From figuei@lutece.rutgers.edu Fri Nov 10 00:32:49 1995 Received: from lutece.rutgers.edu for figuei@lutece.rutgers.edu by www.ccl.net (8.6.10/950822.1) id AAA11674; Fri, 10 Nov 1995 00:21:14 -0500 Received: by lutece.rutgers.edu (931110.SGI/940423 - Rutgers University Department of Chemistry) for chemistry@www.ccl.net id AA15051; Fri, 10 Nov 95 00:20:26 -0500 Date: Fri, 10 Nov 95 00:20:26 -0500 From: figuei@lutece.rutgers.edu (Francisco Figueirido) Message-Id: <9511100520.AA15051@lutece.rutgers.edu> To: mam@atc.atccu.chula.ac.th Cc: chemistry@www.ccl.net In-Reply-To: <9511101046.AA25482@atc.atccu.chula.ac.th> (mam@atc.atccu.chula.ac.th) Subject: Re: CCL:Software of Molecular Dynamics Simulation Reply-To: figuei@lutece.rutgers.edu I once saw a program called MOLDY that was designed just for what you want. The author is Keith Refson (keith@earth.ox.ac.uk). I never used it because we do simulations in liquids, not solids, but it looks rather good. -- Francisco Figueirido email: figuei@lutece.rutgers.edu phone: (908)445-3278 From joubert@ext.jussieu.fr Fri Nov 10 04:02:52 1995 Received: from shiva.jussieu.fr for joubert@ext.jussieu.fr by www.ccl.net (8.6.10/950822.1) id DAA13953; Fri, 10 Nov 1995 03:55:45 -0500 Received: from idf.ext.jussieu.fr (idf.ext.jussieu.fr [134.157.81.129]) by shiva.jussieu.fr (8.6.10/jtpda-5.1) with ESMTP id JAA11672 for ; Fri, 10 Nov 1995 09:55:18 +0100 Received: from 134.157.11.17 by idf.ext.jussieu.fr (8.6.10/jtpda-4.0) with SMTP; Fri, 10 Nov 1995 09:55:17 +0100 Message-Id: <199511100855.JAA27569@idf.ext.jussieu.fr> Date: Fri, 10 Nov 95 08:59:08 -0100 From: JOUBERT laurent Organization: ENSCP X-Mailer: Mozilla 1.12(Macintosh; I; 68K) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: effective core potentials X-URL: http://www.ccl.net/ccl/welcome.html#1 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Hi ! I'm beginning to work on Neodymium complexes.(chlorides and fluorides) I'm looking for an effective core potential working with Nd. All those I found work only with La (but not with the other lanthanides Waiting for somebody's answer. ********************************************************* * JOUBERT laurent * * Tel:47-27-67-27 * * * * E-MAIL : joubert@ext.jussieu.fr * * * * ECOLE NATIONALE SUPERIEURE DE CHIMIE DE PARIS * * LABORATOIRE DE MODELISATION APPLIQUEE A LA CHIMIE * * 11, RUE PIERRE ET MARIE CURIE * * 75232 PARIS CEDEX 05 * * FRANCE * ********************************************************* From owner-chemistry@ccl.net Fri Nov 10 04:32:51 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id EAA14206; Fri, 10 Nov 1995 04:23:01 -0500 Received: from earth.ox.ac.uk for Keith.Refson@earth.ox.ac.uk by bedrock.ccl.net (8.7.1/950822.1) id EAA27085; Fri, 10 Nov 1995 04:22:57 -0500 (EST) Received: from rahman.earth.ox.ac.uk by earth.ox.ac.uk; Fri, 10 Nov 1995 09:21:17 GMT Date: Fri, 10 Nov 95 09:21:16 GMT Message-Id: <21371.9511100921@rahman.earth.ox.ac.uk> From: Keith Refson Subject: CCL:Software of Molecular Dynamics Simulation To: chemistry@ccl.net Organisation: Earth Sciences Department, Oxford University. Francisco Figueirido wrote: > I once saw a program called MOLDY that was designed just for what you > want. The author is Keith Refson (keith@earth.ox.ac.uk). I never used it > because we do simulations in liquids, not solids, but it looks rather good. If anyone is interested in using Moldy it is freely available (under the GNU Public License) from our Web server http://www.earth.ox.ac.uk/~keith/moldy or by anonymous ftp ftp://ftp.earth.ox.ac.uk/pub/moldy-2.9.tar.Z Incidentally it will simulate both solids and liquids; the main restrictions are that it handles atoms, ions and rigid molecules, and it is currently limited to pairwise central forces. I keep a list of email addresses for mailing about any new versions or bug reports. If you want to be included in this, please send me an email and ask. sincerely Keith Refson ------------------------------------------------------------------------------ | Email : keith@earth.ox.ac.uk | Dr Keith Refson, Dept of Earth Sciences| | TEL(FAX): +44 1865 272026 (272072)| Parks Road, Oxford OX1 3PR, UK | ------------------------------------------------------------------------------ From owner-chemistry@ccl.net Fri Nov 10 06:32:56 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id GAA15434; Fri, 10 Nov 1995 06:27:44 -0500 Received: from sun2.nsfnet-relay.ac.uk for awhit@dir.manchester-computing-centre.ac.uk by bedrock.ccl.net (8.7.1/950822.1) id GAA27424; Fri, 10 Nov 1995 06:27:37 -0500 (EST) Via: uk.ac.manchester-computing-centre.dir; Fri, 