be/u/thys/index.html > BELGIUM > ---------------------------------------------------------------------------- > > #3 ************************************ > From: IN%"nielsl@sci.kun.nl" "Niels van der Laag" 14-MAR-1995 01:56:44.96 > > Hi there, > > I'm a student at the university of Nijmegen, The Netherlands. > > The students here have there WWW-pages. Unfortunaly the depart- > ment not yet. > > The address is: > http://www.sci.kun.nl/sigma/ > > Succes > Niels van der Laag > student computational chemistry > > #4 ************************************ > From: IN%"noy@tci002.uibk.ac.at" 14-MAR-1995 02:57:20.92 > > Hi!, > An very complete, but not exhaustive index lists are of > chemistry homepage is at > > http://www.chem.ucla.edu/chempointers.html > > take care. > Noy > ---------------------------------------------------------------------------- > E-mail: noy@tci2.uibk.ac.at (University of Innsbruck) > noy@atc.atccu.chula.ac.th (Bangkok) (Permanent E-mail address) > Homepage http://www-c724.uibk.ac.at/noy/ > http://atc.atccu.chula.ac.th/noyhome/ > ----------------------------------------------------------------------------- > *** Love is easy to start but hard to stop > > #5 ******************************************** > From: IN%"ostertag@alf.biochem.mpg.de" "Georg Ostertag" 14-MAR-1995 03:49:04.11 > > I send you the adresses of 4 chemistry - www servers in germany which are my > preferred: > > http://www.chemie.fu-berlin.de/index.html > Freie Universitaet Berlin CHEMnet WWW Entry Point > ==> outfit very interesting! > > http://www.pc.chemie.th-darmstadt.de/ > Physical Chemistry, Technische Hochschule Darmstadt > > http://derioc1.organik.uni-erlangen.de/ccc-welcome.html > CCC (Computer Chemistry Club) Erlangen HOMEPAGE > > http://pctc.chemie.uni-erlangen.de/fakultaet/chemie.html > Erlangen - Chemie > > Hope this helps. > > Georg. > > #6 ************************************** > From: IN%"webmastr@organik.uni-erlangen.de" "CCC Webmaster" 14-MAR-1995 06:01:35.78 > > You are invited to have a look at the WWW pages of the > CCC (Computer Chemistry Center) in Erlangen URL = > http://www.organik.uni-erlangen.de/ > > Good webbing A.Dransfeld as > ( webmastr@ccc.uni-erlangen.de ) > > #7 *************************************** > From: IN%"rs0thp@rohmhaas.com" 14-MAR-1995 06:59:32.20 > > Chemistry Home Page > > Some sites > > Phoenix Polymers, Inc., a compounder of proprietary engineering thermoplastics > Lists of Internet Chemistry Resources at > University of Texas at Austin Chemistry Library. > Northern Illinois University, Department of Chemistry > Periodic Table of Elements, > Guide > Northern Illinois University Chemistry Server > Ohio SuperComputer Comp. Chem. (CCL) (Jan Labanowski's) Chem Page > Chemistry Servers from UCLA > > Anonymous FTP Servers > > QCPE > OSC Chemistry Archive > Simtel DOS/Windows Chemistry Software > MacSciTech, Chemistry Software > U Mich, Chemistry Software > Sumex Macintosh Science Software > Chemistry tutorials > > -- > Sincerely, Thomas Pierce - THPierce@RohmHaas.Com - Computational Chemist > "These opinions are those of the writer and not the Rohm and Haas Company." > > > > #8 ****************************************************** > From: IN%"rosas@irisdav.chem.vt.edu" "Victor M. Rosas Garcia" 14-MAR-1995 07:40:29.09 > > You can get started with these sites: > > Ohio Supercomputer Center

> WWW Chem Servers

> Chemistry > Page (EINET)

> Cambridge Crystallographic Data > Center

> The Geometry Center

> Magnetic Resonance Home > Page

> WSU Computer > Animations

> > Hope this helps. > > Victor. > > > #9 ***************************************** > From: IN%"nauss@ucmod2.che.uc.EDU" 14-MAR-1995 08:07:05.73 > > You can try our site (which has not been officially opened to the > public) at http://ucmodl.che.uc.edu/ucchem.html. > > Also, many people find the UCLA site useful > (http://www.chem.ucla.edu/chempointers.html). Personally, I find it > too cluttered. > > Two other places you may like are: > > Duke - http://www.chem.duke.edu/ > SUNY-Binghamton - http://chemiris.chem.binghamton.edu:8080/ > > Good luck. > > Jeff Nauss > > **************************************************************************** > * UU UU Jeffrey L. Nauss, PhD * > * UU UU Director, Molecular Modeling Services * > * UU UU Department of Chemistry * > * UU UU CCCCCCC University of Cincinnati * > * UU UU CCCCCCCC Cincinnati, OH 45221-0172 * > * UUUU CC * > * CC Telephone: 513-556-0148 Fax: 513-556-9239 * > * CC * > * CCCCCCCC e-mail: nauss@ucmod2.che.uc.edu * > * CCCCCCC http://ucmodl.che.uc.edu/~nauss/homepage.html * > **************************************************************************** > > > > #10 ******************************************** > From: IN%"LSTEFFEN@fair1.fairfield.edu" 14-MAR-1995 09:13:06.03 > > Here two good sites to get you started: > > http://akebono.stanford.edu/yahoo/Science/Chemistry/ > > http://www.chem.ucla.edu/chempointers.html > > and a couple of my all time favorites: > > http://www.nih.gov/molecular_modeling/gateway.html > > http://www.ch.ic.ac.uk/GIC/ > > Hope this helps get you started, > > L. Kraig Steffen > Assistant Professor of Chemistry > Fairfield University, > Fairfield CT 06430 > > 203 254-4000 ext 2254 > lsteffen@fair1.fairfield.edu > lsteffen@aol.com > > > > #11 *********************************************** > From: IN%"ezequiel@wucmd.wustl.edu" "Ezequiel Q. Morales" 14-MAR-1995 11:22:38.17 > > Hi, > I have several addresses that can be interesting for you: > > Scientific Web Resources > http://boris.qub.ac.uk/edward/index.html > Science:Chemistry > http://akebono.stanford.edu/yahoo/Science/Chemistry > Organic Chemistry Resources > http://www.chem.vt.edu/chem-ed/org-home.html > NMR Information Server > http://micro.ifas.ufl.edu > Chemist's Art Gallery > http://www.csc.fi/lul/chem/graphics.html > > Enjoy them > > ------------------------------------------------------------------------------- > Ezequiel Quintana Morales > Washington University, School of Medicine > Dept. of Molecular Biology and Pharmacology > Campus Box 8103, 660 S. Euclid Ave. > St. Louis, MO 63110 > Tel: + 1 314 362 29 87 > Fax: + 1 314 362 70 58 > e-Mail: ezequiel@wucmd.wustl.edu > ------------------------------------------------------------------------------- > > > > #12 ****************************************** > From: IN%"Jeffrey.Gosper@brunel.ac.uk" 14-MAR-1995 11:25:09.49 > > Try > http://akebono.stanford.edu/yahoo/Science/Chemistry/ > and > http://wwwhost.cc.utexas.edu/world/instruction/index.html > and > http://www.ch.ic.ac.uk/local/organic/ > > if you produce a list please let me know. > > > > ######################################################### > # Dr. Jeff Gosper # > # Dept. of Chemistry # > # BRUNEL University # > # Uxbridge Middx UB8 3PH # > # voice: 0895 274000 x2187 # > # facsim: 0895 256844 # > # internet/email/work: Jeffrey.Gosper@brunel.ac.uk # > # internet/WWW: http://http2.brunel.ac.uk:8080/~castjjg # > ######################################################### > > > > #13 ******************************************************** > From: IN%"bear@ellington.pharm.arizona.edu" 14-MAR-1995 12:49:36.44 > > you may look at my page of net link tools > http://copsg2.pharm.arizona.edu/~bear > please leave an email there to let me know what you think > > bear > > ___ __ ___ _____ ___ _____ ___ > (___ l .) /\ \ / \ \#\ \ / \ \/\ \ / > ___)OARING |__)EAR /\ \ / \ \#\ \ / \ \ \ \ > Cyber-Chemist, Molecular Design \__\/ \__\#\_.\/ \__\ \__\/ > bear@ellington.pharm.arizona.edu N+ O-Tyr-topo > UA New Pharmacy 404 Tucson 85721 > Topoisomerase reference URL: http://copsg2.pharm.arizona.edu/~bear/top/top > * / > \|/ Listening may be the most important thing we do today! (=) > > > > #14 ******************************************** > From: IN%"D.Winkler@chem.csiro.au" 14-MAR-1995 18:35:03.99 > > Try http://www.rpi.edu/dept/chem/cheminfo/chemres.html > > > Cheers, > > Dave > __________________________________________________________________________ > > Dr. David A. Winkler Voice: 61-3-542-2244 > Principal Research Scientist Fax: 61-3-543-8160 > CSIRO Division of Chemicals and Polymers > Private Bag 10 CSIRO: http://www.csiro.au > Clayton, Australia. > > > > #15 **************************************** > From: IN%"zhy@pchsgi25.IPC.PKU.EDU.CN" 14-MAR-1995 18:48:33.95 > > I know a place in stanford which provides rich informations on chemistry > http://akebono.stanford.edu/yahoo/Science/Chemistry/ > > ---------------------------------------------------------------------- > Henry Hongyu Zhang | zhy@pchsgi25.ipc.pku.edu.cn > Molecular Design Laboratory | Tel: 861-2501490 > Institute of Physical Chemistry | Fax: 861-2501725 > Peking University | > Peking 100871 , China | > > > > #16 ********************************************** > From: IN%"pateta@vents.uji.es" 15-MAR-1995 00:37:51.40 > > you can find in: > > http://akebono.stanford.edu/yahoo/ > > an interactive index about any field. > > About chemistry, one good site to jump to another is : > > http://www2.shef.ac.uk/chemistry/chemistry-home.html > > Have a nice trip ... > > Augusto Cesar > > ----------------------------------------+--------------------------------------- > | > Augusto Cesar de Camargo Neto - Pateta | Keith Nelson: You can't judge a > Universitat Jaume I | ------------- book by its cover ... > Departament de Ciencies Experimentales | > Grupo de Quimica Quantica | Watts: Yeah, but you can tell how > Apartat 224 | ----- much it's gonna cost. > 12008 - Castello | > Spain | in Some Kind of Wonderfull (1987) > |--------------------------------------- > Phone: +34 64 34-5700 ext. 2309 | > Fax: +34 64 34-5654 | John Keating: Carpe diem !!! > | ------------ > e-mail: pateta@migjorn.uji.es | > | in Dead Poets Society (1989) > ----------------------------------------+--------------------------------------- > > > > #17 ******************************************** > From: IN%"wtwinter@mailbox.syr.edu" "William T. Winter" 15-MAR-1995 01:40:32.88 > > > http://glucose.esf.edu > > which I have not announced publicly but which does have