From toukie@zui.unizh.ch Mon Jan 8 02:31:39 1996 Received: from rzusuntk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.6.10/950822.1) id CAA09451; Mon, 8 Jan 1996 02:30:55 -0500 Received: by rzusuntk.unizh.ch (4.1/SMI-4.1.9) id AA13341; Mon, 8 Jan 96 08:30:53 +0100 X-Nupop-Charset: Swiss Date: Mon, 8 Jan 1996 09:31:32 +0100 (MET) From: "Hr Dr. S. Shapiro" Sender: toukie@zui.unizh.ch Reply-To: toukie@zui.unizh.ch Message-Id: <34293.toukie@zui.unizh.ch> To: chemistry@www.ccl.net Subject: ? re STERIMOL notation, pt. 2 The following question was posted on CCL, I believe, before Xmas. As of this writing the response has been underwhelming. I am therefore taking this opportunity to repeat it. Any authoritative answers by persons knowl- edgeable about STERIMOL would be sincerely appreciated. Dear Colleagues; For those of you who are familiar with the STERIMOL molecular steric parameter programme: is HC2(H)RDC2(H)RC(H,H)RC6(X1)RDC6(OH)RDC6(H)RDC6(DC6(H)RDC6(H)RDX1)H* a proper STERIMOL linear input structure for o-allylphenol? If it is indeed correct, please confirm; if it is not, where have I erred? Thanks in advance to all responders. Sincerely, (Dr.) S. Shapiro ZH, CH toukie@zui.unizh.ch From chatt@tniri.go.jp Mon Jan 8 03:16:41 1996 Received: from ripspost.aist.go.jp for chatt@tniri.go.jp by www.ccl.net (8.6.10/950822.1) id DAA09720; Mon, 8 Jan 1996 03:13:43 -0500 Received: from tnhost.tniri.go.jp by ripspost.aist.go.jp (8.6.9+2.4W/TISN-1.3/R2-AIST) id RAA08333; Mon, 8 Jan 1996 17:13:37 +0900 Received: by tnhost.tniri.go.jp (4.1/6.4J.6-tniri.MASTER) id AA24786; Mon, 8 Jan 96 17:12:26 JST Date: Mon, 8 Jan 96 17:12:26 JST From: chatt@tniri.go.jp (Abhijit Chatterjee) Message-Id: <9601080812.AA24786@tnhost.tniri.go.jp> To: chemistry@www.ccl.net Subject: PORPHYRIN Dear Collegues, C I am looking for Mg-porphyrin crystal structure can anybody help me in this regard? Please , With regards A. Chatterjee email : chatt@tniri.go.jp From toukie@zui.unizh.ch Mon Jan 8 07:16:44 1996 Received: from rzusuntk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.6.10/950822.1) id HAA10987; Mon, 8 Jan 1996 07:02:24 -0500 Received: by rzusuntk.unizh.ch (4.1/SMI-4.1.9) id AA24061; Mon, 8 Jan 96 13:02:14 +0100 X-Nupop-Charset: Swiss Date: Mon, 8 Jan 1996 14:02:53 +0100 (MET) From: "Hr Dr. S. Shapiro" Sender: toukie@zui.unizh.ch Reply-To: toukie@zui.unizh.ch Message-Id: <50573.toukie@zui.unizh.ch> To: chemistry@www.ccl.net Subject: ? re partial atomic charges Dear Colleagues; For some calculations that I wish to perform, I need to have partial atomic charges; these I can generate without problems using MOPAC. However, some of the molecules in which I am interested have a lone electron pair on an unionised phenolic group, and the software which I am using requires that I enter a partial atomic charge for this lone pair. Since my MOPAC (AM1) calculations only generated partial atomic charges for the hydrogen and heavy (carbon, oxygen) atoms, is there a single "standard" value for the partial atomic charge on this lone pair that I should use, or will the par- tial atomic charge on the lone pair vary substantially with the pattern of substitution around the phenol ring? Or should it simply be set equal to zero? I thank all responders in advance for kindly sharing their information and thoughts on this matter with me. Respectfully, (Dr.) S. Shapiro Inst. f. orale Mikrobiol. u. allg. Immunol. Zent. f. Zahn-, Mund- u. Kieferheilkd. der Univ. ZH Plattenstr. 