10 Nov 1995 11:26:00 +0000 Date: Fri, 10 Nov 95 11:25:52 GMT Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable To: chemistry@ccl.net From: awhit@dir.manchester-computing-centre.ac.uk Subject: 2nd INT. CONF. FOR CHEMICAL INFO. USERS- FINAL NOTICE =46INAL NOTICE, STILL A FEW PLACES LEFT AT THE: 2nd INTERNATIONAL CONFERENCE for CHEMICAL INFORMATION USERS Tuesday 14th and Wednesday 15th November 1995 MANCHESTER, UK ***************************************************************** TO REGISTER, EMAIL OR FAX NOW!!!!!!!!!!!!!!!! Ms H Schofield, Chemistry Department Library, UMIST, PO Box 88, Manchester M60 1QD, UK, Tel: +44(0) 161 200 4420, =46ax: +44(0)161 200 4941 Email: helen.schofield@umist.ac.uk OR visit the UMIST Chemistry Department HOME PAGE at http://uchsg11.ch.umist.ac.uk for further details, cost and registration form. COST: =A3195 for conference registration and meals. =A357 per night for b&b. **************************************************************** The Conference comprises of five sessions. CONFERENCE PROGRAMME Tuesday 14 November 11.00 - 13.00 Arrival and Registration: Manchester Conference Centre-Weston Building, UMIST 12.00 Buffet Lunch in the Exhibition Hall - Weston Building Assemble in Weston Lecture Theatre, Weston Building 13.00 Introduction: "Two years is a long time in chemical information" Dr John M Barnard (Barnard Chemical Information Ltd, Sheffield) SESSION 1 - Use and Manipulation of Molecular Strucuture CHAIRMAN: Professor Peter Willett 13.30 "Applications of 3D structural databases in chemistry and drug design" Dr Frank H Allen (Cambridge Crystallographic Data Centre) 14.00 "Bioinfomatics in the UK" Dr Alan Bleasby (Daresbury Laboratory, EPSRC) 14.30 "Mass spectrometry databases: current position and future requirements" Professor Jim H Scrivens (ICI Chemicals and Polymers, Wilton) 15.00 Tea in the Exhibition Hall 15.30 "Automated structure elucidation with SpecInfo 3" Dr Mickael Penk (Chemical Concepts GmbH, Germany) 16.00 "A review of programs for de novo drug design" Dr Val Gillet (University of Sheffield) 16.30 "The role of chemical information in computer-aided drug discovery" Dr Darren Green (Glaxo-Wellcome Medicines Research Centre, Stevenage) 17.00 End of Session 19.00 Sherry Reception sponsored by Synopsys Scientific Systems Ltd in the Exhibition Hall 20.00 Conference Dinner in the Restaurant Wednesday 15 November SESSION 2 - New Directions for Chemical Information CHAIRWOMAN: Dr Diana M Leitch 08.45 "Electronic chemistry libraries: problems and changes" Dr Engelbert Zass (Chemie-Bibliothek, ETH, Z=C5rich) 09.30 "SciFinder: the Glaxo-Wellcome experience" Dr Stephanie North (Glaxo-Wellcome Medicine Research Centre, Stevenage) 10.00 "Recent developments in similarity and dissimilarity searching" Professor Peter Willett (University of Sheffield) 10.30 Coffee in the Exhibition Hall 11.00 "A chemical information sabbatical: information provision and training in an academic setting" Mr Roger Beckman (Indiana University, USA) 11.30 "Electronic journals in chemistry" Mr Fytton Rowland (Loughborough University of Technology) 11.55 "The CLIC project (Cambridge, Leeds, Imperial, Cambridge)" Dr Henry S Rzepa (Imperial College London) 12.15 Academic Forum Dr Diana M Leitch (John Rylands University Library of Manchester) Dr Henry Rzepa (Imperial College, University of London) 12.45 Lunch in the Exhibition Hall SESSION 3 - Information and Safe Chemical Practice CHIARMAN: Richard Stephenson 13.30 "Superhighway access to OSH, environment and fire information" Mrs Sheila Pantry OBE (Sheila Pantry Associates, Sheffield) 14.15 "IUCLID - a database on chemical substances information as a tool for the EU risk assessment programme" Mr Christian Heidorn (European Chemicals Bureau, Italy) SESSION 4 - Developments in Chemical Patent Information 14.45 "The importance of patents and patent information for academics" Helen Schofield (UMIST, Manchester) 15.15 Tea in the Exhibition Hall 15.45 "Searching full text documents in chemistry" John Brennan (European Patent Office, The Hague) 16.15 "Impact of new technologies: chemical patent information products" Dr Bill G Town (Derwent Information Ltd, London) SESSION 5 - The Way Forward CHAIRMAN: Dr John M Barnard 17.00 Discussion/Forum Mr Stephen Briggs Dr Darren Green Dr Diana M Leitch Dr Engelbert Zaas 17.30 Closing Remarks and Conclusion of Conference CURRENT LIST OF CONFERENCE EXHIBITORS BEILSTEIN INSTITUTE CHAPMAN & HALL LTD CHEMICAL CONCEPTS GmbH DERWENT INFORMATION LTD EPSRC, DARESBURY LABORATORY INSTITUTE OF SCIENTIFIC INFORMATION