From craig@hobbes.gh.wits.ac.za Wed Mar 1 01:08:35 1995 Received: from hobbes.gh.wits.ac.za for craig@hobbes.gh.wits.ac.za by www.ccl.net (8.6.10/930601.1506) id BAA13502; Wed, 1 Mar 1995 01:04:57 -0500 Received: (from craig@localhost) by hobbes.gh.wits.ac.za (8.6.9/8.6.9) id IAA01078; Wed, 1 Mar 1995 08:02:17 +0200 Date: Wed, 1 Mar 1995 08:02:16 +0200 From: Craig Taverner Subject: code for atomic hartree-fock To: computational chemistry Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I asked a question about this a while back, but didn't word myself too well. I'm interested in C code for the calculation of atomic hartree-fock self-consistent-field wave functions. I need code that I can modify, and/or incorporate into a bigger program. Any ideas? Thanks, Craig "If God had meant us to be naked, we would have been born that way." Craig Taverner Structural Chemistry, University of the Witwatersrand, South Africa From craig@hobbes.gh.wits.ac.za Wed Mar 1 01:16:44 1995 Received: from hobbes.gh.wits.ac.za for craig@hobbes.gh.wits.ac.za by www.ccl.net (8.6.10/930601.1506) id BAA13483; Wed, 1 Mar 1995 01:02:23 -0500 Received: (from craig@localhost) by hobbes.gh.wits.ac.za (8.6.9/8.6.9) id HAA01070; Wed, 1 Mar 1995 07:59:22 +0200 Date: Wed, 1 Mar 1995 07:59:21 +0200 From: Craig Taverner Subject: code for xray structure factors To: computational chemistry Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I'm interested in calculating atomic structure factors for use in X-ray crystallographic structure refinements. Does anyone know of any C code out there to do it? I expect the input to the code to be atomic wavefunctions or electron densities. I'm particularly interested in C code that I can modify myself. Thanks, Craig "If God had meant us to be naked, we would have been born that way." Craig Taverner Structural Chemistry, University of the Witwatersrand, South Africa From jeremy@med.su.oz.au Wed Mar 1 02:08:36 1995 Received: from blackburn.med.su.oz.au for jeremy@med.su.oz.au by www.ccl.net (8.6.10/930601.1506) id BAA13861; Wed, 1 Mar 1995 01:48:53 -0500 Received: (jeremy@localhost) by blackburn.med.su.oz.au (8.6.8.1/8.6.4) id RAA13613 for chemistry@ccl.net Wed, 1 Mar 1995 17:48:50 +1100 From: Jeremy R Greenwood Message-Id: <199503010648.RAA13613@blackburn.med.su.oz.au> Subject: 2nd summary: Modelling protein under point mutation To: chemistry@ccl.net Date: Wed, 1 Mar 1995 17:48:50 +1100 (EST) X-Mailer: ELM [version 2.4 PL23] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 3740 Following my previous summary, I have received further advice. The original question concerned techniques for modelling structural and functional changes in a protein which has undergone any one of a number of single point mutations, and for which the X-ray crystal structure is known. Thanks again for all your help, Jeremy --------------------------------------------------------------------------- From arne@hodgkin.mbi.ucla.edu Sat Feb 25 10:07:56 1995 I think you missed a few points in the summaries you got. (or I missed to read about them) However there are a few references that I think you should read. If you are interested in structure & stability 1. The work by Christopher Lee (and subbiah and Levitt) the latest reference is JMB(1994) 236, 918-939 Look also at their Nature paper and the JMB paper by Mark & van Gunsteren) 2. Koehl and DeLarue Proteins(1994) 20:264-278 and an article in latest issue of Nature structural Biology (1995:1 ?) I would (almost) bet my house (if I had one) that these methods are way much better to predict protein stability than perturbation with md methods. Structure only 3. Filippis, Sander, Vriend Protein Engineering (1994)7,10(1203-1208) I bet this method will beat any molecular mechanics method. good luck, sorry I waited with the reply arne --------------------------------------------------------------------------- From Gert.Vriend@EMBL-Heidelberg.DE Fri Feb 24 23:47:07 1995 Saw you needed mutation structure prediction. See protein engineering 1994 7 1203-1208 The software used is available as shareware. Gert. --------------------------------------------------------------------------- From wyl@pchindigo2.IPC.PKU.EDU.CN Thu Feb 23 22:48:51 1995 Hi, Heremy, Many people have given you very usefull suggestions in responsing your questions about how to predict a mutant structure and the property changed after mutation. They provided some software such as Whatif, Quanta/Charmm, Sybyl, and Insight II. However, if you want to gain some general concept about the mutant structure prediction methods, I would like to suggest you to read a paper by Prof. Chris Sander, which was published in Protein Engineering, Vol.7, No. 10, pp.1203~1208. In addition, simple point mutation, especially the mutation such as from a charged residue to a uncharged residue will bring some change to the protein, and many people are working on such property change prediction, in fact, some methods have been developed to predict the quality change, even though it seems a little difficult comparing to the development of structure prediction methods, typically, some methods on electrostatic calculation have been developed, such as those by Prof. Barry Honig in Columbia University, and Dr. Donald in Scrippt Institute, also the software DELPHI to study the electrostatic property has been included in Insight II (Biosym Inc. software). I am sure once more experiments on mutation have been carried out, people will get more rules, all these will promote the methods for property prediction. Yanli Wang, Peking University, Beijing e-mail: wyl@pchindigo2.ipc.pku.edu.cn ---------------------------------------------------------------------------- From parry@cthulu.med.jhu.edu Thu Feb 23 17:41:58 1995 Hello Jeremy, You do have some good answers already to get you on your way. There are several ways to approach this problem, and the good thing is that you do have a crystal structure. I have begun working on a similar project. This will be brief: For a very very general review see Chemical Reviews (1994) 94,2183-2239. See especially p2218. Sincerely, Christian. ----------------------------------------------------------------------------- From jmolmod@organik.uni-erlangen.de Wed Mar 1 05:08:37 1995 Received: from faui45.informatik.uni-erlangen.de for jmolmod@organik.uni-erlangen.de by www.ccl.net (8.6.10/930601.1506) id EAA15264; Wed, 1 Mar 1995 04:44:07 -0500 Received: from derioc1.organik.uni-erlangen.de by uni-erlangen.de with SMTP; id AA01389 (5.65c-6/7.3w-FAU); Wed, 1 Mar 1995 10:43:55 +0100 Received: by organik.uni-erlangen.de; id AA14880 (5.64/7.3n-FAU); Wed, 1 Mar 95 10:43:54 +0100 From: Journal of Molecular Modeling Message-Id: <9503010943.AA14880@derioc1.organik.uni-erlangen.de> Subject: J.Mol.Mod.: Finally we made it To: Chemistry@ccl.net Date: Wed, 1 Mar 95 10:43:53 MET X-Mailer: ELM [version 2.3 PL11] *************************************** * * * The Journal of Molecular Modeling * * * *************************************** Well here we are - the first electronic chemistry journal. What started as an idea at an ACS meeting has developed into an experiment in which we are very much learning as we go along. The results of this learning process are now available on the server and we are officially (and only 6 weeks late) "up and running". I have tried to emphasize from the beginning that the purpose