11 Postfach CH-8028 ZH 7 Internet: toukie@zui.unizh.ch FAX-nr: ( ... + 1) 261'56'83 From peon@medchem.dfh.dk Mon Jan 8 08:31:45 1996 Received: from danpost.uni-c.dk for peon@medchem.dfh.dk by www.ccl.net (8.6.10/950822.1) id IAA11446; Mon, 8 Jan 1996 08:28:58 -0500 Received: from medchem.dfh.dk (medchem.dfh.dk [130.225.177.15]) by danpost.uni-c.dk (8.6.4/8.6) with ESMTP id OAA23589 for <@danpost.uni-c.dk:chemistry@www.ccl.net>; Mon, 8 Jan 1996 14:28:57 +0100 Received: from [130.225.177.59] by medchem.dfh.dk via SMTP (940816.SGI.8.6.9/940406.SGI) for id PAA08493; Mon, 8 Jan 1996 15:13:04 +0100 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Mon, 8 Jan 1996 14:28:59 +0100 To: chemistry@www.ccl.net From: peon@medchem.dfh.dk (Per-Ola Norrby) Subject: Re: CCL:M:? re partial atomic charges Dr. Shapiro asked: > For some calculations that I wish to perform, I need to have partial >atomic charges; these I can generate without problems using MOPAC. However, >some of the molecules in which I am interested have a lone electron pair >on an unionised phenolic group, and the software which I am using requires >that I enter a partial atomic charge for this lone pair. Since my MOPAC >(AM1) calculations only generated partial atomic charges for the hydrogen >and heavy (carbon, oxygen) atoms, is there a single "standard" value for the >partial atomic charge on this lone pair that I should use, or will the par- >tial atomic charge on the lone pair vary substantially with the pattern of >substitution around the phenol ring? Or should it simply be set equal to >zero? It all hangs on what you are going to use the charges for. I assume it's a molecular mechanics/dynamics calculation; in that case, the charges to use are very much dependent on which force field you want to use. Not all force fields will work well with semi-empirically determined charges, and indeed, "charges from MOPAC" is a very fuzzy term. Are you talking about some kind of ESP charges, or are you using (shudder :-) raw Mulliken charges, or what? I only know about lone pairs in the MM2 paradigm. There, they are included mainly to reproduce an anisotropic van der Waals surface, and should not participate in electrostatics at all. Of course, MM2 does not use partial charges for it's electrostatics, so the paradigm might be different... Doesn't the program come with a recommendation for situations like this? If not, I'd start by guessing no partial charge on the lone pairs. Per-Ola Norrby ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ --- Bureaucracy is a challenge to be conquered with a righteous attitude, a tolerance for stupidity, and a bulldozer when necessary -- Peter's Law 15. * Per-Ola Norrby * The Royal Danish School of Pharmacy, Dept. of Med. Chem. * Universitetsparken 2, DK 2100 Copenhagen, Denmark * tel. +45-35376777-506, +45-35370850 fax +45-35372209 * Internet: peon@medchem.dfh.dk, peo@compchem.dfh.dk From shenkin@still3.chem.columbia.edu Mon Jan 8 11:01:47 1996 Received: from mailhub.cc.columbia.edu for shenkin@still3.chem.columbia.edu by www.ccl.net (8.6.10/950822.1) id KAA12586; Mon, 8 Jan 1996 10:50:18 -0500 Received: from still3.chem.columbia.edu (still3.chem.columbia.edu [128.59.112.36]) by mailhub.cc.columbia.edu (8.7.3/8.7.3) with SMTP id KAA05774; Mon, 8 Jan 1996 10:50:14 -0500 (EST) Received: by still3.chem.columbia.edu (931110.SGI/930416.SGI.AUTO) for @mailhub.cc.columbia.edu:peon@medchem.dfh.dk id AA05231; Mon, 8 Jan 96 10:50:14 -0500 Date: Mon, 8 Jan 96 10:50:14 -0500 From: shenkin@still3.chem.columbia.edu (Peter Shenkin) Message-Id: <9601081550.AA05231@still3.chem.columbia.edu> To: chemistry@www.ccl.net, peon@medchem.dfh.dk (Per-Ola Norrby) Subject: Re: CCL:M:? re partial atomic charges > Date: Mon, 8 Jan 1996 14:28:59 +0100 > From: peon@medchem.dfh.dk (Per-Ola Norrby) > Dr. Shapiro asked: > > For some calculations that I wish to perform, I need to have partial > >atomic charges; these I can generate without problems using MOPAC. However, > >some of the molecules in which I am interested have a lone electron pair... ... > ... the > charges to use are very much dependent on which force field