MICROINFO QUESTEL-ORBIT ROYAL SOCIETY OF CHEMISTRY STN INTERNATIONAL SYNOPSYS SCIENTIFIC SYSTEMS LTD LINKED MEETINGS (independent of the conference) The following meetings will be held: Wednesday 14 November 10.00 - 12.00 STN User Meeting Conference Room 6: refreshments and online demonstrations(open forum) 17.10 Chemical Structures Association, Annual General Meeting (open to Association members only) 18.00 BIDS User Meeting Speakers: Chris Cooksey - "Jewels from the mailbox", Terry Morrow - "The chemistry of BIDS" (open forum) Registration for the conference is not necessary for attendance at these linked meetings. END*********************************************************************** =A7=A7=A7=A7=A7=A7=A7=A7=A7=A7=A7=A7=A7=A7=A7=A7=A7=A7=A7=A7=A7=A7=A7=A7=A7= =A7 Dr Andy Whiting Chemistry Department =46araday Building UMIST PO Box 88 Manchester M60 1QD UK Tel. (0161)200 4524 =46ax. (0161)236 7677 Email. awhit@dir.mcc.ac.uk =A7=A7=A7=A7=A7=A7=A7=A7=A7=A7=A7=A7=A7=A7=A7=A7=A7=A7=A7=A7=A7=A7=A7=A7=A7= =A7 From owner-chemistry@ccl.net Fri Nov 10 07:47:54 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id HAA16393; Fri, 10 Nov 1995 07:45:39 -0500 Received: from earn.cvut.cz for strajbl@silicon.karlov.mff.cuni.cz by bedrock.ccl.net (8.7.1/950822.1) id HAA27650; Fri, 10 Nov 1995 07:45:35 -0500 (EST) Received: from ns.karlov.mff.cuni.cz by earn.cvut.cz (IBM VM SMTP V2R1) with TCP; Fri, 10 Nov 95 13:45:05 MET Received: from silicon.karlov.mff.cuni.cz by ns.karlov.mff.cuni.cz id aa20258; 10 Nov 95 13:43 MEZ Received: by silicon.karlov.mff.cuni.cz (931110.SGI/930416.SGI) for @NS.KARLOV.MFF.CUNI.CZ:CHEMISTRY@ccl.net id AA25362; Fri, 10 Nov 95 14:33:43 -0800 Date: Fri, 10 Nov 95 14:33:43 -0800 From: Marek Strajbl Message-Id: <9511102233.AA25362@silicon.karlov.mff.cuni.cz> To: CHEMISTRY@ccl.net Subject: force field and sugar puckering Dear netters, can someone give hints, what force field or semiempirical method are best for predicting of sugar puckering of ribose (deoxyribose) in nucleosides. Thanks, Marek Strajbl --------------------------------- Marek Strajbl Institute of Physics of CU, Prague, CZ e-mail: --------------------------------- From talafous@coil.com Fri Nov 10 09:32:56 1995 Received: from bronze.coil.com for talafous@coil.com by www.ccl.net (8.6.10/950822.1) id JAA17315; Fri, 10 Nov 1995 09:17:58 -0500 Received: from mail.coil.com ([205.133.97.120]) by bronze.coil.com (8.6.4/8.6.12) with SMTP id JAA23472 for ; Fri, 10 Nov 1995 09:17:24 -0500 Date: Fri, 10 Nov 1995 09:17:24 -0500 Message-Id: <199511101417.JAA23472@bronze.coil.com> X-Sender: talafous@mail.coil.com X-Mailer: Windows Eudora Version 1.4.4 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@www.ccl.net From: talafous@coil.com (Joseph Talafous) Subject: book ref Dear CCLer's: Does anyone have an ISBN number for the following? Oxford University Press says that they don't have it... Chang, W. et. al. (1994), "Design and Application of PDBLib, a C++ Macromolecular Class Library", Oxford University Press. Thanks fellows, Joe Talafous TAU Consulting From xiaopeng@astro.ocis.temple.edu Fri Nov 10 09:47:59 1995 Received: from astro.ocis.temple.edu for xiaopeng@astro.ocis.temple.edu by www.ccl.net (8.6.10/950822.1) id JAA17410; Fri, 10 Nov 1995 09:28:02 -0500 Received: (from xiaopeng@localhost) by astro.ocis.temple.edu (8.7.1/8.7.1) id JAA07587; Fri, 10 Nov 1995 09:27:00 -0500 (EST) Date: Fri, 10 Nov 1995 09:26:59 -0500 (EST) From: Peking To: chemistry@www.ccl.net Subject: summary--3d graph and 2d contour (fwd) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII ---------- Forwarded message ---------- Date: Thu, 9 Nov 1995 14:10:23 -0500 (EST) From: Peking To: chemistry@www.ccl.net Subject: 3d graph and 2d contour Hello, Dear CCLs, I am looking for a PC or SGI software that can show a 3-dimension optential surface and its 2-d contour on the same graph. Anybody can kindly give me info? Thanks! xiaopeng xiaopeng@astro.ocis.temple.edu Thanks for the help of ccls. Here is what I got for the questions above. Matlab can do this. There are version for windows and UNIX work station. gnuplot can do this. gnuplot can be ftp from the following address: ftp.dartmouth.edu under the directory: pub/gnuplot/gnuplot3.5.tar.z or ftp prep.ai.mit.edu under the directory /pub/gnu From sylee@sorak.kaist.ac.kr Fri Nov 10 10:47:56 1995 Received: from sorak.kaist.ac.kr for sylee@sorak.kaist.ac.kr by www.ccl.net (8.6.10/950822.1) id KAA18031; Fri, 10 Nov 1995 10:40:45 -0500 Received: (from sylee@localhost) by sorak.kaist.ac.kr (8.6.12H1/8.6.12) id AAA15841 for