lots of pointers. > you are welcome to look > warning, since I am still doing a lot of tinkering, this site shuts down > without warning aperiodically > =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= > Dr. William T. Winter Phone: (315)470-6876 > 315 Baker Lab FAX: (315)470-6856 > SUNY-ESF Internet: wtwinter@mailbox.syr.edu > Syracuse, NY 13210-2786 > > > > > #18 ***************************************** > From: IN%"arthur@pchindigo2.IPC.PKU.EDU.CN" "Wang Arthur" 15-MAR-1995 02:09:13.85 > > You will find the following address helpful: > http://www.rpi.edu/dept/chem/cheminfo/chemres.html > > Good luck. > > Arthur > > +-----------------------------------------------------------+ > | | > | Arthur Wang Doctoral Candidate | > | | > | Molecular Design Lab | > | Institute of Physical Chemistry, Peking University | > | Beijing 100871, P.R.China | > | | > | E-mail: arthur@pchindigo2.ipc.pku.edu.cn | > | Telephone: 86-1-2501490 | > | WWW: ftp://162.105.177.1/sys/www/arthur/homepage.html | > | http://www.ipc.pku.edu.cn/arthur/homepage.html | > | | > +-----------------------------------------------------------+ > > > > > #19 ***************************************** > From: IN%"szilagyi@indy.mars.vein.hu" "Robert K. Szilagyi" 16-MAR-1995 01:25:36.52 > > Try our server! We have some excellent links to chemistry related documents! > > Good luck, > > Rob > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > Robert K. Szilagyi University of Veszprem METMOD FF > research fellow Dept. Org. Chem. L1 > Email: szilagyi@miat0.vein.hu Veszprem, H-8201 L2 | R1 > szilagyi@indy.mars.vein.hu Egyetem u. 10 >W=C< > Phone: +36-(88)-422022/137 P.O.Box 158 L3 | R2 > FAX: +36-(88)-426016 HUNGARY L4 > http://indy.mars.vein.hu:8000/molmod.html > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: 5GK9SUNJ@VMS.CSD.MU.EDU > -- Original Sender From: Address: 5GK9SUNJ@VMS.CSD.MU.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 > > Previous message: Garrett M. Morris: "CCL:malloc etc. on DEC Alpha" > From hinsenk@ERE.UMontreal.CA Fri Mar 17 11:13:51 1995 Received: from condor.CC.UMontreal.CA for hinsenk@ERE.UMontreal.CA by www.ccl.net (8.6.10/930601.1506) id LAA13329; Fri, 17 Mar 1995 11:09:21 -0500 Received: from eole.ERE.UMontreal.CA by condor.CC.UMontreal.CA with SMTP id AA18009 (5.65c/IDA-1.4.4 for chemistry@ccl.net); Fri, 17 Mar 1995 11:07:06 -0500 Received: from cyclone.ERE.UMontreal.CA by eole.ERE.UMontreal.CA (940406.SGI/5.17) id AA13400; Fri, 17 Mar 95 11:07:04 -0500 Received: by cyclone.ERE.UMontreal.CA (940406.SGI/5.17) id AA27235; Fri, 17 Mar 95 11:07:03 -0500 Date: Fri, 17 Mar 95 11:07:03 -0500 From: hinsenk@ERE.UMontreal.CA (Hinsen Konrad) Message-Id: <9503171607.AA27235@cyclone.ERE.UMontreal.CA> To: chemistry@ccl.net In-Reply-To: <199503170923.JAA00975@vision.soton.ac.uk> (S.R.Kilvington@soton.ac.uk) Subject: Re: CCL:malloc etc. on DEC Alpha "Simon Kilvington" wrote: you should all read a book called "Code Complete" by Steve McConnell, published by the Microsoft Press. An excellent suggestion! Be warned, however, that this book is written for C programmers. Although many topics discussed in it are equally valid for programming in Fortran or any other "standard" programming language, you probably need some basic knowledge of C to profit from the book. However, it doesn't hurt to know something about C anyway, even if you don't intend to use it much. One of the best introductions to C for those who already know some other programming language is still the good old Kernighan & Ritchie ("The C Programming Language", by B. Kernighan and D. Ritchie; make sure to get the second edition that deals with ANSI C). I remember having seen a book that deals with good programming style in Fortran, but I do not have a reference. Many Fortran textbooks unfortunately give a lot of bad advice - often for the sake of "efficiency", but most of these tricks give no advantages with most modern compilers. Obviously it is much more difficult to write safe code in Fortran, since you have to deal with all the silly limitations of a stone-age language. This makes it all the more important to have tools to help you, and by far the most important one is ftnchek (available from AT&T's netlib), which checks your for semantic errors that compiler normally don't detect (like passing wrong parameters to subroutines). It's free, it works, and it is easy to use - so there is no excuse for not using it. ------------------------------------------------------------------------------- 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 muguet@poly.polytechnique.fr Fri Mar 17 13:13:14 1995 Received: from polytechnique.polytechnique.fr for muguet@poly.polytechnique.fr by www.ccl.net (8.6.10/930601.1506) id MAA15175; Fri, 17 Mar 1995 12:48:09 -0500 Received: from poly.polytechnique.fr (poly.polytechnique.fr [192.48.98.1]) by polytechnique.polytechnique.fr (8.6.11/8.6.9) with ESMTP id TAA16323 for ; Fri, 17 Mar 1995 19:02:07 +0100 Received: (from muguet@localhost) by poly.polytechnique.fr (8.6.10/8.6.6) id