you want to > use. Not all force fields will work well with semi-empirically determined > charges, and indeed, "charges from MOPAC" is a very fuzzy term. Are you > talking about some kind of ESP charges, or are you using (shudder :-) raw > Mulliken charges, or what? All true, but independent of the lone-pair problem. > I only know about lone pairs in the MM2 paradigm. ... By the way, Amber, until Amber94, used lone pairs on S. >...There [[ i.e., in MM2 ]], they are > included mainly to reproduce an anisotropic van der Waals surface, and > should not participate in electrostatics at all. Of course, MM2 does not > use partial charges for it's electrostatics, so the paradigm might be > different... MM2 electrostatics, by default, uses bond moments interacting as dipoles, and bonds to lone pairs do have moments in MM2. So the lone pairs do indeed contribute to electrostatics in MM2. What I'd do is take whatever bond moments your force-field uses for the X-Lp bonds and apply them to your semi-empirical charge distribution. This will distribute charge between each X and its Lp's, keeping the net charge on each X and its associated Lp's equal to the original semi-empirical charge on X. This assumes that your semi-empirical charge distribution makes sense in the first place. (If you've obtained torsional profiles using semi-empirical methods, you'd probably then want to go back and "trim" the torsional parameters so that the overall shape of the molecular mechanics torsional profile is matched by the force-field when all terms, including electrostatic and vdW, are used.) -P. * It's not the road, not the journey, it's the shock absorbers. (H.T.Deane)* *** Peter S. Shenkin, Box 768 Havemeyer Hall, Chemistry, Columbia Univ., *** *** NY, NY 10027; shenkin@columbia.edu; (212)854-5143; FAX: 678-9039 *** *** MacroModel home page: www.cc.columbia.edu/cu/chemistry/mmod/mmod.html*** From owner-chemistry@ccl.net Mon Jan 8 12:16:48 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id MAA13493; Mon, 8 Jan 1996 12:11:02 -0500 Received: from monge.brunel.ac.uk for Jeffrey.Gosper@brunel.ac.uk by bedrock.ccl.net (8.7.1/950822.1) id MAA20277; Mon, 8 Jan 1996 12:10:57 -0500 (EST) Received: from chem-pc-18.brunel.ac.uk by monge.brunel.ac.uk with SMTP (PP) id <01254-0@monge.brunel.ac.uk>; Mon, 8 Jan 1996 17:00:12 +0000 Date: Mon, 8 Jan 1996 16:59:57 GMT From: Jeffrey J Gosper Reply-To: Jeffrey.Gosper@brunel.ac.uk Subject: Re: CCL:xmol for MS-Windows? To: Tony Dyson cc: Computational Chemistry List Message-ID: Priority: Normal MIME-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Dear Anthony and other computational chemists. > I'm looking for a MS-Windows program that has the functionality of xmol - > specifically, the ability to animate multi-step cartesian trajectories. > Has anybody come across such a thing? It need not be free. > I have developed just such a program called Re_View. The major input type is a multistructure XYZ file but it will also accept certain MOPAC output files directly. OVERVIEW RE_VIEW is essentially a molecular viewer, animator, analyzer, and MOPAC reaction path converter. The program runs under Windows 3.x and Windows 95, and although the program definitely benefits from 8 Mbytes (or even more memory) the minimum recommended memory is 4 Mbytes. The major functions of RE_VIEW include the ability to: 1) Display and manipulate molecules in 3D; 2) Animate reaction pathways; 3) Align the steps/frames within an animation, along a vectors or onto a plane; 4) Animate normal modes of vibration; 5) Monitor geometries (lengths, angles and dihedrals); 6) Provide tabulated geometrical data (which can be readily incorporated into spreadsheets) and graphical displays of such geometrical data; and 7) Automatically produce high quality 'ray-traced' images and