of the Journal of Molecular Modeling is not to be an electronic journal, but rather to be a good scientific journal that happens to be published electronically. This should be a motivation to contributors to give their best, taking advantage of the possibility to publish high quality presentation material. The Journal of Molecular Modeling is a non-commercial journal operated by the Computer-Chemie-Centrum at the Institut fuer Organische Chemie of the Friedrich-Alexander-Universitaet Erlangen-Nuernberg in cooperation with Megalon S.A. and the Springer Verlag (Heidelberg). In the unlikely event that we ever make a profit, it will be used to finance research, graduate student travel to conferences etc. Nevertheless, we realise that we need professional help to produce a quality journal and are grateful to Megalon for their expertise in providing the InterNet access to the Journal itself and to Springer, who patiently taught us what a real Journal looks like. The goal is to convert the Journal of Molecular Modeling, which has now in the beginning a conservative "book-like" format, into something approaching an interactive journal in which the reader will have the possibility to rotate graphics, extract diagrams etc. The technology for this sort of application will be developed over the years and we will try to keep pace with its progress. However, we will do our very best to incorporate anything that our authors would like to have included, beginning with videos as a logical first step. Finally, a word of thanke to Henryette Roth, without whom none of this would have happened. She has worked above and beyond the call of duty to get us this far. Tim Clark, Erlangen, February 25th 1995 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ^ Journal of Molecular Modeling ^ Tel: [+49](0)9131 / 85-2948 ^ ^ Computer-Chemie-Centrum ^ [+49](0)9131 / 85-6581 ^ ^ Universitaet Erlangen-Nuernberg ^ ^ ^ Naegelsbachstrasse 25 ^ Fax: [+49](0)9131 / 85-6565 ^ ^ D-91052 Erlangen ^ ^ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ^ email: jmolmod@organik.uni-erlangen.de ^ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ From jaouad@ugr.es Wed Mar 1 06:08:38 1995 Received: from ocelote.cica.es for jaouad@ugr.es by www.ccl.net (8.6.10/930601.1506) id FAA15433; Wed, 1 Mar 1995 05:17:15 -0500 Received: (from ean@localhost) by ocelote.cica.es (8.6.9/8.6.9) id LAA08939 for CHEMISTRY@ccl.net; Wed, 1 Mar 1995 11:09:49 +0100 X400-Received: by mta rica in /PRMD=/ADMD=/C=/; Relayed; Wed, 1 Mar 1995 11:09:38 UTC+0100 X400-Received: by /PRMD=iris/ADMD=mensatex/C=es/; Relayed; Wed, 1 Mar 1995 11:09:38 UTC+0100 X400-Received: by /PRMD=es/ADMD=/C=/; Relayed; Wed, 1 Mar 1995 11:10:08 UTC+0200 Date: Wed, 1 Mar 1995 11:10:08 UTC+0200 X400-Originator: jaouad@ugr.es X400-Recipients: non-disclosure:; X400-Content-Type: P2-1984 (2) X400-MTS-Identifier: [/PRMD=es/ADMD=/C=/;950301111008] Content-Identifier: 42 Conversion: Prohibited From: Jaouad el bahraoui To: CHEMISTRY@ccl.net (confirm) Message-ID: <42*/S=jaouad/O=ugr/PRMD=iris/ADMD=mensatex/C=es/@MHS> Subject: SUMMARY DGAUS and G92/DFT Return-Receipt-To: Jaouad el bahraoui MIME-Version: 1.0 (Generated by Ean X.400 to MIME gateway) Dear CCLers First, thanks to those who responded to my query. the original message as well as the responses are at the and of this mail. ******************************************************************************** EL BAHRAOUI JAOUAD Ph.D.STUDENT Instituto de Biotecnologia Grupo de Modelizacion y Diseno Molecular Universidad de GRANADA,Facultad de Ciencias, GRANADA 18071,Spain TEL: 34-58-243186. FAX: 34-58-243186 EMAIL: jaouad@ugr.es ******************************************************************************** the original question and the answers: I'm doing some calculations with G92/DFT and I'want to performe it with DGAUS basis set, knowing that gaussian dont accept auxiliary basis set Do you know if it possible. thanks in advance. jaouad ******************************************************************************************************** From: Clifford LeMaster: CLEMAST@quartz.es I would like to hear the replies. I am also interested in DFT *************************************************************************************** From: steinke@ZIB-Berlin.DE I can't suggest this in generally since the DGauss basis set is specially developed for the "DFT-LDA method" and it makes no sense for me (at least theoretically) to use such a basis set in a HF-based density approach like the implementation in G92/DFT. I'll expect some curious results using such a "mixed" approach. The auxiliary basis set is used for the representation of the one-electron density in a set of analytically based functions for a slightly better integral computation. Best regards, Thomas ***************************************************************************************************************************************************** From: m10!aefrisch@uunet.uu.net Yes, it is possible; Gaussian does allow you to read in a basis set for the calculation. Look at the discussion of the Gen keyword in the G92/DFT manual to see the format that is required. **************************************************************************************************************************************** From: dobbskd@esvax.dnet.dupont.com Yes, it is possible. I have been doing it for well over 6 months now. G92/DFT does not need auxiliary basis sets. DGauss basis sets work fine, but do not expect DGauss energies/structures to be exactly the same as those of G92/DFT since they each implement the DFT code differently. ****************************************************************************************************************************************** From: "Oscar N. Ventura" Dear Jaouad, I can not help you with that topic because I don't have the necessary experience. However, I have performed DFT calculations using G92/DFT and conventional ab initio basis sets. My experience with some hydrogen-bonded complexes, organic radical cations and some organometallics is that you can obtain accurate results in such a manner. If you are interested I can send you some numbers. Best regards, O. *********************************************************************************************************************** From: Nathaniel Malcolm as far as i am aware Gaussian does allow the use of general basis sets with the keyword "gen" instead of a standard basis set (see the users manual) NOJ Malcolm *********************************************************************************************** From: I do not think G92 currently accepts auxillary functions for DFT calculations. However, there is the program DeFT of Alain St.