SAA22348 for chemistry@ccl.net; Fri, 17 Mar 1995 18:51:28 +0100 Date: Fri, 17 Mar 1995 18:51:28 +0100 From: muguet francis Message-Id: <199503171751.SAA22348@poly.polytechnique.fr> To: chemistry@ccl.net Subject: BSSE update Dear CCL fans In relation to the last question CCL/BSSE As another post suggested, there have been sometimes ago a debate on BSSE on CCL. Pls consult the CCL archives. I would just add some comments. The BSSE is the subject of a somewhat heated debate. There have been unconvincing claims that the "problem was solved". One must be very cautious. I would suggest to read 2 very recent references with a somewhat different point of view, to say the least : van Duijneveldt Chem. Rev. 94, 1873-1885 (1994) An updated review. I. Mayer Chem. Phys. Lett 224, 166-174 (1994) The first stands for the standard correction CP method, while the other stands for an interesting yet complex a priori method. Also to read Feller JCP,96(8),6104 (1992) discuss Basis set completeness/BSSE Saebe JCP,98(3),2170 (1993) (I found this ref. quite recently) It seems to offer an interesting suggestion to correct, what I call the CSE (Configuration or Excitation Superposition error) and which Pulay and coworkers call the 'BSSE at the Correlated level'. This latter correction is added to the 'BSSE at the SCF level' correction. The CP is missing a real key point: The interacting partner is absent while computing the BSSE correction. This point of view is expressed in my paper, just published. JCP 102(9),3648-3654. FLAMEGUARD: Now, I don't claim to be a messiah, I don't claim to have "solved entirely" the BSSE problem. Note the title : TOWARDS In competition with other research interests, I am currently improving my scheme. Cheers to the CCL, and PLEASE send your letters of support. 20% is not enough. Francis ====================================================================== Francis F. Muguet Ph.D Research Scientist L.O.A Ecole Polytechnique - ENSTA Centre de l'Yvette 91120 PALAISEAU FRANCE Ph: (33) (1) 60.10.03.18 ext. 12.76 Fax: (33) (1) 60.10.60.85 E-mail : muguet@poly.polytechnique.fr ===================================================================== From pat@mercury.aichem.arizona.edu Fri Mar 17 14:13:13 1995 Received: from mercury.aichem.arizona.edu for pat@mercury.aichem.arizona.edu by www.ccl.net (8.6.10/930601.1506) id NAA15988; Fri, 17 Mar 1995 13:35:28 -0500 Received: by mercury.aichem.arizona.edu (5.65/DEC-Ultrix/4.3) id AA04632; Fri, 17 Mar 1995 11:32:07 -0700 Date: Fri, 17 Mar 1995 11:32:05 -0700 (MST) From: Pat Walters To: chemistry@ccl.net Subject: Re: CCL:malloc etc. on DEC Alpha In-Reply-To: <9503171607.AA27235@cyclone.ERE.UMontreal.CA> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I can't resist throwing in my $0.02 on this subject. In addition to "Code Complete" I'd recommend Writing Solid Code Steve Maguire Microsoft Press ISBN 1-55615-551-4 Also ... There is an excellent commercial package called MemCheck which can be a tremendous aid in debugging malloc problems. Not only will MemCheck find things like overwrites, it will also find "leaks" caused by memory you forgot to free. MemCheck is available for Unix, DOS and Windows. It costs about $200.00 (cheaper if you ask for an academic discount), and it's worth every cent. You can get MemCheck from StratosWare (1-800-WE-DEBUG). My only association with StratosWare is as a VERY satisfied customer. Pat _________________________________________________________________________ W. Patrick Walters pat@mercury.aichem.arizona.edu Graduate Student http://mercury.aichem.arizona.edu/pat.html Laboratory for Artificial Intelligence in Chemistry * Dept of Chemistry * * * University of Arizona, Tucson AZ 85721 * * * Voice : 602-621-6334 FAX : 602-621-8407 *** "At least it's a dry heat" * _______________________________________________________*__________________ From tripos!rigel!david@uunet.uu.net Fri Mar 17 14:17:09 1995 Received: from relay3.UU.NET for tripos!rigel!david@uunet.uu.net by www.ccl.net (8.6.10/930601.1506) id NAA16151; Fri, 17 Mar 1995 13:48:24 -0500 Received: from uucp5.UU.NET by relay3.UU.NET with SMTP id QQyhmh20136; Fri, 17 Mar 1995 13:48:17 -0500 Received: from tripos.UUCP by uucp5.UU.NET with UUCP/RMAIL ; Fri, 17 Mar 1995 13:48:18 -0500 Received: from rigel.tripos by tripos (4.1/SMI-4.0) id AA14076; Fri, 17 Mar 95 12:21:38 CST Received: by rigel.tripos (940816.SGI.8.6.9/5.6) id SAA11707; Fri, 17 Mar 1995 18:21:59 GMT Date: Fri, 17 Mar 1995 18:21:59 GMT From: tripos!rigel!david@uunet.uu.net (David Mosenkis) Message-Id: <199503171821.SAA11707@rigel.tripos> To: uunet!tessa.iaf.uiowa.edu!jstevens@uunet.uu.net Subject: Re: knowledge based protein modeling Cc: uunet!ccl.net!chemistry@uunet.uu.net Michelle, > Is it possible to generate a very crude model for a small protein (95 aa) > if you know the following: hydrophobic/hydrophilic regions, antibody > binding epitopes, carbohydrate linkage sites, and disulfide linkages? > If this is possible could you provide me with some