animation sequences. I am distributing the program directly at present the cost is 50 pounds (GB) for a single user licence and 500 pounds for a departmental licence. For this you get the program, help file, a number of data files and a manual. Feel free to contact me for further information. /\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\ Dr. Jeff Gosper Dept. of Chemistry BRUNEL University Uxbridge Middx UB8 3PH, UK voice: 01895 274000 x2187 facsim: 01895 256844 internet/email/work: Jeffrey.Gosper@brunel.ac.uk internet/WWW: http://http2.brunel.ac.uk:8080/~castjjg \/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/ From gnetua!qnet.odessa.ua!kruglyak@iron.tenet.odessa.ua Mon Jan 8 13:31:49 1996 Received: from relay2.UU.NET for gnetua!qnet.odessa.ua!kruglyak@iron.tenet.odessa.ua by www.ccl.net (8.6.10/950822.1) id NAA14227; Mon, 8 Jan 1996 13:22:39 -0500 Received: from nipple.TeNeT.Odessa.UA by relay2.UU.NET with ESMTP id QQzxqv08306; Mon, 8 Jan 1996 13:21:54 -0500 (EST) Received: from ignet.ignet.odessa.ua (root@tenet.ignet.odessa.ua [194.44.73.200]) by nipple.TeNeT.Odessa.UA (8.6.12/8.6.9) with ESMTP id UAA08216 for ; Mon, 8 Jan 1996 20:19:42 +0200 Received: (from uuqnet@localhost) by ignet.ignet.odessa.ua (8.6.9/8.6.9) id UAA27245 for chemistry@www.ccl.net; Mon, 8 Jan 1996 20:17:11 +0200 Received: by ignet.ignet.odessa.ua (uumail v1.5/ache) with UUCP id AA27238; Mon, 8 Jan 1996 20:17:07 +0200 Received: by qnet.odessa.ua (dMail for DOS v1.23, 15Jun94); Mon, 8 Jan 1996 20:19:15 +0200 To: chemistry@www.ccl.net Message-Id: Organization: QuantumNet Date: Mon, 8 Jan 1996 20:19:15 +0200 (EET) Reply-To: kruglyak@qnet.odessa.ua From: "Yuri Kruglyak" X-Mailer: dMail [Demos Mail for DOS v1.23] Subject: Request to inform all U.S. Members of CCL Lines: 280 RE: To Those U.S. Members of Computational Chemistry List Who are Concerned REQUEST: We are looking for U.S.Co-Investigator to submit together one of the following Projects-on-Line at Department for Molecular Electronics Odessa State University, UA kruglyak@qnet.odessa.ua to Cooperative Grants Program of U.S. Civilian Research and Development Foundation for the Independent States of the FSU/CRDF E-mail: information@crdf.org Fax: 703/526 9721 Tel: 703/526 9720 Details of the Projects are available on request. PUBLIC ASSOCIATION QuantumNet ------------------------------------------------------------------------------ QNet1: Photocatalysis on Dispersed Titanium Dioxide Surface: QuantumChemical Study Participants: Dr. Viktor V.Lobanov, Institute of Surface Chemistry, National Academy of Sciences, Kiev, UA Prof. Yurii A.Kruglyak, Department of Molecular Electronics Odessa State University ------------------------------------------------------------------------------ QNet2: Gas-Phase Spontaneous and E-Field Induced Rearrangements of Neutrals C6H5-R (R = CH2, NH, O, S) and Their Charged Ions: QuantumChemical Study Participants: Prof. Yurii A. 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RECENT INTERESTS: Research Project: ________________________________________________________ Teaching: _________________________________________________________________ Others: ___________________________________________________________________ ___________________________________________________________________ end of file From ripoll@TC.Cornell.EDU Mon Jan 8 15:01:51 1996 Received: from theory.tc.cornell.edu for ripoll@TC.Cornell.EDU by www.ccl.net (8.6.10/950822.1) id OAA15716; Mon, 8 Jan 1996 14:52:13 -0500 Received: (from ripoll@localhost) by theory.tc.cornell.edu (8.6.9/8.6.6) id OAA25666; Mon, 8 Jan 1996 14:52:03 -0500 Date: Mon, 8 Jan 1996 14:52:03 -0500 From: Daniel Ripoll Message-Id: <199601081952.OAA25666@theory.tc.cornell.edu> To: chemistry@www.ccl.net Subject: Symposium on Protein Folding Cc: ripoll@TC.Cornell.EDU International Symposium on THEORETICAL AND EXPERIMENTAL ASPECTS OF PROTEIN FOLDING June 17 - 21, 1996 Universidad Nacional de San Luis, San Luis - Argentina Organizing Committee Scheraga, H.A. (Cornell) Skolnick, J. (California) Vila, J. (San Luis) Ripoll, D. (Cornell) Ciuffo, G. (San Luis) Alessandrini, J. (La Plata) Benegas, J. (San Luis) San Luis, December 1995 Dear Colleague: This is our second announcement with information about the International Symposium on Theoretical and Experimental Aspects of Protein Folding to be held in San Luis, Argentina, during June 17-21, 1996. We have already received an important number of contributions indicating that the Symposium has raised great interest in the Biophysical Chemistry community. Posters sessions will be an important means for attendees to share ideas and techniques. We encourage you to submit a manuscript by the deadline of April 15, 1996. The registration fee has been fixed at U$ 350 for participants and accompanying persons. This includes lodging and meals at the international Hotel Potrero de Los Funes during the Symposium. To help us to obtain a better organization, please read carefully the enclosed information. We look forward to meet you in San Luis. Sincerely yours The Organizing Committee _______________________ For Information Contact: Prof. J. Vila Protein Folding - UNSL Instituto de Matematica Aplicada San Luis Ejercito de Los Andes 950 (5700) San Luis - Argentina or through Email to: protein@unsl.edu.ar More detailed information can also be found at our WWW page: http://linux0.unsl.edu.ar/sym/ GENERAL INFORMATION The goal of this Symposium is to provide an objective assessment of our current ability to predict protein three dimensional structure from amino acid sequence. The main subjects to be cover by the invited speakers are: Prediction of Secondary and Tertiary Structure - Empirical Potentials - Multiple Minima Problem - Molecular Dynamics and Molecular Mechanics Simulations - NMR and CD Applications - Structural Basis of Drug Design - Site Directed Mutagenesis. The Symposium is organized by the Universidad Nacional de San Luis on behalf of the International Centre for Genetic Engineering and Biotechnology (ICGEB) Trieste, Italy. Co-sponsoring institutions and agencies are: the Gobierno de La Provincia de San Luis (Argentina), Fundacion Antorchas (Argentina), Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Instituto de Matematica Aplicada San Luis (IMASL), International Union for Pure and Applied Chemistry (IUPAC). At his time is under consideration the co-sponsorships of the Third World Academy of Sciences (TWAS) and of the International Union for Pure and Applied Biophysics (IUPAB). "IUPAC sponsorship implies that entry visas will be granted to all bona fide chemists provided application is made not less than three months in advance. If a visa is not granted one month before the meeting, the IUPAC Secretariat should be notified without delay by the applicant". GUEST SPEAKERS Cohen, F.E., University of California at San Francisco -USA `Protein Structure Prediction: Prions and Parasitic Disease' Dill, K. A., University of California at San Francisco-USA `A Simple Model Perspective on Protein Folding' Erijman, L., Instituto de Investigaciones en Ingenieria Genetica y Biologia Molecular CONICET-ARGENTINA (*) Ermacora, M., Instituto de Quimica y Fisico-Quimica Biologicas CONICET-ARGENTINA `Mapping the Structure of Protein Nonnative States Using Reactive Oxygen Species as a Probe' Fersht, A., University of Cambridge- ENGLAND (*) Go, N., Faculty of Science, Kyoto University- JAPAN `Harmonic and Anharmonic Aspects of Conformational Dynamics of Native Protein' Grigera, R., Instituto de Fisica de Liquidos y Sistemas Biologicos CONICET-ARGENTINA `Electrical Interactions in