-Amant at Ottawa that does. DGAUSS, DEMON, and DeFT all take auxillary functions....for good reason...St-Amant wrote DEMON and DeFT, and there are many similarities with DGAUSS. Regards, John ***************************************************************************************************** From: Dear Jaouad, The DGauss basis set can be used in G92. But you need to modify it into acceptable format to be read into G92. G92 doesn't use fitting for the charge density. (This is one of the reasons DGauss is so much faster). Therefore, the auxiliary basis set, which is used only for the density fitting, is not needed in G92 DFT calcultions. Please let us know if you have any further questions. Regards, Susan -------------------------------------------------------- Susan M. Gustafson, Ph.D. Phone: (612) 683-3662 Cray Research, Inc. e-mail: sgustaf@cray.com -------------------------------------------------------- ******************************************************************************************* From: Hola, Si es posible usar las bases de dgauss, yo hecho un par de calculos con G92/DFT usando las bases de dgauss, todo lo que tienes que hacer es ignorar las "auxiliary basis set". Ademas tienes que traducir el formato que usa dgauss con el que usa G92/DFT. Si tienes mas preguntas enviamelas directamente, yo trabajo con Gaussian en Cray. Tuve el placer de conocer tu Universidad hace mas de un anyo. Saludos. From chpajt@bath.ac.uk Wed Mar 1 07:08:39 1995 Received: from goggins.bath.ac.uk for chpajt@bath.ac.uk by www.ccl.net (8.6.10/930601.1506) id GAA16175; Wed, 1 Mar 1995 06:28:23 -0500 Received: from bath.ac.uk (actually mary.bath.ac.uk) by goggins.bath.ac.uk with SMTP (PP); Wed, 1 Mar 1995 11:26:41 +0100 Date: Wed, 1 Mar 1995 11:27:26 +0000 (GMT) From: A J Turner To: Chemistry@ccl.net Subject: Prof W.H. Gerwick - address Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi! Thank-you for your excellent help on the parametes for charmm, I shall be putting the results in my world wide webb page soon. In the mean time, can anyone help me by sending the E-mail adress to Professor W.H. Gerwick Colledge Of Pharmacy and Department of Biochemistry and Biophysics, Oregon State University. Cheers Alex +--------------------------------------------------+ |Alternate E-mail A.J.Turner@Bath.ac.uk | |www home @ http://www.bath.ac.uk/~chpajt/home.html| +--------------------------------------------------+ From yuan@nka1.med.uc.edu Wed Mar 1 11:08:53 1995 Received: from nka1.med.uc.edu for yuan@nka1.med.uc.edu by www.ccl.net (8.6.10/930601.1506) id KAA20059; Wed, 1 Mar 1995 10:43:07 -0500 Received: by nka1.med.uc.edu (920330.SGI/921111.SGI.AUTO) for chemistry@ccl.net id AA06086; Wed, 1 Mar 95 10:44:22 -0500 Date: Wed, 1 Mar 1995 10:44:14 -0500 (EST) From: Jie Yuan To: Computational Chemistry List Subject: for those seeking email address of someone Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII If that person is a faculty/student/postdoc/staff at an educational institution, I think you can find out his/her email address by calling the department where he/she works if you don't know his/her phone number. The phone numbers for the departments and many individuals can be found in many directories. For example, If it is an institution in the USA/Canada, Peterson's Guides for Graduate Studies is a good starting point, so is the ACS directory of graduate programs if it is a chemistry department. Would you please use those sources before considering the CCL? BTW, I think the publishers of those directories should seriously consider including email addresses in the books. How can we voice our concerns to them? Regards, Jie -- Dr. Jie Yuan - Pharmacology & Cell Biophysics - U. Cincinnati -- -- Phone: 513-558-2352 -- Fax: x-1169 -- Email: Jie.Yuan@UC.Edu -- -- P.O. Box 670575, 231 Bethesda Ave., Cincinnati, OH 45267-0575 -- From mmadrid@gardel.psc.edu Wed Mar 1 11:20:04 1995 Received: from gardel.psc.edu for mmadrid@gardel.psc.edu by www.ccl.net (8.6.10/930601.1506) id KAA19565; Wed, 1 Mar 1995 10:21:28 -0500 Received: by gardel.psc.edu (931110.SGI/930416.SGI.AUTO) for chemistry@ccl.net id AA29415; Wed, 1 Mar 95 10:22:24 -0500 From: "Marcela Madrid" Message-Id: <9503011022.ZM29413@gardel.psc.edu> Date: Wed, 1 Mar 1995 10:22:17 -0500 X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: chemistry@ccl.net Subject: CCL: NMR workshop offered at PSC Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 STRUCTURE DETERMINATION FROM NMR Pittsburgh Supercomputing Center June 25-28, 1995 Pittsburgh Supercomputing Center (PSC) is offering biomedical researchers a "Structure Determination From NMR" Workshop. The objective is to introduce participants to the different techniques for the elucidation of solution structures of biological macromolecules from nuclear magnetic resonance data. The workshop is free to academic participants. The worskhop will consist of lectures and extensive hands-on sessions. The programs AMBER, Mardigras and MidasPlus will be discussed. Hands-on sessions will be emphasized. Participants will be able to work on the examples provided or on their own experimental data. No prior supercomputing experience is necessary. Workshop leaders are: Dr. David Case, The Scripps Research Institute; and Drs Thomas James, Julie Newdoll and Uli Schmitz, University of California, San Francisco. This workshop is funded by a grant from the Biomedical Research Technology Program, National Center for Research Resources, National Institutes of Health. Travel, meals and hotel accommodations for researchers affilated with U.S. academic institutions are supported by this grant. Enrollment is limited to 20. An application form is included. Deadline for applications is: April 28, 1995. Additional information about this workshop can be found in http://pscinfo.psc.edu/biomed/workshops95.html * * * * * * * * * * PITTSBURGH SUPERCOMPUTING CENTER BIOMEDICAL INITIATIVE STRUCTURE DETERMINATION USING NMR June 25-28, 1995 APPLICATION Name:________________________________________________________________________ Affiliation:_________________________________________________________________ Address:_____________________________________________________________________ (Business) _____________________________________________________________________________ ____________________________________________________________________________ (Home) ____________________________________________________________________________ Telephone: ____________________ ______________________ (Business) (Home) *Social Security Number: _______-_____-_______ Citizenship: ____________ Electronic Mail Address:____________________________________________________ Status: ___Graduate ___Post-doctoral Fellow ___Faculty ___Other (specify) Please indicate specifically any special housing, transportation or dietary arrangements you will need: _______________________________________________ How did you learn about this workshop? _____________________________________ REQUIREMENTS: Applicants must submit a completed application form and a cover letter. The letter should describe, in one or two paragraphs, your current research and how participating in the workshop will enhance this research. Please include a brief statement describing your level of experience with computers. Faculty members, staff and post-docs should provide a curriculum vita. Graduate students must have a letter of recommendation from a faculty member. Please return all application materials by APRIL 28, 1995 to: Biomedical Workshop Applications Committee Pittsburgh Supercomputing Center 4400 Fifth Avenue, Suite 230C Pittsburgh, PA 15213 Direct inquiries to: Nancy Blankenstein, blankens@psc.edu or 412/268-4960. *Disclosure of Social Security Number is voluntary. PSC does not discriminate on the basis of race, color, religion, sex, age, creed, national or ethnic origin, or handicap. From mmadrid@gardel.psc.edu Wed Mar 1 11:20:54 1995 Received: from gardel.psc.edu for mmadrid@gardel.psc.edu by www.ccl.net (8.6.10/930601.1506) id