CHEMISTRY@www.ccl.net; Sat, 11 Nov 1995 00:42:34 +0900 Date: Sat, 11 Nov 1995 00:42:34 +0900 From: sang-yeon lee Message-Id: <199511101542.AAA15841@sorak.kaist.ac.kr> To: CHEMISTRY@www.ccl.net Subject: Looking for a code for scaled quantum mechanical force field Dear CCls; I am looking for freeware/shareware for the generation of scaled quantum mechanical force field from the cartesian force constants computed with Gaussian 94. Could anybody give me the information ? Thank you very much in advance. Sincrely yours Sang Yeon Lee ========================================================================= Mr Sang Yeon Lee e-mail) sylee@sorak.kaist.ac.kr Center for Molecular Science KAIST, Taejon, 305-701 Republic of Korea ========================================================================= From owner-chemistry@ccl.net Fri Nov 10 11:17:58 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id LAA18446; Fri, 10 Nov 1995 11:09:31 -0500 Received: from gtc05f for vis@gensia.com by bedrock.ccl.net (8.7.1/950822.1) id LAA28580; Fri, 10 Nov 1995 11:09:28 -0500 (EST) Received: from genny (genny.res.gensia.com) by gtc05f (5.x/SMI-SVR4) id AA12419; Fri, 10 Nov 1995 08:04:13 -0800 Received: by genny (940816.SGI.8.6.9/930416.SGI.AUTO) id LAA02691; Fri, 10 Nov 1995 11:01:08 GMT Date: Fri, 10 Nov 1995 03:01:07 +48000 From: Viswanadhan To: chemistry@ccl.net Subject: Re: Zinc parametrization Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi Netters: With regard to my question on parametrizing Zinc (vdW radius & charge) at the active site of an enzyme, I received a number of responses. Several refer to the papers of Merz & coworkers, but these authors do not use CHELPG and Gaussian to get the charges, and they constrain the residues. If the metal ion and the neighboring residues are constrained, it really does not matter that much what radius and charge are used in the simulation (to preserve the active site geometry though the final energies depend on these parameters). The charges on the interacting residues that coordinate with Zinc also need to be altered when deriving a model. I thank all of those who responded to my question. Here are the responses: ---------------------------------------------------------------------------------------------------- Vis: Goldschmidt (Naturwissenschaften 14:477, 1926 I think) gives the empirical radius of Zn2+ to be 0.83 ang while Pauling (JACS 49:763, 1927) computes 0.74 ang. For the CHELPG method, I don't believe that it hurts to choose a radius too large, but do not choose one that is too small! The important thing is the charge "felt" by neighboring atoms. So, choose a radius slightly smaller than the closest approach that you would expect from any other atoms. From the literature, the Zn-O distances in the first hydration shell are about 2.0 to 2.2 angstroms (see Chem Rev 93:1173, 1993), so I should think that your 1.39 angstrom value would work fine. Best of luck, Brian J. Teppen teppen@srel.edu Advanced Analytical Center for Environmental Sciences Savannah River Ecology Laboratory University of Georgia Drawer E Aiken, SC 29802 On Nov 6, 4:49am, Viswanadhan wrote: > Subject: CCL:G:Parametrization for Zinc / charges & vdW radius > I would like to use CHELPG charges which necessitates the use of right > vdW radii. For neutral Zinc, the Bondi radius (J. Phys. Chem. 68. 441) > is 1.39 A, which is clearly not appropriate. Can any one point to recent > references or suggest a method? I will be happy to summarize the > responses (with regard to vdW radii & modeling the charge in the active > site of an enzyme for the Zinc ion). Merz and coworkers have addressed the problem of zinc parameters for their study of human carbonic anhydrase II, JACS, 1991, 113, 8262-8270. Dave Huhta, now at Biosym/MSI, I believe, also worked on this issue with a different approach, JACS, 1990, 112, 4759-4767. Lee Bartolotti addressed the issue of the 6-12 potentials in J. Comp. Chem., 1991, 12(9), 1125-8. A formidable problem...best of luck. Regards, James jbrown@iris7.carb.nist.gov ------------------- Dr. Viswanadhan - While I offer no solutions, I do offer a caution: I would be careful when using CHELPG charges for the system you have described. In this system, it seems to me that the zinc ion would be fairly well buried. CHELPG produces charges which reproduce the electrostatic potential outside the molecule. Unfortunately, atoms that are buried inside the molecule do not affect the electrostatic potential much. The result is that CHELPG charges for buried atoms can vary over a wide range without changing the outcome much. This often leads to unreasonable charges on the buried atom. Dave Giesen Hi Vish, Sal Profeta here. Hope you and the group out there are doing well. I think the person who can best answer your query is Kenny Merz at Penn State. He's done a lot of work with zinc-containing systems within AMBER, and has published a few papers in JACS and JCC in the last 5 years on this. According to the Directory of Grad REsearch his eamil is: merz@retina.chem.psu.edu Good luck! Cheers, Sal ++++++De mortuis nil nisi bonum.