Proteins and the Folding Process' Kidera, A., Biomolecular Engineering Research Institute - JAPAN `Enhanced Conformational Sampling in Monte Carlo and Molecular Dynamics Simulations: Applications of Multicanonical (entropy sampling) algorithm' Liwo, A., University of Gdansk - POLAND `A Knowledge-Based United-Residue Force Field for Off-Lattice Calculations of Protein - Structure that Recognizes Native Folds' Maigret, B., University of Nancy - FRANCE `Computer Modeling of G Protein-Coupled Receptors: Promises and Drawbacks' Montelione, G., Rutgers University - USA `Dynamics in Protein-Protein Complexes' Sander, C., European Molecular Biology Laboratory - GERMANY `From Genome Sequence to Protein Function' Scheraga, H.A., Cornell University - USA `Approaches to the Multiple-Minima Problem in Global Optimization' Skolnick, J., Scripps Research Institute - USA `Design Principles of Globular Proteins' Sussman, J.L., Weizmann Institute of Science - ISRAEL and Protein Data Bank, Brookhaven National Laboratory - USA `AChE in 3D: New Mysteries Revealed from the Crystal Structure' Vasquez, M., Protein Design Laboratory - USA `Monte Carlo Methods for Peptides and Protein Modeling' Warshel, A., University of Southern California - USA `On the Relationship Between Folding Energy and Enzyme Catalysis' Wodak, S., Universite Libre de Bruxelles - BELGIUM `The Role of Local Interactions in Protein Structure Prediction and Protein Folding' Wuthrich, K., Swiss Federal Institute of Technology, Zurich - SWITZERLAND `NMR studies of the chaperone DnaJ(2-108): Implications for the action of the Hsp70 chaperone machine' REGISTRATION FORM (You can submit your application via Email to: protein@unsl.edu.ar) Deadline for applications: March 15, 1996. International Symposium on Theoretical and Experimental Aspects of Protein Folding June 17 - 21, 1996 Universidad Nacional de San Luis, Argentina Last Name First Name Agency/Institution Street Address City State Zip/Postal Code Country Telephone Fax E-mail Address A limited number of fellowships will be available for young participants from Latin American countries to cover lodging and meals at the International Hotel Potrero de Los Funes during the Symposium. Request of Fellowship : Yes / No . If affirmative, please submit also a detailed Curriculum Vitae (in English). From dgregory@biosym.com Mon Jan 8 18:16:53 1996 Received: from nic.cerf.net for dgregory@biosym.com by www.ccl.net (8.6.10/950822.1) id SAA17309; Mon, 8 Jan 1996 18:03:39 -0500 Received: from biff.biosym.com (biff.biosym.com [146.202.0.225]) by nic.cerf.net (8.7.3/8.6.9) with SMTP id PAA06695 for ; Mon, 8 Jan 1996 15:03:24 -0800 (PST) Received: from [146.202.14.2] by biff.biosym.com (4.1/SMI-4.1) id AA24389; Mon, 8 Jan 96 14:59:31 PST Message-Id: <9601082259.AA24389@biff.biosym.com> Date: Mon, 8 Jan 1996 15:03:58 -0500 To: chemistry@www.ccl.net From: dgregory@biosym.com (Don Gregory) X-Sender: dgregory@146.202.0.225 Subject: Re: CCL:CHARMm and CHARMM differences? At 11:57 AM 1/4/96 +0100, Eldbjoerg S. Heimstad wrote: >I have been using the MSI-version CHARMm and Harvard version >CHARMM for simulations and see from the topology files (top_all22_prot.inp >and AMINO(H).RTF) that there are some differences in atomic >charges for the amino acids (I have not yet looked at the parameters). > >Is there any significant important differences in topology and parameters >between these two versions? > [From D.Gregory: Protein & Simulations Product Marketing Manager, Biosym/MSI] The most significant difference between these two "versions", is that they are, in fact, different force-fields. This brings up a whole, interesting discussion about what "tranferrablility" means in force-field technology. Often times, I hear of people asking for parameters for some molecule, or element, without