references and what > programs are being used. I currently have access to most modules for > sybyl 6.10 which are running on various SGI platforms. I know that > homology modeling is possible using "composer", "homology", etc., but in > this case there are no related or homologous (based 20 % homology > cut-off). We don't need an "acurate" model, rather a very crude "first" > approximation which should provide us with the gross anatomy of the > protein. Knowledge of the hydrophobic regions, binding sites, and disulfides, by itself, will not be sufficient to produce even a rough 3D model. The only hope is if there is a protein of known structure that has a similar structure to yours. How to find if such a protein exists? Certainly the logical first step is to search the database of known structures for any with high sequence similarity, as you have done. In this case, you found no matches down to 20% sequence identity. I have seen a few cases where jumbling the alignments can detect a significant sequence relationship even with sequence identity as low as the high teens. So you could try lowering your % identity cutoff to 15%, and see if Composer's sequence homology search turns up any sequences with a significance score of at least 4 (i.e. native alignment score is > 4 standard deviations better than jumbled versions of same sequences). Another approach to locating a protein with the same fold is to use the inverse folding approach, which tries threading a sequence through known protein folds, and seeing if any of them accomodates the sequence extremely well. Such methods have been published by a number of groups, including those of Eisenberg, Thornton, Crippen, Sippl, and Bryant, Johnson, and Skolnick. I was involved in development of a Tripos product called MatchMaker that implements the Skolnick group approach to this problem[1,2,3], and includes analysis tools for reliably assessing the correctness of a match of your sequence to a known 3D structure. If a strong match is found, the result is just the sort of crude structural model of your sequence that you are seeking, that provides the "gross anatomy of the protein". Contact me or Tripos for more information. Good luck, David Mosenkis (david@tripos.com) Tripos, Inc. 1. Godzik, A., Kolinski, A., and Skolnick, J. (1992) "Topology Fingerprint Approach to the Inverse Protein Folding Problem", J. Mol. Biol. 227, 227-238. 2. Gozdik, A. and Skolnick, J. (1992) "Sequence-structure matching in globular proteins: Application to supersecondary and tertiary structure determination", Proc. Natl. Acad. Sci., Vol. 89, pp. 12098-12102. 3. Godzik, A., Kolinski, A., and Skolnick J. (1993) "De novo and inverse folding predictions of protein structure and dynamics", J. Comp. Aid. Mol. Design, Vol. 7, pp. 397-438. From MARYJO@neu.edu Fri Mar 17 15:13:23 1995 Received: from nuhub.dac.neu.edu for MARYJO@neu.edu by www.ccl.net (8.6.10/930601.1506) id OAA16745; Fri, 17 Mar 1995 14:16:02 -0500 From: Received: from neu.edu by neu.edu (PMDF V4.3-7 #7628) id <01HO8ULKUPLS93KSZ5@neu.edu>; Fri, 17 Mar 1995 14:20:29 EST Date: Fri, 17 Mar 1995 14:20:29 -0500 (EST) Subject: chiral intermolec potentials? To: chemistry@ccl.net Message-id: <01HO8ULKWL4293KSZ5@neu.edu> X-Envelope-to: chemistry@ccl.net X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-transfer-encoding: 7BIT Hello Everybody! I am asking this question on behalf of a local experimentalist. Has anybody done intermolecular potentials between two CHIRAL molecules? If so, do you have a reference? Is your program available to the public? Thank you. Mary Jo Ondrechen From feaster@tessa.iaf.uiowa.edu Fri Mar 17 15:20:55 1995 Received: from ns-mx.uiowa.edu for feaster@tessa.iaf.uiowa.edu by www.ccl.net (8.6.10/930601.1506) id OAA16846; Fri, 17 Mar 1995 14:18:56 -0500 Received: from tessa.iaf.uiowa.edu by ns-mx.uiowa.edu (8.6.10/19950309.1) on Fri, 17 Mar 1995 13:18:37 -0600 id NAA28439 with SMTP Received: by tessa.iaf.uiowa.edu (920330.SGI/891024) on Fri, 17 Mar 95 13:16:16 -0600 id AA25822 Date: Fri, 17 Mar 1995 13:07:36 -0600 (CST) From: shawn feaster Subject: protein modeling To: Sybyl List , Computational Chemistry List , BIOSYM Mailing List , Charmm List , Amber Mailing List Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all, Is it possible to force a complex of 3 proteins to have a triple helix conformation without having the original tertiary structures? It is know from CD that they do form a triple helix complex, the regions of the proteins which interact are known, and you can also see this from scanning em. If this is possible, what software should be used? I do know that de novo protein folding is computationally "impossible". Thanks, Shawn Feaster feaster@tessa.iaf.uiowa.edu From mmccar@postman.essex.ac.uk Thu Mar 16 15:07:21 1995 Received: from postman.essex.ac.uk for mmccar@postman.essex.ac.uk by www.ccl.net (8.6.10/930601.1506) id PAA28067; Thu, 16 Mar 1995 15:07:17 -0500 Received: from postman.essex.ac.uk by postman.essex.ac.uk with SMTP (PP) id <04496-0@postman.essex.ac.uk>; Thu, 16 Mar 1995 19:50:03 +0000 From: Mccarron M Date: Thu, 16 Mar 95 19:50:02 GMT Message-Id: <28566.9503161950@solb1.essex.ac.uk> To: chemistry Subject: CHARMM does someone know how to use the eavg command and the tsm command together like the block module says you can. I have run a simulation and want to carry out free energy component anlysis by thermodynamic integration. thanks in advance Matthew McCarron e-mail mmccar@essex.ac.uk From frits@rulglq.LeidenUniv.nl Fri Mar 17 10:13:11 1995 Received: from rulglq.leidenuniv.nl for frits@rulglq.LeidenUniv.nl by www.ccl.net (8.6.10/930601.1506) id JAA11179; Fri, 17 Mar 1995 09:44:42 -0500 Received: by rulglq.leidenuniv.nl (AIX 3.2/UCB 5.64/4.03) id AA15342; Fri, 17 Mar 1995 15:45:38 +0100 Date: Fri, 17 Mar 1995 15:45:38 +0100 From: frits@rulglq.LeidenUniv.nl (Frits Daalmans (4505)) Message-Id: <9503171445.AA15342@rulglq.leidenuniv.nl> To: chemistry@ccl.net, kreidler@hp817s.rz.uni-duesseldorf.de Subject: Re: CCL:rotamers in n.m.r. experiment I know of an NMR measurement that showed what was presumably slow exchange in N,N-di-isopropyl benzamide. The rotation around the CONH amide bond was so slow (at ambient temperature) that 2 different rotamers could indeed be seen. reference: C. Altona, R. Francke, R. de Haan, J.H Ippel, G.J Daalmans, A.J.A Westra Hoekzema, J. van Wijk, Mag. Res. Chem 32, p. 670-678 (1994) title: Empirical group electronegativities for vicinal NMR proton-proton couplings along a C-C bond: Solvent effects and reparameterization of the Haasnoot equation. good luck, Frits OH: PS: the solvent was CDCl3, concentration about 5 vol. % From tripos!ananke!shuston@uustar.starnet.net Fri Mar 17 18:13:25 1995 Received: from uustar.starnet.net for tripos!ananke!shuston@uustar.starnet.net by www.ccl.net (8.6.10/930601.1506) id RAA21491; Fri, 17 Mar 1995 17:28:12 -0500 Received: from tripos.UUCP by uustar.starnet.net with UUCP id AA12610 (5.67b/IDA-1.5); Fri, 17 Mar 1995 16:17:23 -0600 Received: from ananke.tripos by tripos (4.1/SMI-4.0) id AA16819; Fri, 17 Mar 95 16:10:27 CST Received: from localhost.SGI by ananke.tripos (931110.SGI/5.6) id AA26271; Fri, 17 Mar 95 16:10:26 -0600 Message-Id: <9503172210.AA26271@ananke.tripos> To: feaster@tessa.iaf.uiowa.edu, sybyl@quant.chem.rpi.edu, chemistry@ccl.net Subject: Re: protein modeling In-Reply-To: Your message of Fri, 17 Mar 1995 13:07:36 -0600 (CST) X-Mailer: exmh version 1.5gamma 8/15/94 Date: Fri, 17 Mar 95 16:10:25 -0600 From: Shawn Huston Dear Shawn, You can do this simply in Sybyl, starting from the primary sequence. All you need to do is to rotate the successive monomers by the correct transformation matrix. All the details are in Sundararajan and Marchessault Can. J. Chem. Vol. 53 1975 page 3563. I used this method to create a 6-fold sugar triplex, and will include the SPL for this. Your case will differ in that you will have a differend periodicity and you will not have a homopolymer, but this is easily modifed in the spl. Good Luck, Shawn Huston ### ### Triple Helix Construction ### ### Virtual Bond Method of Merchessault and Sundararajan ### Can. J. Chem. vol 53 p. 3563 1975 ### ### ( assumes use of the MERGE default tailor variables as listed in ### the Sybyl 6.1 Manual) # # Read in Asymmetric Residue, color and label atom names # ZAP (*) DEFAULT m1 MOL MULT_IN M1 /usr/ananke/shuston/presales/mansur/tripos_ff/Asym_Res.mol2 #COLOR TYPE M1 #LABEL NAME M1(*) # # Determine Helical Parameter h # SETVAR an_id 8 SETVAR a1_id 10 SETVAR zn_id %atom_info($an_id z) SETVAR z1_id %atom_info($a1_id z) SETVAR h %math( $z1_id - $zn_id ) ECHO 'Helix Parameter h is' $h # # Get the ID number of the O2 Oxygen atom # FOR i in %range( 1 %mol_info(m1 natoms) ) if %streql( %atom_info($i name) "O2") DEFINE STATIC_SET atom $i O2SET O2_atoms ENDIF ENDFOR # # copy M1 to M2, Apply Helix Symmetry Operation to M2 (residue 2) # COPY M1 M2 STATIC ROTATE D2 0.0 0.0 60.0 STATIC TRANSLATE D2 0.0 0.0 $h FREEZE molecule D2 # # copy M2 to M3, Apply Helix Symmetry Operation to M3 (residue 3) # COPY M2 M3 STATIC ROTATE D3 0.0 0.0 60.0 STATIC TRANSLATE D3 0.0 0.0 $h FREEZE molecule D3 # # copy M3 to M4, Apply Helix Symmetry Operation to M4 (residue 4) # COPY M3 M4 STATIC ROTATE D4 0.0 0.0 60.0 STATIC TRANSLATE D4 0.0 0.0 $h FREEZE molecule D4 # # There are no more Display areas so do some building here: # # # Freeze M2 and Merge M2 to M1 (O(1)-C(n) bond will form automatically # MERGE m2 m1 ZAP m2 # # Freeze M3 and Merge M3 to M1 (O(1)-C(n) bond will form automatically # FREEZE molecule D3 MERGE m3 m1 ZAP m3 # # copy M4 to M2, Apply Helix Symmetry Operation to M2 (residue 5) # COPY M4 M2 STATIC ROTATE D2 0.0 0.0 60.0 STATIC TRANSLATE D2 0.0 0.0 $h FREEZE molecule D2 # # copy M2 to M3, Apply Helix Symmetry Operation to M3 (residue 6) # COPY M2 M3 STATIC ROTATE D3 0.0 0.0 60.0 STATIC TRANSLATE D3 0.0 0.0 $h FREEZE molecule D3 # # Freeze M4 and Merge M4 to M1 (O(1)-C(n) bond will form automatically # FREEZE molecule D4 MERGE m4 m1 ZAP m4 # # Freeze M2 and Merge