++++++++++* Dr. Salvatore Profeta, Jr. Computational Polymorphism, Ltd. Research Computing & Consulting 104 Cottage Lane Durham, NC 27713-9387 (919) 544-2299/5304 (Fax) email: profeta~s@glaxo.com (courtesy acct) ++++++Sic transit gloria mundi++++++++++++ Viswanadhan wrote: : : : I would like to use CHELPG charges which necessitates the use of right : vdW radii. For neutral Zinc, the Bondi radius (J. Phys. Chem. 68. 441) : is 1.39 A, which is clearly not appropriate. Can any one point to recent : references or suggest a method? I will be happy to summarize the : responses (with regard to vdW radii & modeling the charge in the active : site of an enzyme for the Zinc ion). : : Vellarkad N. Viswanadhan : Yes, what does constitute "good" vdW radii. In our work on Fe-S centers in proteins we've noticed that the actual charges calculated by CHELPG vary significantly depending on whether you use Breneman&Wiberg radii or Gavizotti&Spackman radii. Generally, Breneman & Wiberg based charges seem "better behaved" in our systems. Also, we've noticed that many groups use radii designed for other purposes and "plug" these into the CHELPG algorithm. What are the rationals people use in choosing their radii? -Brian -- ============================================================================= | .---------.| Brian W. Beck | E-mail Addresses: | |/\ | ||--------------------| brian@bert.chem.wsu.edu | || \\ WSU || Biochem/Biophysics | brian_beck@wsu.edu | |\ - *|| WSU , 206 Fulmer | URL http://elmo.chem.wsu.edu/~brian | | | || Pullman, WA | VOICE (509) 335-4083 | | \___________|| 99164-4660 | FAX (509) 335-9688 | ============================================================================= Hi, You might want to look at the following reference in which charges and force field params for Zinc and for surrounding atoms are determined for the zinc finger in the DBD of the glucocorticoid receptor. M.A.L. Eriksson, T. Hard and L. Nilsson (1995) Biophys. J. vol68, pp 402-426. Molceular dynamics simulations of the glucocorticoid receptor DNA-Binding Domain in complex with DNA and free in solution. Charges were obtained from full geometry optimization of model system in the MOPAC/MNDO/ESP calcn. The Lennard-Jones params for Zn were taken from K. Merz (1991) J. Amer. Chem. Soc. 113:406-411. Hope this helps Laurent ********************************************************************** ** Laurent Chiche !! e-mail: ** ** !! chiche@cbs.univ-montp1.fr ** ** Centre de Biochimie Structurale !! ** ** Faculte de Pharmacie !! Tel: (33) 67.04.34.32 ** ** 15 Ave. Charles Flahault !! ** ** 34060 Montpellier - France !! Fax: (33) 67.52.96.23 ** ********************************************************************** From owner-chemistry@ccl.net Fri Nov 10 12:48:00 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id MAA19620; Fri, 10 Nov 1995 12:44:56 -0500 Received: from scisun.sci.ccny.cuny.edu for box@scisun.sci.ccny.cuny.edu by bedrock.ccl.net (8.7.1/950822.1) id MAA29153; Fri, 10 Nov 1995 12:44:54 -0500 (EST) Received: by scisun.sci.ccny.cuny.edu (4.1/SMI-4.1-CCNY-Science) id AA17227; Fri, 10 Nov 95 12:44:47 EST Date: Fri, 10 Nov 95 12:44:47 EST From: box@scisun.sci.ccny.cuny.edu (Vernon G. Box) Message-Id: <9511101744.AA17227@scisun.sci.ccny.cuny.edu> To: CHEMISTRY@ccl.net, strajbl@silicon.karlov.mff.cuni.cz Subject: Re: CCL:force field and sugar puckering Hi You can try STR3DI.EXE which has a new force field specifically designed to incorporate lone pairs into molecular mechanics. Look at the web page for Exorga Inc., who are the distributors of the program. http://pages.prodigy.com/NJ/exorga/exorga.html VB From patterson@chem.wisc.edu Fri Nov 10 13:18:00 1995 Received: from chem.wisc.edu for patterson@chem.wisc.edu by www.ccl.net (8.6.10/950822.1) id NAA20009; Fri, 10 Nov 1995 13:04:37 -0500 From: Received: from evp by chem.wisc.edu; Fri, 10 Nov 95 12:04 CST Message-Id: <25111012043415@chem.wisc.edu> Date: Fri, 10 Nov 1995 12:03:47 -0600 Subject: MC-SCF summary To: chemistry@www.ccl.net Dear CCL: Some time ago I posted a question concerning tutorial