KAA19576; Wed, 1 Mar 1995 10:22:25 -0500 Received: by gardel.psc.edu (931110.SGI/930416.SGI.AUTO) for chemistry@ccl.net id AA29554; Wed, 1 Mar 95 10:23:30 -0500 From: "Marcela Madrid" Message-Id: <9503011023.ZM29552@gardel.psc.edu> Date: Wed, 1 Mar 1995 10:23:22 -0500 X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: chemistry@ccl.net Subject: MM/MD of Biopolymers workshop Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 "METHODS OF MOLECULAR MECHANICS AND DYNAMICS OF BIOPOLYMERS" WORKSHOP Pittsburgh Supercomputing Center August 16-19, 1995 The Pittsburgh Supercomputing Center (PSC) is hosting a workshop on "Methods of Molecular Mechanics and Dynamics of Biopolymers," August 16-19, 1995. The workshop will familiarize biomedical researchers with computational methods and provide practice in applying supercomputing resources to problems of concern in molecular mechanics. Practical experience on our supercomputers will be gained in the application to: (1) the theory and practice of molecular mechanics and dynamics; (2) the development and refinement of molecular mechanics force fields; (3) the problem of conformation mapping and analysis of polypeptide structures, including the refinement of structure from measured NMR data; and (4) computation of interaction energies and free energies for protein-drug interactions and conformational thermodynamics. Workshop leaders are Dr. Charles L. Brooks III, The Scripps Research Institute and Dr. Alexander D. MacKerell Jr., University of Maryland at Baltimore. The worskhop will consist of lectures and extensive hands-on sessions. General aspects of molecular mechanics software will be discussed and a number of packages are available for use at the PSC. However, the programs CHARMM and QUANTA will be utilized most extensively in demonstrations. Hands-on sessions will be emphasized. Participants will be able to work on the examples provided or on their own experimental data. No prior supercomputing experience is necessary. This workshop is funded by a grant from the Biomedical Research Technology Program, National Center for Research Resources, National Institutes of Health. Travel, meals and hotel accommodations for researchers affilated with U.S. academic institutions are supported by this grant. Enrollment is limited to 20. An application form is included. Deadline for applications is: June 22, 1995. Please direct inquires or send the following application form to blankens@psc.edu. Additional information about this workshop can be found in http://pscinfo.psc.edu/biomed/workshops95.html PITTSBURGH SUPERCOMPUTING CENTER BIOMEDICAL INITIATIVE ************************************** August 16-19, 1995 APPLICATION Name:________________________________________________________________________ Affiliation:_________________________________________________________________ Address:_____________________________________________________________________ (Business) _____________________________________________________________________________ ____________________________________________________________________________ (Home) ____________________________________________________________________________ Telephone: ____________________ ______________________ (Business) (Home) *Social Security Number: _______-_____-_______ Citizenship: ____________ Electronic Mail Address:____________________________________________________ Status: ___Graduate ___Post-doctoral Fellow ___Faculty ___Other (specify) Please indicate specifically any special housing, transportation or dietary arrangements you will need: _______________________________________________ How did you learn about this workshop? _____________________________________ REQUIREMENTS: Applicants must submit a completed application form and a cover letter. The letter should describe, in one or two paragraphs, your current research and how participating in the workshop will enhance this research. Please include a brief statement describing your level of experience with computers. Faculty members, staff and post-docs should provide a curriculum vita. Graduate students must have a letter of recommendation from a faculty member. Please return all application materials by June 22, 1995 to: Biomedical Workshop Applications Committee Pittsburgh Supercomputing Center 4400 Fifth Avenue, Suite 230C Pittsburgh, PA 15213 Direct inquiries to: Nancy Blankenstein, blankens@psc.edu or 412/268-4960. *Disclosure of Social Security Number is voluntary. PSC does not discriminate on the basis of race, color, religion, sex, age, creed, national or ethnic origin, or handicap. From mmadrid@gardel.psc.edu Wed Mar 1 11:21:35 1995 Received: from gardel.psc.edu for mmadrid@gardel.psc.edu by www.ccl.net (8.6.10/930601.1506) id KAA19605; Wed, 1 Mar 1995 10:23:47 -0500 Received: by gardel.psc.edu (931110.SGI/930416.SGI.AUTO) for chemistry@ccl.net id AA29695; Wed, 1 Mar 95 10:24:44 -0500 From: "Marcela Madrid" Message-Id: <9503011024.ZM29693@gardel.psc.edu> Date: Wed, 1 Mar 1995 10:24:37 -0500 X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: chemistry@ccl.net Subject: CCL: Sequence Analysis workshop Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 NUCLEIC ACID AND PROTEIN SEQUENCE ANALYSIS WORKSHOP FOR BIOMEDICAL RESEARCHERS Pittsburgh, Pennsylvania June 4-9, 1995 Pittsburgh Supercomputing Center (PSC) is offering a five-day workshop on "Nucleic Acid and Protein Sequence Analysis," June 4-9, 1995. It is funded by a grant from the National Center for Human Genome Research of the National Institutes of Health. The workshop will familiarize biomedical researchers with computational methods and provide practice in applying supercomputing resources to problems of concern in macromolecular sequence analysis. Emphasis will be on alignment of and pattern extraction from multiple sequences. Participants will gain practical experience on PSC's Cray C-90 and T3D in (1) comparing and aligning sequences, (2) identifying informative patterns in a set of sequences; and (3) using extracted informative patterns to identify related sequences. Researchers will also learn several approaches to database searching and multiple sequence alignment, how to use profile analysis effectively, and how to identify patterns in their sequences. Participants are encouraged to bring sequence analysis problems from their current research. Extensive documentation will be given at the outset on the PSC computing environment as well as on the specific programs to be employed in the workshop. No prior supercomputing experience is required. Workshop leaders are Dr. Gary Churchill, Cornell University, Dr. Michael Gribskov, San Diego Supercomputing Center, and Dr. Hugh Nicholas, PSC. A limited number of grants to cover travel and hotel accommodations are available for U.S. academic participants. ALL PARTICIPANTS ARE REQUIRED TO PAY A $135 REGISTRATION FEE, IN ADVANCE, UPON ACCEPTANCE INTO THE WORKSHOP. The deadline for submitting applications is April 17, 1995. Enrollment is limited to 20 participants. Additional information about this workshop can be found in http://pscinfo.psc.edu/biomed/workshops95.html * * * * * PITTSBURGH SUPERCOMPUTING CENTER NUCLEIC ACID AND PROTEIN SEQUENCE ANALYSIS WORKSHOP FOR BIOMEDICAL RESEARCHERS June 4-9, 1995 APPLICATION Name: ________________________________________________________________ Affiliation: ________________________________________________________________ Address: ________________________________________________________________ (Business) ________________________________________________________________ ________________________________________________________________ (Home) ________________________________________________________________ Telephone: ____________________________ ______________________________ (Business) (Home) *Social Security Number: _______-_____-_______ Citizenship:___________________ Electronic Mail Address:_______________________________________________________ Status: ___Graduate ___Post-doctoral Fellow ___Faculty ___Other (specify) In order to attend the workshop, will you need funds for travel?