M2 to M1 (O(1)-C(n) bond will form automatically # FREEZE molecule D2 MERGE m2 m1 ZAP m2 # # Freeze M3 and Merge M3 to M1 (O(1)-C(n) bond will form automatically # FREEZE molecule D3 MERGE m3 m1 ZAP m3 # # The single strand is now built. Make 2 copies of this, and rotate them # by +- 120.0 deg. about the helix (z) axis in order to produce the triple # helix. # COPY M1 M2 STATIC ROTATE D2 0.0 0.0 120.0 COPY M1 M3 STATIC ROTATE D3 0.0 0.0 -120.0 FREEZE molecule ALL MERGE M2 M1 MERGE M3 M1 ZAP M2 ZAP M3 # # Add the remaining Hydrogens # BIO ADDH * ALL # # Name the Residues and Label the 3 distinct chains # MODIFY substructure name * sequential_auto BIO SET chainname 7,8,9,10,11,12 B BIO SET chainname 13,14,15,16,17,18 C # # Define each chain as a set # # # Create the set of all O2 atoms # FOR i in %range( 1 %mol_info(m1 natoms) ) if %streql( %atom_info($i name) "O2") MODIFY LOCAL_SET definition O2SET $i YES ENDIF ENDFOR From huang@mazda.wavefun.com Fri Mar 17 20:13:25 1995 Received: from volvo.wavefun.com for huang@mazda.wavefun.com by www.ccl.net (8.6.10/930601.1506) id TAA23149; Fri, 17 Mar 1995 19:28:08 -0500 Received: from mazda.wavefun.com by volvo.wavefun.com via SMTP (931110.SGI/930416.SGI) for chemistry@ccl.net id AA11070; Fri, 17 Mar 95 16:28:19 -0800 Received: by mazda.wavefun.com (931110.SGI/930416.SGI) for workshop@wavefun.com id AA04617; Fri, 17 Mar 95 16:28:06 -0800 From: "Wayne Huang" Message-Id: <9503171628.ZM4615@mazda.wavefun.com> Date: Fri, 17 Mar 1995 16:28:04 -0800 Reply-To: huang@wavefun.com X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: chemistry@ccl.net, spartan@wavefun.com Subject: Computational Chemistry Workshop Cc: workshop@wavefun.com Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 I am pleased to announce the upcoming spring quarter schedule for ... ------------------------------------ | COMPUTATIONAL CHEMISTRY WORKSHOP | ------------------------------------ Intensive 3-day workshops focus on the application of modern electronic structure methods to chemistry. Lectures will describe underlying theory, assess the performance of modern electronic structure methods, outline practical strategies for doing calculations, and illustrate results of applications to diverse chemical problems. Laboratories provide hands-on experience using a wide selection experiments, as well as ample time to explore your own chemistry. Visualization and animation will also be presented for both educational demonstration and research presentation. Here are the summary of workshop information: _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ _/ _/ COMPUTATIONAL CHEMSITRY WORKSHOP _/ _/ _/ _/ Format: 3-day intensive workshop on electronic structure methods _/ _/ and applications, and hands-on molecular modeling _/ _/ laboratory on individual workstations. It will provide: _/ _/ _/ _/ o Concise summary of modern electronic structure methods _/ _/ o Assessment of range and performance of their applications_/ _/ o Hands-on experience in molecular modeling _/ _/ o Graphical Analysis of results _/ _/ o Visualization and animation of structures and reactions _/ _/ _/ _/ Schedule: March Workshop: March 29, 30, 31, 1995 (Full) _/ _/ April Workshop: April 26, 27, 28, 1995 _/ _/ May Workshop: May 22, 23, 1995 (Yorktown, NY) _/ _/ June Workshop: June 14, 15, 16, 1995 _/ _/ _/ _/ Instructors: Lecture Section - Prof. Warren J. Hehre _/ _/ Lab Section - Dr. Wayne Huang _/ _/ _/ _/ Location: Wavefunction, Inc. Irvine, California, USA _/ _/ _/ _/ Fee: $1000 (50% off for academics, $500), which includes course _/ _/ registration, three computational textbooks ("Practical _/ _/ strategy of electronic structure calculations", _/ _/ "Chemistry with Computation" and "Experiments in _/ _/ Computational Chemistry"), breakfasts and lunches. _/ _/ _/ _/ Information: Contact Wayne Huang for further information including _/ _/ detailed brochure and course curriculum. _/ _/ Tel: (714)955-2120 Fax: (714)955-2118 _/ _/ E-mail: workshop@wavefun.com _/ _/ http://wavefun.com _/ _/ _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ +---------------------------------------------------------------------+ | Wayne Huang, Ph.D. | /--- ----\ /---/ ---\ ----- /---/ /| / | | Computational Chemist | \ / / / / / / / / / / | / | | Wavefunction, Inc. | \ /---/ /---/ /---/ / /---/ / | / | | huang@wavefun.com |---/ / / / / \ / / / / |/ | +---------------------------------------------------------------------+ | Wavefunction, Inc., 18401 Von Karman, Suite 370, Irvine, CA 92715 | | Telephone: (714)955-2120 Fax: (714)955-2118 | +---------------------------------------------------------------------+ -- +-------------------------------------------------------------------+ | Wayne Huang, Ph.D. | /--- ----\ /---/ ---\ ----- /---/ /| / | | Support Scientist | \ / / / / / / / / / / | / | | Wavefunction, Inc. | \ /---/ /---/ /---/ / /---/ / | / | | huang@wavefun.com |---/ / / / / \ / / / / |/ | +-------------------------------------------------------------------+ | Wavefunction, Inc., 