examples for MC-SCF and related methods. Here are the most important responses. Thanks to everyone who responded. You have helped me greatly. Also, several people mentioned the upcoming Gaussian workshop on CASSCF at Pacifichem. Anybody have a spare plane ticket to Hawaii :) ? ======== response 1 Hi Eric, if you are dealing mainly with small to medium sized molecules then you should probably give MOLPRO94 a try. Documentation for this program is available from http://tcibm.mols.sussex.ac.uk/molpro/molpro.html If you want to download a copy of the manual to get an idea of the capabilities of this ab initio package you can do so at http://www.zib-berlin.de/German/Vektor/ZIBdoc/Anwendungssoftware/Chemie/AbIn itio/ I myself have been using this program quite a bit lately an got the impression that it is one of the best on the market, specially if you are concerned with the calculation of highly correlated wavefunctions via MCSCF, CASSCF, MRCI, etc. Methods. The articles cited in the MOLPRO94 manual are often very tutorial. I can also strongly recommend the following: o Lecture Notes in Quantum Chemistry, (European Summer School in Quantum Chemistry) B. O. Roos (Ed.) Springer Verlag Berlin, 1992 o Lecture Notes in Quantum Chemistry, (European Summer School in Quantum Chemistry) B. O. Roos (Ed.) Springer Verlag Berlin, 1994 Best Wishes Stefan =-=-=-=-this message is transmitted on 100% recycled electrons=-=-=-=-= | | | | sschulz@chemie.fu-berlin.de | Stefan Schulz | | Tel. ++49/30/838 5384 | FU Berlin - Theoretical Chemistry | | ++49/30/838 2351 | Takustrasse 3 | | FAX. ++49/30/838 4792 | D-14195 Berlin | =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= ===== response 2 I would recommend that you look in the volume 69 of the Advances of Chemical Physics. In that volume there are the three articles of R. Shepard, H.J. Werner and B.O. Roos, which may give a good introduction. More on the didactical side there was recently the publication of the sommer school at the Lund university in 2 Lecture Notes in Chemistry (B.O. Roos (ed.), Springer, Berlin), which may also be interesting for you. with best regards, H.U. Suter ===== response 3 There's a fairly recent review paper by Bartlett on correlated methods but I don't have the reference right off hand. A good place to start for CAS is Pulay and Hamilton, J. Chem. Phys. _88_, 4926 (1988) For MRCI, get the Columbus suite and check out the references there. You may want to see what Gaussian 94 has to say about CASPT2. Dave Heisterberg ===== response 4 You might want to contact Prof. W.A.Goddard at Cal. Tech. When I worked for him in graduate school we used to teach a course on how to use GVB methods. The course emphasized a qualitative approach to analyzing bonding with valence bond methods. There was also a lab for the course. The "lab" focused on using the Cal Tech programs which included GVB calculations (which are very simple multiple configuration calculations). The course notes may have evolved over the last decade to include multiple reference calculations. Prof. Goddard wrote a series of lecture notes which are very readable and useful. I wrote the first version of a series a tutorials on how to used the GVB programs back in the early '80's. You should be able to purchase (or borrow) the course notes >from Cal. Tech. The course and the notes were entitled "The Nature of the Chemical Bond". Although this is not a direct hit on what you asked for in your note. I believe that the concepts presented in the lecture notes provide an approach to selecting "active spaces" for CAS or other MRCI calculations in a chemically reasonable way. John J. Low UOP Research Center Des Plaines, IL ===== response 5 I assume by CASSCF that you mean MCSCF. In any case, I published a couple of papers last year in a NATO workshop that you might find useful. They are in "Relativistic and Electron Correlation Effects in Molecules and Solids", edited by G. L. Malli, Plenum Press, New York, 1994 (NATO ASI Series B: Physics Vol. 318). The first is "A Discussion of Some Aspects of the MCSCF Method" on page 161, and the other is "An Introduction to GUGA in the COLUMBUS Program System" on page 447. There are other chapters that you might also find interesting. Good Luck, -Ron shepard@tcg.anl.gov ======================================================================== >From the desk of: Eric Patterson voice: (608) 262-0599 Department of Chemistry FAX: (608) 265-4534 University of Wisconsin - Madison email: patterson@chem.wisc.edu 1101 University Ave. Madison, WI 53706 ======================================================================== From raman@bioc01.uthscsa.edu Fri Nov 10 16:33:00 1995 Received: from ELZIP.UTHSCSA.EDU for raman@bioc01.uthscsa.edu by www.ccl.net (8.6.10/950822.1) id QAA24683; Fri, 10 Nov 1995 16:30:44 -0500 Received: from bioc01.uthscsa.edu by uthscsa.edu (PMDF V4.3-13 #8477) id <01HXHEH0LTWG001ZYD@uthscsa.edu>; Fri, 10 Nov 1995 15:30:24 -0500 (CDT) Received: by bioc01.uthscsa.edu (4.1/SMI-4.1) id AA04911; Fri, 10 Nov 95 15:30:16 CST Date: Fri, 10 Nov 1995 15:30:15 -0600 (CST) From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Subject: Re: C++ macromolecular query database - book To: chemistry@www.ccl.net Message-id: <9511102130.AA04911@bioc01.uthscsa.edu> X-Envelope-to: chemistry@www.ccl.net X-Mailer: ELM [version 2.4 PL3] Content-type: text Content-transfer-encoding: 7BIT Content-length: 2370 Joe: > Does anyone have an ISBN number for the following? > Oxford University Press says that they don't have it... > Chang, W. et. al. (1994), "Design and Application of > PDBLib, a C++ Macromolecular Class Library", Oxford > University Press. Is it possible that you have a journal article confused with the title of a book? I am not aware of a book with this title, but, would recommend the following articles: Chang W; Shindyalov IN; Pu C; Bourne PE. Design and application of PDBlib, a C++ macromolecular class library. Computer Applications in the Biosciences, 1994 Dec, 10(6):575-86. Shindyalov IN; Chang W; Pu C; Bourne PE. Macromolecular query language (MMQL): prototype data model and implementation. Also, this library, which was formerly available from Columbia U., has since moved to UCSD. Contact is Phil Bourne at UCSD. Hope this helps Cheers -raman -- _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ _/ _/ C.S.RAMAN _/ _/ Department of Biochemistry _/ _/ University of Texas Health Science Center _/ _/ 7703 Floyd Curl Drive _/ _/ San Antonio, TX 78284-7760 _/ _/ USA _/ _/ _/ _/ Tel: (210) 567-6623 _/ _/ Fax: (210) 567-6595 _/ _/ E-mail: raman@bioc01.uthscsa.edu _/ _/ _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ _/ _/ How can it be that mathematics, a product of human thought _/ _/ independent of experience, is so admirably adapted to the _/ _/ objects of reality? -Albert Einstein _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ From SHAUN@jason.uthct.edu Fri Nov 10 18:33:01 1995 Received: from jason.uthct.edu for SHAUN@jason.uthct.edu by www.ccl.net (8.6.10/950822.1) id SAA26012; Fri, 10 Nov 1995 18:22:22 -0500 Date: Fri, 10 Nov 1995 17:22:40 -0600 (CST) From: "Shaun D. Black" To: chemistry@www.ccl.net Message-Id: <951110172240.2196@jason.uthct.edu> Subject: Extinction Coefficient for p-Nitroanisole Dear Colleagues, Is anyone aware of an empirical or computed extinction coefficient for p-nitroanisole at 403nm, in aqueous medium (preferably a phosphate buffer). The compound is only sparingly soluble in water, but it is soluble enough to achieve about 20 OD-403nm when saturated. I've looked everywhere without success, and I hope someone can help. Thanks, in advance. -Shaun =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= = Shaun D. Black, PhD | Internet address: shaun@jason.uthct.edu = = Dept. of Biochemistry | University of Texas Health Center, at Tyler = =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From schrecke@zinc.chem.ucalgary.ca Fri Nov 10 19:18:02 1995 Received: from zinc.chem.ucalgary.ca for schrecke@zinc.chem.ucalgary.ca by www.ccl.net (8.6.10/950822.1) id TAA26454; Fri, 10 Nov 1995 19:08:54 -0500 From: Received: by zinc.chem.ucalgary.ca (AIX 3.2/UCB 5.64/4.03) id AA33639; Fri, 10 Nov 1995 17:03:43 -0700 Message-Id: <9511110003.AA33639@zinc.chem.ucalgary.ca> Subject: NMR shift calculation (G94)? To: chemistry@www.ccl.net Date: Fri, 10 Nov 1995 17:03:42 -0700 (MST) Reply-To: schrecke@zinc.chem.ucalgary.ca (Georg Schreckenbach) X-Mailer: ELM [version 2.4 PL23] Content-Type: text Content-Length: 1416 Hi everybody, this is a question to the GAUSSIAN user's community. I understand that G94 can calculate NMR chemical shifts with the GIAO scheme. Now I would like to know whether the shift calculation is possible only on some levels of theory, and if so, on which ones. E.g., I don't think that -- say -- Coupled Cluster methods and shift calculations are compatible yet in G94. In particular, I'd like to know wether G94/DFT and shift calculations go together or not. Any references to papers using G94 for shift calculations would be of interest, too. I am not a GAUSSIAN user, therefore I thought I ask the net; I do so out of pure curiosity. For