___ lodging?___ Please indicate specifically any special housing, transportation or dietary arrangements you will need: __________________________________________ How did you learn about this workshop:_________________________________________ REQUIREMENTS: Applicants must submit a completed application form and a cover letter. The letter should describe, in one or two paragraphs, the sequence analysis problems encountered in your research, and how participating in the workshop will enhance this research. Please include a brief statement describing your level of experience with computers. Faculty members, staff and post-docs should provide a curriculum vita. Graduate students must have a letter of recommendation from a faculty member. If you have requested travel funds, please include the cost of roundtrip air fare from your home to Pittsburgh and indicate the amount of travel funds you will need. ALL PARTICIPANTS WILL BE REQUIRED TO PAY A $135 ADVANCE REGISTRATION FEE UPON ACCEPTANCE INTO THE WORKSHOP. Please return all application materials by APRIL 17, 1995 to: Biomedical Workshop Applications Committee Pittsburgh Supercomputing Center 4400 Fifth Avenue, Suite 230C Pittsburgh, PA 15213 Direct inquiries to: Nancy Blankenstein, blankens@psc.edu or 412/268-4960. *Disclosure of Social Security Number is voluntary. PSC does not discriminate on the basis of race, color, religion, sex, age, creed, national or ethnic origin, or handicap. From thys@schs.uia.ac.be Wed Mar 1 11:22:17 1995 Received: from sch2.uia.ac.be for thys@schs.uia.ac.be by www.ccl.net (8.6.10/930601.1506) id KAA19305; Wed, 1 Mar 1995 10:08:57 -0500 Received: by sch2.uia.ac.be (8.6.10/Ultrix3.0-C) id QAA01172; Wed, 1 Mar 1995 16:06:01 +0100 Date: Wed, 1 Mar 1995 16:05:59 +0100 (MET) From: Gerd Thys X-Sender: thys@sch2.uia.ac.be To: CCL Subject: Summary: Semi-empirical methods + CI Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all, Two weeks ago, I posted a question concerning Semi-empirical methods and CI ... Thanks to all who did reply. They were really elucidating. Gerd ********************* ORIGINAL POSTING ************************************ I'm using PM3 and AM1 followed by MECI (as implemented in MOPAC) to calculate excitation-energies of a series of (large) closed-shell organic molecules. As a test, I did some MECI calculation including 3 up to 8 orbitals to correct for the correlation energy (In MOPAC: MECI C.I.=3 to C.I.=8). I was told to be careful no to add too much orbitals in de MECI-calculation, since part of the correction for the correlation energy is already included in the AM1/PM3 (and any other) parameterization. Adding too much orbitals would overestimate the excitation energy. In some cases, the first singlet-singlet excitation energy at a given number of orbitals results in the following: PM3: C.I.=5 E= 3.571 eV (347 nm) C.I.=6 E= 3.624 eV (342 nm) C.I.=7 E= 3.472 eV (366 nm) C.I.=8 E= 3.436 eV (361 nm) In other words, at a given # of orbitals (in this case C.I.=6), the energy reaches a maximum. Normally I would expect energy to lower with adding orbitals (and most of the time this is the case). Now my question to you all: Is this 'going through a maximum' an effect of the overcompensation of the correlation energy? Are there any other effects (depending on the electronic structure of the molecule)? Thanks for your reaction, Gerd **************************************************************************** From grzesb@asp.biogeo.uw.edu.plWed Mar 1 15:34:52 1995 Date: Wed, 22 Feb 95 11:23:08 +0100 From: Grzegorz Bakalarski To: thys@reks.uia.ac.be Dear Mr. Thys, Maybe a key point is the version of MOPAC you use. I was told ( but I have never checked this by myself) that in version 6 (or less) of MOPAC the C.I. routine has implemented wrong formulas ( only diagonal elemets of matrix). I know that in MOPAC 7 (or MOPAC 93) this was corrected. Hope this helps. Grzegorz Bakalarski P.S> Could you send me summary if you find a solution of your question ? ***************************************************************************** From gedeck@pctc.chemie.uni-erlangen.deWed Mar 1 15:34:56 1995 Date: Wed, 22 Feb 1995 14:15:22 +0100 (NFT) From: Peter Gedeck To: Gerd Thys Subject: Re: CCL:Semi-empirical methods + CI Hello Gerd, There is another aspect that needs to be considered, when talking about the CI-implementation in mopac. Usually the conformations used in the CI-calculation are ordered by there energy and then the CI-expansions are truncated, so that only the lowest 100 conformations are considered. If you look now at the type of conformations that are included in the CI-expansion, more and more conformations are included that are only single-excitations, while the number of double and higher excitations is reduced. The single-excitations will not contribute to the correlation energy of your ground state and therefore the correlation energy or the lowering of the ground state will be reduced. If you consider even more orbitals (I know this is not possible in mopac 6 without changing the source), while keeping the number of conformations in your CI-calculation constant, you will find, that the S1<-S0 absorption energy approaches the value it will have for a SCI-calculation. I hope this will be of any help for you, Peter Peter Gedeck Inst. f. Physikalische Chemie I Egerlandstrasse 3 91058 Erlangen Germany Tel: ++9131 - 85 7335 Fax: ++9131 - 85 8307 E-Mail: gedeck@pctc.chemie.uni-erlangen.de WWW: http://pctc.chemie.uni-erlangen.de/~gedeck/gedeck.html ************************************************************************** From H1376May@huella.bitnetWed Mar 1 15:35:01 1995 Date: 22 Feb 95 17:01:43 +0100 From: H1376May@huella.bitnet To: thys@sch2.uia.ac.be Subject: Re: Semiempirical methods + CI Dear Gerd, If I have correctly understood, you have observed a 'going through a maximum' effect in the EXCITATION ENERGY. If so, then nothing unexpected is there: variation principle states that the energy of the ground state should go down with the increasing CI size; with some conditions, the same holds for the first excited singlet. But nothing is known concerning their distance. What I said above is independent whether you use ab initio or semiempirical theory. Do not mix over with the problem of "overcompensation of the correlation energy" - the latter is connected with the relation to the experimental data: if an effect is already included in the parameters, then its explicit inclusion may deteriorate the agreement between theory and experiment. Prof. I. Mayer Budapest ************************************************************************ From Matthew.Harbowy@tjlus.sprint.comWed Mar 1 15:35:07 1995 Date: Wed, 22 Feb 1995 08:51:00 -0500 From: Matthew.Harbowy@tjlus.sprint.com To: thys@reks.uia.ac.be Subject: CCL:Semi-empirical methods + CI Remember: it is the total energy that should be lowered. Be very, very, careful with MECI: Actual use should be C.I.