specifying what force field they intend to use with these parameters. Big mistake. For example, take these two force fields, the Harvard/Karplus-CHARMM force-field supplied with CHARMM, and the B/MSI force-field, supplied with CHARMm. Are they similar? Yes. Are their parameters interchangable? Now there is a tougher question. My caution would be to say no, not so simply. The B/MSI-CHARMm used the Harvard/Karplus-CHARMM force field as a starting point, but then went on to add new parameters, and refine existing parameters quite independently. The reasons for this? Primarily because [then] MSI felt a strong desire by our customers to have a single force-field that would be generally applicable to a wide variety of molecules, especially mixed complexes of classic molecule types, such as protein-drug, protein-nucleic_acids, carbohydrates, etc. To be sure, others have developed related force fields that are much more specific to a particular class of molecules (note the SHAPES and CHEAT force fields for metals and sugars respectively). In developing a force field that could more confidently be used with these types of complexes, and perhaps be slightly less accurate with pure peptide systems, the overall character of the force field changed. This is at the heart of the internally "consistent force field" concept that was begun decades ago. In the latest version of the MSI-CHARMm force-field, some of the most significant changes have taken place in the radii of ions and metals, while there have also been numerous, perhaps less significant changes elsewhere. Whenever a new version of the B/MSI-CHARMm force field is distributed, we try to make a loud, bold statement to our existing users that they SHOULD continue to use the previous force-field to complete the projects they are currently working upon. One of the last things you ever want to do, is to change force fields in the middle of a project. It is up to companies such as ourselves, to ensure that classic problems and benchmarks are still valid with each new force field, so that customers can confidently use a new force-field when it is made available. > >I have used MSI-topology and parameters files with a parallel version >of (academic) CHARMM -could that cause any problems? > As far as we know, the only difficulty anyone might have, in using the MSI-CHARMm force-field within the CHARMM program, is that one might run out of array space when loading in the much larger MSI-CHARMm parameter set. If not, there should be virtually no difficulty. If anyone does find any problems, we hope they alert us through any of the standard channels: mail to myself: "dgregory@biosym.com" mail to the support hotline: "support@msi.com" or through the 1800 number, i.e. 1 800 756 4MSI (756-4675) Don Gregory From owner-chemistry@ccl.net Mon Jan 8 19:01:53 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id SAA17649; Mon, 8 Jan 1996 18:55:50 -0500 Received: from vmsuser.acsu.unsw.EDU.AU for P8946019@vmsuser.acsu.unsw.EDU.AU by bedrock.ccl.net (8.7.1/950822.1) id SAA26482; Mon, 8 Jan 1996 18:55:46 -0500 (EST) From: Received: from vmsuser.acsu.unsw.EDU.AU by vmsuser.acsu.unsw.EDU.AU (PMDF V4.3-13 #6323) id <01HZSYDS96HK8WXXOT@vmsuser.acsu.unsw.EDU.AU>; Tue, 09 Jan 1996 11:00:56 +1000 Date: Tue, 09 Jan 1996 11:00:56 +1000 Subject: Symmetry and 2e integrals To: chemistry@ccl.net Message-id: <01HZSYDS96HM8WXXOT@vmsuser.acsu.unsw.EDU.AU> X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Dear computational chemist How does one best use symmetry to reduce the number of two-electron integrals in a molecular calculation? If one decides to use group theory and finds the symmetry adapted basis in terms of the starting AO basis then how is it used to simplify things? Any help will be appreciated greatly. Yours sincerely Hugh