my part, I am working on the development of a DFT-GIAO method for the chemical shift (shielding, to be more precisely). It is therefore interesting to know what other people out there are doing. Thank you and have a nice weekend! Yours, Georg P.S. Please reply to me; I shall summarize to the net as usual. ============================================================================== Georg Schreckenbach Tel: (Canada)-403-220 8204 Department of Chemistry FAX: (Canada)-403-289 9488 University of Calgary Email: schrecke@zinc.chem.ucalgary.ca 2500 University Drive N.W., Calgary, Alberta, Canada, T2N 1N4 ============================================================================== From ui22204@sunmail.lrz-muenchen.de Fri Nov 10 19:33:02 1995 Received: from cd1.lrz-muenchen.de for ui22204@sunmail.lrz-muenchen.de by www.ccl.net (8.6.10/950822.1) id TAA26706; Fri, 10 Nov 1995 19:32:01 -0500 Received: from sun2.lrz-muenchen.de by cd1.lrz-muenchen.de; Sat, 11 Nov 95 01:31:16 +0100 Received: by sun2.lrz-muenchen.de (4.1/SMI-4.1) id AA05483; Sat, 11 Nov 95 01:31:15 +0100 Date: Sat, 11 Nov 1995 01:31:15 +0100 (MET) From: Eugene Leitl X-Sender: ui22204@sun2 To: /G=Matthew/S=Harbowy/OU=LIPTONUS-EC02/O=TMUS.TJL/@LANGATE.gb.sprint.com Cc: chemistry@www.ccl.net Subject: Re: CCL:Global minimum not-so-philosophical problem... In-Reply-To: <"Wed Nov 8 15:06:37 199500*/G=Matthew/S=Harbowy/OU=LIPTONUS-EC02/O=TMUS.TJL/PRMD=LANGATE/ADMD=TELEMAIL/C=GB/"@MHS> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Wed, 8 Nov 1995 /G=Matthew/S=Harbowy/OU=LIPTONUS-EC02/O=TMUS.TJL/@LANGATE.gb.sprint.com wrote: > It is not always desired to reach the global minimum. One needs to > understand what geometries are realistic and applicable to > experimental problems. It is not necessarily the case that a protein > will be formed in its global minimum: it my have been formed into a > specific conformation and the barrier to transition is too high to > permit movement into the minimum. Also, the arrangement of atoms may > be arranged into a lower energy state, but obviously one does not want > to break chemical bonds during minimization. Or, you may be interested > in the properties of cis-butane or boat-cyclohexane, whose > conformations we know and can reach. I think Matthew is right. I understand it is the current dogma that the protein native structure is an attractor, and resides at global energetic minima. However, there seems to be little evidence to that claim. The state or phase space of energetically attainable conformations is much too big to be sampled in its entirety. During its evolution the system is myopic inasmuch as it perceives purely local portion of the Hamiltonian. Hence it remains entirely under kinetic, not thermodynamic control. Since the number of denaturated conformations is a great many whereas the target conformation is but one and an attractor at that, we have obviously an converging statespace evolution. The energy gradient is surely very steep at initial stages. However, the final stages are purported to have a rugged energy landscape and very little energetical difference between neighbouring minima. If true, and provided, the final plateau is big enough to evade the subspace total search by means of what is then essentially an unbiased random walk, the question whether the target structure is a local or global minimum appears pointless. It can be one. Yet only facultatively so. Provided, above views are not erroneous, they might provide a new angle of attack upon the protein folding problem: namely by explicit traversal of the statespace (ESTM). Instead of using energy minimization as in the conservative molecular dynamics approach, an essentially CA-like encoding of a particle/potential well system appears viable, with the transition rule being the hamiltonian. I am convinced that by means of scaled integers, lookup tables and clever algorithmics a physically correct simulation up to microsecond range can be done upon a standard workstation at tolerable run time. Another potentially fruitful thought might be a GP calibration of endgame potentials using low-amplitude randomly distorted PDB structures. Have I made some erroneous assumptions? Inasmuch? Has anyone in here been thinking along the same lines? Is there even, perchance, some references available on ESTM protein folding? Has anybody references to phase space approach to the PFP? Thanks, -- Eugene > It would seem, philosophically, that the search for global minima of > massive proteins does not have a demonstrated value-added application > as yet. > > matt > [...]