=(x,y), where x is the number of orbitals and y is the number of singly occupied orbitals. I've seen cases where I've gotten a third of an electron or a fourth of an electron scattered among orbitals, which is a completely unphysical and spurious result and results in higher energies. The individual orbitals movce up and down with mixing, and can result in transitions moving in (seemingly) odd directions, either bathochromic or hypsochromic. matt **************************************************************************** From ZUILHOF@rulgca.LeidenUniv.nlWed Mar 1 15:35:25 1995 Date: Wed, 01 Mar 1995 01:02:20 +0100 (MET) From: Han Zuilhof To: thys@reks.uia.ac.be Subject: MOPAC and CI Dear Gerd, In regard of your CCL question about the use of explicit CI in the calculation of excitation properties of organic molecules, I would like to ask you whether you would be willing to give a summary of the responses, either to the net or to me personally. I have used PM3 with small CI's several times quite succesfully, but almost always more in a qualitative than quantitative sense. Not too long ago a discussion of the role of correlation energy in semiempirical calculations was given by Tim Clark in the Israel Journal of Chemistry. That had -either in 1993 or 1994, and I think the latter- two special issues on quantum chemistry. It is in the second. Hope this helps a bit. Best regards, Han ****************************************************************************** ** Dr. Han Zuilhof ** e-mail: ZUILHOF@chem.chem.rochester.edu ** ** Department of Chemistry ** (optional: ZUILHOF@rulgca.leidenuniv.nl) ** ** University of Rochester ** ** ** Rochester, NY, 14627 ** Fax: (716) 473-6889 ** ** USA ** Voice: (716) 275-2219 ** ****************************************************************************** ** ** ** "Excite a photochemist!" ** ** ** ****************************************************************************** ---------------------------------------------------------------------------- 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 ---------------------------------------------------------------------------- From mburson@southwind.net Wed Mar 1 12:08:56 1995 Received: from onyx.southwind.net for mburson@southwind.net by www.ccl.net (8.6.10/930601.1506) id MAA22075; Wed, 1 Mar 1995 12:05:26 -0500 Received: from localhost (mburson@localhost) by onyx.southwind.net (8.6.5/8.6.5) id LAA15012; Wed, 1 Mar 1995 11:02:32 -0600 Date: Wed, 1 Mar 1995 11:02:31 -0600 (CST) From: Max Burson To: Chemistry@ccl.net Subject: Software Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Friends University's chemistry faculty are seeking information on computer software programs that enable students to simulate usage of several peices of equipment, such as NMR, and infrared and mass spectroscopy and qualitative analysis. They would like to know what software is available ahd how to contact the manufacturers. Feedback from users of such programs is also sought. All replies should be forwarded to mburson@southwind.net by March 10. Please, if possible, include your telephone number and address so that faculty members can contact you for more information. Thanks for your help in advance. Max M. Burson Public Sevices Librarian Friends University Wichita, KS 67213 From Don_Gregory@msi.com Wed Mar 1 13:10:01 1995 Received: from msi.com for Don_Gregory@msi.com by www.ccl.net (8.6.10/930601.1506) id MAA22935; Wed, 1 Mar 1995 12:44:59 -0500 Received: from qmail-gw.msi.com by msi.com (4.1/SMI-4.1) id AA04248; Wed, 1 Mar 95 12:44:21 EST Message-Id: <9503011744.AA04248@msi.com> Date: 1 Mar 1995 12:40:16 +0000 From: "Don Gregory" Subject: None To: "Comp. Chem. Listserver" Subject: Time:12:35 PM OFFICE MEMO None Date:3/1/95 On March 1, McCarron wrote: "Has anyone out there carried out amino acid mutations using BLOCK If so do you know how to get around the problem of having interactions between three blocks (blocks 2 and 3 containing different side chains)"? Matthew, When using the BLOCK facility within CHARMm, if you've successfully assigned atoms to block 2 and 3 (by default, all atoms are initially placed into block 1), and assigned a "lambda" value, then interactions between blocks 2 & 3 are *already* excluded. So I'm not quite sure what difficulties you are having. Another consideration you may wish to make, is that one is not restricted to only 3 blocks, but can define numerous blocks. In this instance however, you must use the explicit 'COEFF" commands to specify the coefficients between each block. If, however, you're doing a classic alchemical perturbation, using 3 blocks, the lambda value will result in (for a lambda of 0.1), interactions between block 1 and 2 = 0.1 interactions between block 1 and 3 = 0.9 interactions between block 2 and 3 = 0.0 This should be apparent in the matrix printout when leaving the block facility in the CHARMm output file. Don Gregory Mgr. Life Science Applications Molecular Simulations, Inc. From ar1z+@andrew.cmu.edu Wed Mar 1 13:19:07 1995 Received: from po8.andrew.cmu.edu for ar1z+@andrew.cmu.edu by www.ccl.net (8.6.10/930601.1506) id NAA23380; Wed, 1 Mar 1995 13:01:48 -0500 Received: (from postman@localhost) by po8.andrew.cmu.edu (8.6.9/8.6.9) id NAA06985 for chemistry@ccl.net; Wed, 1 Mar 1995 13:01:45 -0500 Received: via switchmail; Wed, 1 Mar 1995 13:01:43 -0500 (EST) Received: from unix4.andrew.cmu.edu via qmail ID ; Wed, 1 Mar 1995 13:00:57 -0500 (EST) Received: from unix4.andrew.cmu.edu via qmail ID ; Wed, 1 Mar 1995 13:00:51 -0500 (EST) Received: from mms.4.60.Jan.26.1995.18.44.27.pmax.ul4.EzMail.2.0.CUILIB.3.45.SNAP.NOT.LINKED.unix4.andrew.cmu.edu.pmax.ul4 via MS.5.6.unix4.andrew.cmu.edu.pmax_ul4; Wed, 1 Mar 1995 13:00:50 -0500 (EST) Message-ID: Date: Wed, 1 Mar 1995 13:00:50 -0500 (EST) From: "Alexander J. Ropelewski" To: chemistry@ccl.net Subject: CCL:Molecular Mechanics and Dynamics workshop Annoucement "METHODS OF MOLECULAR MECHANICS AND DYNAMICS OF BIOPOLYMERS" WORKSHOP Pittsburgh Supercomputing Center August 16-19, 1995 The Pittsburgh Supercomputing Center (PSC) is hosting a workshop on "Methods of Molecular Mechanics and Dynamics of Biopolymers," August 16-19, 1995. The workshop will familiarize biomedical researchers with computational methods and provide practice in applying supercomputing resources to problems of concern in molecular mechanics. Practical experience on our supercomputers will be gained in the application to: (1) the theory and practice of molecular mechanics and dynamics; (2) the development and refinement of molecular mechanics force fields; (3) the problem of conformation mapping and analysis of polypeptide structures, including the refinement of structure from measured NMR data; and (4) computation of interaction energies and free energies for protein-drug interactions and conformational thermodynamics. Workshop leaders are Dr. Charles L. Brooks III, The Scripps Research Institute and Dr. Alexander D. MacKerell Jr., University of Maryland at Baltimore. The worskhop will consist of lectures and extensive hands-on sessions. General aspects of molecular