18401 Von Karman, Suite 370, Irvine, CA 92715 | | Telephone: (714)955-2120 Fax: (714)955-2118 | +-------------------------------------------------------------------+ From y_zheng@ccmail.pnl.gov Fri Mar 17 21:13:19 1995 Received: from pnl.gov for y_zheng@ccmail.pnl.gov by www.ccl.net (8.6.10/930601.1506) id UAA23935; Fri, 17 Mar 1995 20:40:30 -0500 From: Received: from ccmail.pnl.gov by pnl.gov (PMDF V4.3-13 #6012) id <01HO91LDAU5C00004U@pnl.gov>; Fri, 17 Mar 1995 17:39:04 -0800 (PST) Date: Fri, 17 Mar 1995 17:36 -0800 (PST) Subject: Consistent force field To: chemistry@ccl.net, amber@cgl.ucsf.edu Message-id: <01HO91LDESCY00004U@pnl.gov> MIME-version: 1.0 Content-transfer-encoding: 7BIT Hi, I need a copy of the manual for Rasmussen's consistent force field program. The file I down loaded is somehow corrupted and I could not read it. I would appreciate if some one could send me the manual in a text file format. Thanks in advance. Yajun From b_duke@lacebark.ntu.edu.au Fri Mar 17 21:23:58 1995 Received: from lacebark.ntu.edu.au for b_duke@lacebark.ntu.edu.au by www.ccl.net (8.6.10/930601.1506) id UAA23997; Fri, 17 Mar 1995 20:45:58 -0500 From: Received: by lacebark.ntu.edu.au (AIX 3.2/UCB 5.64/4.03) id AA07973; Sat, 18 Mar 1995 10:06:48 +1000 Message-Id: <9503180006.AA07973@lacebark.ntu.edu.au> Subject: NBO in G92 To: CHEMISTRY@ccl.net (chemistry) Date: Sat, 18 Mar 1995 10:06:47 +1000 (EET) X-Mailer: ELM [version 2.4 PL21] Content-Type: text Content-Length: 704 Hi folks, One can use the NBO package in G92 by putting pop=nbo in the command line. I want to give NBO the RESONANCE keyword. Does anyone know how this is done? It was suggested to me that one could put $NBO RESONANCE $END at the end of the data. It does not work. Does anyone have any ideas? Thanks for any help. I will summarise any useful responses. Cheers, Brian. -- NOTE - Change of School name and University address from 1/1/95. Associate Professor Brian Salter-Duke (Brian Duke) School of Mathematical and Physical Sciences, Northern Territory University, Darwin, NT 0909, Australia. Phone 089-466702 e-mail: b_duke@lacebark.ntu.edu.au or b_duke@uncl04.ntu.edu.au From b_duke@lacebark.ntu.edu.au Fri Mar 17 21:34:58 1995 Received: from lacebark.ntu.edu.au for b_duke@lacebark.ntu.edu.au by www.ccl.net (8.6.10/930601.1506) id VAA24118; Fri, 17 Mar 1995 21:00:41 -0500 From: Received: by lacebark.ntu.edu.au (AIX 3.2/UCB 5.64/4.03) id AA08773; Sat, 18 Mar 1995 10:21:31 +1000 Message-Id: <9503180021.AA08773@lacebark.ntu.edu.au> Subject: A BLYP/Becke3LYP frequency problem in G92/DFT To: CHEMISTRY@ccl.net (chemistry) Date: Sat, 18 Mar 1995 10:21:31 +1000 (EET) X-Mailer: ELM [version 2.4 PL21] Content-Type: text Content-Length: 1111 Hi folks, I have been using BLYP and Becke3LYP for some large systems where MP2 frequencies are not feasible here with some success. With one system I have a problem. The molecule has D2h symmetry and is like diborane. Experimentally we know this but are using theory to help the neutron diffraction studies and to sort out the i.r./Raman bands. SCF gives reasonable results with two basis sets. BLYP and Becke3LYP give similar geometries to the SCF but the SCF gives one imaginary frequency. However the 3 "zero" rotational frequencies are roughly -30, -20 and -8. The imag freq is -40. I used opt=tight and Int=FineGrid. The frequency run still shows the forces and predicted displacements to be good. Can anyone sugest what is going on? I will post a summary. Thanks, Brian. -- NOTE - Change of School name and University address from 1/1/95. Associate Professor Brian Salter-Duke (Brian Duke) School of Mathematical and Physical Sciences, Northern Territory University, Darwin, NT 0909, Australia. Phone 089-466702 e-mail: b_duke@lacebark.ntu.edu.au or b_duke@uncl04.ntu.edu.au From wyl@pchindigo2.IPC.PKU.EDU.CN Fri Mar 17 22:13:22 1995 Received: from pchindigo2.IPC.PKU.EDU.CN for wyl@pchindigo2.IPC.PKU.EDU.CN by www.ccl.net (8.6.10/930601.1506) id VAA24588; Fri, 17 Mar 1995 21:47:28 -0500 Received: by pchindigo2.IPC.PKU.EDU.CN (920330.SGI/911001.SGI) for CHEMISTRY@ccl.net id AA03865; Sat, 18 Mar 95 10:33:31 +0800 Date: Sat, 18 Mar 1995 10:33:30 +0800 (SST) From: Wang Yanli To: shawn feaster Cc: Sybyl List , Computational Chemistry List , BIOSYM Mailing List , Charmm List , Amber Mailing List Subject: examples of protein refolding experiments in vitro In-Reply-To: Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear netters, I am interested in protein folding study, indeed I am interested in theoritical method. So I need experiment data to test my methods. I know some examples, such as ribonuclease, BPTI, cytochrome, but I need more other ones. Could anybody provide me examples of proteins, for which refolding experiments have been carried out in vitro, I will need not only successful examples, but as well as those failed. Any information from you will be highly appreciated. Thanks a lot in advance. Yanli Wang Molecular Design Lab. Peking University e-mail: wyl@pchindigo2.ipc.pku.edu.cn