mechanics software will be discussed and a number of packages are available for use at the PSC. However, the programs CHARMM and QUANTA will be utilized most extensively in demonstrations. Hands-on sessions will be emphasized. Participants will be able to work on the examples provided or on their own experimental data. No prior supercomputing experience is necessary. This workshop is funded by a grant from the Biomedical Research Technology Program, National Center for Research Resources, National Institutes of Health. Travel, meals and hotel accommodations for researchers affilated with U.S. academic institutions are supported by this grant. Enrollment is limited to 20. An application form is included. Deadline for applications is: June 22, 1995. Please direct inquires or send the following application form to blankens@psc.edu. Additional information about this workshop can be found in http://pscinfo.psc.edu/biomed/workshops95.html PITTSBURGH SUPERCOMPUTING CENTER BIOMEDICAL INITIATIVE ************************************** August 16-19, 1995 APPLICATION Name:________________________________________________________________________ Affiliation:_________________________________________________________________ Address:_____________________________________________________________________ (Business) _____________________________________________________________________________ ____________________________________________________________________________ (Home) ____________________________________________________________________________ Telephone: ____________________ ______________________ (Business) (Home) *Social Security Number: _______-_____-_______ Citizenship: ____________ Electronic Mail Address:____________________________________________________ Status: ___Graduate ___Post-doctoral Fellow ___Faculty ___Other (specify) Please indicate specifically any special housing, transportation or dietary arrangements you will need: _______________________________________________ How did you learn about this workshop? _____________________________________ REQUIREMENTS: Applicants must submit a completed application form and a cover letter. The letter should describe, in one or two paragraphs, your current research and how participating in the workshop will enhance this research. Please include a brief statement describing your level of experience with computers. Faculty members, staff and post-docs should provide a curriculum vita. Graduate students must have a letter of recommendation from a faculty member. Please return all application materials by June 22, 1995 to: Biomedical Workshop Applications Committee Pittsburgh Supercomputing Center 4400 Fifth Avenue, Suite 230C Pittsburgh, PA 15213 Direct inquiries to: Nancy Blankenstein, blankens@psc.edu or 412/268-4960. *Disclosure of Social Security Number is voluntary. PSC does not discriminate on the basis of race, color, religion, sex, age, creed, national or ethnic origin, or handicap. From ar1z+@andrew.cmu.edu Wed Mar 1 13:25:55 1995 Received: from po8.andrew.cmu.edu for ar1z+@andrew.cmu.edu by www.ccl.net (8.6.10/930601.1506) id MAA22978; Wed, 1 Mar 1995 12:47:28 -0500 Received: (from postman@localhost) by po8.andrew.cmu.edu (8.6.9/8.6.9) id MAA06650 for chemistry@ccl.net; Wed, 1 Mar 1995 12:47:23 -0500 Received: via switchmail; Wed, 1 Mar 1995 12:47:22 -0500 (EST) Received: from unix4.andrew.cmu.edu via qmail ID ; Wed, 1 Mar 1995 12:46:33 -0500 (EST) Received: from unix4.andrew.cmu.edu via qmail ID ; Wed, 1 Mar 1995 12:46:26 -0500 (EST) Received: from mms.4.60.Jan.26.1995.18.44.27.pmax.ul4.EzMail.2.0.CUILIB.3.45.SNAP.NOT.LINKED.unix4.andrew.cmu.edu.pmax.ul4 via MS.5.6.unix4.andrew.cmu.edu.pmax_ul4; Wed, 1 Mar 1995 12:46:26 -0500 (EST) Message-ID: Date: Wed, 1 Mar 1995 12:46:26 -0500 (EST) From: "Alexander J. Ropelewski" To: chemistry@ccl.net Subject: CCL:Sequencing Analysis workshop Annoucement NUCLEIC ACID AND PROTEIN SEQUENCE ANALYSIS WORKSHOP FOR BIOMEDICAL RESEARCHERS Pittsburgh, Pennsylvania June 4-9, 1995 Pittsburgh Supercomputing Center (PSC) is again offering a five-day workshop on "Nucleic Acid and Protein Sequence Analysis," June 4-9, 1995. It is funded by a grant from the National Center for Human Genome Research of the National Institutes of Health. The workshop will familiarize biomedical researchers with computational methods and provide practice in applying supercomputing resources to problems of concern in macromolecular sequence analysis. Emphasis will be on alignment of and pattern extraction from multiple sequences. Participants will gain practical experience on PSC's Cray C-90 and T3D in (1) comparing and aligning sequences, (2) identifying informative patterns in a set of sequences; and (3) using extracted informative patterns to identify related sequences. Researchers will also learn several approaches to database searching and multiple sequence alignment, how to use profile analysis effectively, and how to identify patterns in their sequences. Participants are encouraged to bring sequence analysis problems from their current research. Extensive documentation will be given at the outset on the PSC computing environment as well as on the specific programs to be employed in the workshop. No prior supercomputing experience is required. Workshop leaders are Dr. Gary Churchill, Cornell University, Dr. Michael Gribskov, San Diego Supercomputing Center, and Dr. Hugh Nicholas, PSC. A limited number of grants to cover travel and hotel accommodations are available for U.S. academic participants. ALL PARTICIPANTS ARE REQUIRED TO PAY A $135 REGISTRATION FEE, IN ADVANCE, UPON ACCEPTANCE INTO THE WORKSHOP. The deadline for submitting applications is April 17, 1995. Enrollment is limited to 20 participants. Additional information about this workshop can be found in http://pscinfo.psc.edu/biomed/workshops95.html * * * * * PITTSBURGH SUPERCOMPUTING CENTER NUCLEIC ACID AND PROTEIN SEQUENCE ANALYSIS WORKSHOP FOR BIOMEDICAL RESEARCHERS June 4-9, 1995 APPLICATION Name: ________________________________________________________________ Affiliation: ________________________________________________________________ Address: ________________________________________________________________ (Business) ________________________________________________________________ ________________________________________________________________ (Home) ________________________________________________________________ Telephone: ____________________________ ______________________________ (Business) (Home) *Social Security Number: _______-_____-_______ Citizenship:___________________ Electronic Mail Address:_______________________________________________________ Status: ___Graduate ___Post-doctoral Fellow ___Faculty ___Other (specify) In order to attend the workshop, will you need funds for travel?___ lodging?___ Please indicate specifically any special housing, transportation or dietary arrangements you will need: __________________________________________ How did you learn about this workshop:_________________________________________ REQUIREMENTS: Applicants must submit a completed application form and a cover letter. The letter should describe, in one or two paragraphs, the sequence analysis problems encountered in your research, and how participating in the workshop will enhance this research. Please include a brief statement describing your level of experience with computers. Faculty members, staff and post-docs should provide a curriculum vita. Graduate students must have a letter of recommendation from a faculty member. If you have requested travel funds, please include the cost of roundtrip air fare from your home to Pittsburgh and indicate the amount of travel funds you will need. ALL PARTICIPANTS WILL BE REQUIRED TO PAY A $135 ADVANCE REGISTRATION FEE UPON ACCEPTANCE INTO THE WORKSHOP. Please return all application materials by APRIL 17, 1995 to: Biomedical Workshop Applications Committee Pittsburgh Supercomputing Center 4400 Fifth Avenue, Suite 230C Pittsburgh, PA 15213 Direct inquiries to: Nancy Blankenstein, blankens@psc.edu or 412/268-4960. *Disclosure of Social Security Number is voluntary. PSC does not discriminate on the basis of race, color, religion, sex, age, creed, national or ethnic origin, or handicap. From mburson@southwind.net Wed Mar 1 15:08:53 1995 Received: from onyx.southwind.net for mburson@southwind.net by www.ccl.net (8.6.10/930601.1506) id OAA25078; Wed, 1 Mar 1995 14:13:12 -0500 Received: from localhost (mburson@localhost) by onyx.southwind.net (8.6.5/8.6.5) id NAA20326; Wed, 1 Mar 1995 13:10:14 -0600 Date: Wed, 1 Mar 1995 13:10:13 -0600 (CST) From: Max Burson To: chemistrytm@dhvx20.csudh.edu cc: Chemistry@ccl.net Subject: Software Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Friends University's chemistry faculty are seeking information on computer software programs that enable students to simulate usage of several pieces of equipment, such as NMR, and infrared and mass spectroscopy and qualitative analysis. They would like to know what software is available and how to contact the manufacturers. Feedback from users of such programs is also sought. All replies should be forwarded to mburson@southwind.net by March 10. Please, if possible, include your telephone number and address so that we may contact you for further information. Thanks four your help in advance. Max M. Burson Public Services Librarian Friends University Wichita, KS 67213 From MCARDUCCI@xray0.chem.arizona.edu Wed Mar 1 16:20:10 1995 Received: from xray0.chem.arizona.edu for MCARDUCCI@xray0.chem.arizona.edu by www.ccl.net (8.6.10/930601.1506) id PAA27209; Wed, 1 Mar 1995 15:35:31 -0500 Date: Wed, 1 Mar 1995 13:34:26 MST From: MCARDUCCI@XRAY0.CHEM.ARIZONA.EDU Message-Id: <950301133426.20200d20@XRAY0.CHEM.ARIZONA.EDU> Subject: deformation density calculations To: chemistry@ccl.net X-Vmsmail-To: SMTP%"chemistry@ccl.net" Hi folks, I am attempting to calculate the theoretical deformation densities of a group of molecules. The deformation density is the difference between the total electron density of a molecule (calculated or experimental) and the electron density of "neutral spherical unperturbed atoms" superimposed at the same nuclear positions. I am currently using Fenske-Hall MO calculations to define the molecule and the associated program MOPLOT to subtract the unperturbed density. I have been finding that the Fenske-Hall method overestimates the density in lone pair regions and underestimates that in bonding regions. This problem has been reported in the literature previously for restricted basis sets. The solution has been to move to Ab Initio methods using extended basis sets. So, I am looking for a package that will allow me to calculate deformation densities. Gaussian92 is available in our department, but I have been unable to define/obtain the "neutral unperturbed atom density". (I am a beginner using Ab Initio calculations.) Does anyone know how this may be done in G92? I'd also be interested in any other packages that would allow me to calculate deformation densities. Thanks for your time. ---Mike Carducci Department of Chemistry University of Arizona mcarducci@xray.chem.arizona.edu From rameshg@phar.umich.edu Wed Mar 1 19:08:54 1995 Received: from iris.phar.umich.edu for rameshg@phar.umich.edu by www.ccl.net (8.6.10/930601.1506) id TAA03244; Wed, 1 Mar 1995 19:01:22 -0500 Received: from iris.phar.umich.edu (iris.phar.umich.edu [35.211.128.3]) by iris.phar.umich.edu (8.6.10/8.6.10) with SMTP id TAA12997 for ; Wed, 1 Mar 1995 19:01:20 -0500 Date: Wed, 1 Mar 1995 19:01:19 -0500 (EST) From: Ramesh Gopalaswamy To: chemistry@ccl.net Subject: sybyl command Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello Netters, I am having trouble reading a pdb file (from DGEOM output) using sybyl in command mode. I get a warning "unable to read CONECT records........." However, I could read it in using menu mode. I need to use command mode as I have several pdb files to be minimized and would like to SPL. Your help appreciated very much. Ramesh. **************************************************************************** Ramesh Gopalaswamy, rameshg@phar.umich.edu **************************************************************************** From d3h325@maddog.pnl.gov Wed Mar 1 20:08:50 1995 Received: from pnl.gov for d3h325@maddog.pnl.gov by www.ccl.net (8.6.10/930601.1506) id UAA04095; Wed, 1 Mar 1995 20:05:30 -0500 Received: from maddog.pnl.gov by pnl.gov (PMDF V4.3-13 #6012) id <01HNMNPAE1HS00MEYV@pnl.gov>; Wed, 01 Mar 1995 17:03:56 -0800 (PST) Received: by maddog.pnl.gov (4.1/SMI-4.1) id AA00321; Wed, 1 Mar 95 17:05:12 PST Date: Wed, 01 Mar 1995 17:05:12 -0800 (PST) From: d3h325@maddog.pnl.gov (Jaroslaw Nieplocha) Subject: Global Arrays programming environment To: chemistry@ccl.net Message-id: <9503020105.AA00321@maddog.pnl.gov> Content-transfer-encoding: 7BIT The release 2.0 of the Global Array (GA) toolkit is now available for public distribution. The GA toolkit provides a portable "shared-memory" NUMA programming environment. The GA allows each process in a MIMD parallel program asynchronously access logical blocks of physically distributed matrices, without need for explicit cooperation by other processes. Global Arrays have been used at Pacific Northwest Laboratory, Argonne National Laboratory and elsewhere in several computational chemistry codes for the following problems: Hartree-Fock SCF, Density Functional Theory, second-order Moller-Plesset Perturbation, Multi-Reference Configuration Interaction, and Coupled Cluster. Supported Platforms: Cray T3D, IBM SP-1/2, Intel iPSC/860, Delta, Paragon, KSR-1/2, networks of single- and multi-processor workstations: SUN, IBM, DEC, and SGI (including Power Challenge) Distribution: anonymous ftp: ftp.pnl.gov directory: /pub/global file: global2.0.tar.Z More Information about GA: http://www.emsl.pnl.gov:2080/docs/global/ga.html J.Nieplocha, RJ Harrison, RJ Littlefield, "Global Arrays: a portable 'shared memory' programming model for distributed memory computers", Supercomputing'94, pp. 340-349. (a copy is also distributed with the toolkit) From JeanLuc.Verschelde@rug.ac.be Wed Mar 1 11:07:41 1995 Received: from mserv.rug.ac.be for JeanLuc.Verschelde@rug.ac.be by www.ccl.net (8.6.10/930601.1506) id LAA20592; Wed, 1 Mar 1995 11:07:34 -0500 Received: from allserv.rug.ac.be by mserv.rug.ac.be with SMTP id AA09336 (5.67b/IDA-1.5 for ); Wed, 1 Mar 1995 17:06:00 +0100 Received: by allserv.rug.ac.be (5.x/SMI-SVR4) id AA06160; Wed, 1 Mar 1995 17:07:09 +0100 Date: Wed, 1 Mar 1995 17:07:09 +0100 (MET) From: Jean-Luc Verschelde To: OHIO SUPER Subject: simplex Message-Id: Status: R Hi all, Where can I find minimization algorithms? The simplex procedure would be nice. Jean-Luc