From Patrick.Bultinck@rug.ac.be Fri Apr 26 05:49:03 1996 Received: from mserv.rug.ac.be for Patrick.Bultinck@rug.ac.be by www.ccl.net (8.7.1/950822.1) id FAA07441; Fri, 26 Apr 1996 05:04:24 -0400 (EDT) Received: from hartree1.rug.ac.be by mserv.rug.ac.be with SMTP id AA09510 (5.67b/IDA-1.5 for ); Fri, 26 Apr 1996 11:03:11 +0200 Date: Fri, 26 Apr 1996 11:59:44 +0200 (DFT) From: Patrick Bultinck To: CCL Subject: Direct SCF + Morokuma EDA Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear, I am doing some calculations on complexes with up to a couple of hundred basis functions. For the optimizations etc. I use several techniques based on Direct SCF. I would like to do a Morokuma energy decomposition analysis on the complexes. Most programs I know of, however, do not support the combination of Direct SCF AND Morokuma EDA (e.g. GAMESS says in INPUT.DOC that DIRSCF=.TRUE. and RUNTYP=MOROKUMA are incompatible). Can anybody offer some help ? Are there programs that can handle Direct SCF + Morokuma EDA ? My hard-disk capability (some 4 Gb) cannot handle it because of the fact that GAMESS stores two integral files. I could go in parallel with some other workstations, but it's a speed-heterogeneous network, which makes that one workstation beats the other so badly that the first one fills it's disk and then halts the whole thing. Could an SSA help, and if so what about the current 2Gb filesystem limit ? Thanks a million, Patrick ***************************************************************************** Patrick Bultinck Macrocycles Quantum Chemical Ph. D. Student Calculations Dept. Inorganic & Physical Chemistry University of Ghent Tel. Int'l code/32/9/264.44.44 Krijgslaan 281 (S-3) Fax. Int'l code/32/9/264.49.83 9000 Gent E-mail : Patrick.Bultinck@rug.ac.be Belgium http://allserv.rug.ac.be/~pbultink/ ***************************************************************************** From OLIVER@psipsy.uct.ac.za Fri Apr 26 06:49:05 1996 Received: from uctmail2.uct.ac.za for OLIVER@psipsy.uct.ac.za by www.ccl.net (8.7.1/950822.1) id GAA07920; Fri, 26 Apr 1996 06:05:01 -0400 (EDT) Received: by uctmail2.uct.ac.za (Smail3.1.29.1 #15) id m0uCkO5-0005QHC; Fri, 26 Apr 96 12:04 SAT Message-Id: Received: by uctmail.uct.ac.za (Mort 2.15) id 439 from PSIPSY; Fri Apr 26 12:04:29 1996 From: "Oliver Hill" To: chemistry@www.ccl.net Date: Fri, 26 Apr 1996 12:11:32 SAST-2 Subject: Modelling of Ferrocene - Refs Reply-to: oliver@psipsy.uct.ac.za Priority: normal X-mailer: Pegasus Mail v3.22 Dear CCLs I wonder if someone can help me. I am looking for references on Ab Initio calculations of ferrocene. In particular I am looking for the original papers (if they exist) on RHF calculations which give iron to carbon distances that are too long. Also I am looking for papers on the solution of this problem by including correlation in the calculation. We have run into this problem in calculations of iron alkene complexes and I would like to find the original references. I would be most grateful to anyone who could help me out, and will of course post a summary if anyone is interested. Oliver ______________________________________________________________________ | Oliver Hill | | | Department of Chemistry | "The true scientist never | | University of Cape Town | loses the faculty of | | Rondebosch, 7700 | amazement. It is the essence | | SOUTH AFRICA | of his(her) being." | | oliver@psipsy.uct.ac.za (internet) | - HANS SELYE | | | | | Tel. +27-21-650-2527 | | | Fax. +27-21-650-3788 | | |____________________________________|_______________________________| | http://www.cem.uct.ac.za/PeopleInChemDept/grad/oliver-hill.html | |____________________________________________________________________| From pis_diez@nahuel.biol.unlp.edu.ar Fri Apr 26 09:49:11 1996 Received: from biol.unlp.edu.ar for pis_diez@nahuel.biol.unlp.edu.ar by www.ccl.net (8.7.1/950822.1) id JAA10441; Fri, 26 Apr 1996 09:43:29 -0400 (EDT) Received: from jubert.biol.unlp.edu.ar (jubert.biol.unlp.edu.ar [163.10.7.25]) by biol.unlp.edu.ar (8.6.9/8.6.9) with SMTP id KAA07516 for ; Fri, 26 Apr 1996 10:26:49 -0300 Date: Fri, 26 Apr 1996 10:26:49 -0300 Message-Id: <199604261326.KAA07516@biol.unlp.edu.ar> X-Sender: pis_diez@nahuel.biol.unlp.edu.ar X-Mailer: Windows Eudora Version 1.4.3 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@www.ccl.net From: pis_diez@nahuel.biol.unlp.edu.ar (Reinaldo Pis Diez) Subject: G: Semiempiricals in G92 Dear netters Does anybody know if it is possible to add non-standard parameters to the semiempirical methods included in G92/DFT? If yes, how can we do it? Which keyword must we used? Thanx in advance, Reinaldo From steve@indi.aci.uni-heidelberg.de Fri Apr 26 10:49:07 1996 Received: from relay.urz.uni-heidelberg.de for steve@indi.aci.uni-heidelberg.de by www.ccl.net (8.7.1/950822.1) id JAA10579; Fri, 26 Apr 1996 09:53:17 -0400 (EDT) Received: from sun0.urz.uni-heidelberg.de (root@sun0.urz.uni-heidelberg.de [129.206.100.126]) by relay.urz.uni-heidelberg.de (8.7.5/8.7.4) with SMTP id PAA16064 for ; Fri, 26 Apr 1996 15:53:10 +0200 (MET DST) Received: from mondo (mondo.aci.uni-heidelberg.de) by sun0.urz.uni-heidelberg.de (4.1/URZ-20.03.92) id AA03862; Fri, 26 Apr 96 15:53:06 +0200 Sender: steve@indi.aci.uni-heidelberg.de Message-Id: <3180D59F.41C6@indi.aci.uni-heidelberg.de> Date: Fri, 26 Apr 1996 15:54:39 +0200 From: Stefan Reichling X-Mailer: Mozilla 3.0b2 (X11; I; IRIX 5.3 IP22) Mime-Version: 1.0 To: chemistry@www.ccl.net Subject: polygon search in 3D Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi all, I'm looking for an algorithm to search in a given set of n points in 3D space empty convex polygons, spacifically tetrahedrons and oktahedrons. Any help apreciated steve -- +---------------------------------------------------------------------+ | Stefan Reichling | | Anorganisch-Chemisches Instiut | | Tel +49-6221-548565 Universitaet Heidelberg | | Fax +49-6221-545707 69120 Heidelberg | | e-mail: steve@indi.aci.uni-heidelberg.de Germany | | www: http://ix.urz.uni-heidelberg.de/~il1 | +---------------------------------------------------------------------+ From owner-chemistry@ccl.net Fri Apr 26 12:49:07 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.1/950822.1) id MAA12450; Fri, 26 Apr 1996 12:32:46 -0400 (EDT) Received: from theory.tc.cornell.edu for lscott@tc.cornell.edu by bedrock.ccl.net (8.7.1/950822.1) id MAA04274; Fri, 26 Apr 1996 12:32:39 -0400 (EDT) Received: from [128.84.181.75] (JEANNE.TC.CORNELL.EDU [128.84.181.75]) by theory.tc.cornell.edu (8.6.9/8.6.6) with SMTP id MAA29452; Fri, 26 Apr 1996 12:28:51 -0400 Date: Fri, 26 Apr 1996 12:28:51 -0400 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable To: (Recipient list suppressed) From: lscott@TC.Cornell.EDU (Lisa A. Scott) Subject: Intro. to Computer-Aided Molec. Design Workshop Cornell Theory Center Introduction to Computer-aided Molecular Design Workshop July 10-13, 1996 Cornell University, Ithaca, NY This workshop provides a broad introduction to computer-aided molecular design. We will describe how computational methods can be appropriately applied to real-world problems in the pharmaceutical, biotechnology, and chemical industries. A variety of methods will be discussed, ranging from statistical methods based on experimental data to high-level ab initio quantum chemical calculations. The methods to be introduced include molecular dynamics, quantum chemistry, and dielectric-continuum solvent models. Sections of the workshop will also introduce homology-based protein modeling and general-purpose optimization methods used across a range of computational chemistry methods. The workshop will combine descriptions of methods with applications to specific areas. Applications will include predictions of physical properties of molecules (solubilities, conformations, pKas, diffusion coefficients, etc.) and predictions of binding properties of drugs (binding geometries and energetics). After each method is introduced, it will be illustrated with a case study. The material in the lectures will be reinforced through hands-on computer laboratory sessions, which will include both introductory software tutorials and more extensive "mini-research projects" using the computer resources at the Cornell Theory Center. WHO SHOULD ATTEND * Faculty, postdocs, and graduate students interested in developing chemical modeling skills * Professionals in the pharmaceutical, biotechnology, or chemical industries who are evaluating the usefulness of molecular modeling * Professionals moving into the area of modeling * Modelers who are expert in one field but who wish to broaden their experti= se COURSE OBJECTIVES * How computer modeling can be used to design molecules * How to choose the appropriate modeling method for specific problems * How to apply standard molecular modeling tools * How to assess the accuracy of predictions made by computer models LECTURERS Dr. Michael Colvin Senior member of the technical staff at Sandia National Laboratories, in Livermore, CA. Colvin's main research interest is the application of quantum chemical methods to understand biochemical processes. The nature of these research problems has involved him in more than a decade of research on quantum chemical methods for massively parallel computers and the development of methods for accurately simulating aqueous solvation. Dr. Richard Judson Senior member of the technical staff at Sandia National Laboratories, in Livermore, CA. Judson has twelve years of experience in molecular modeling using quantum mechanics, molecular dynamics, and statistical and optimization methods. At Sandia he has headed a project in computational drug design that produced new methods for drug-docking predictions, NMR data analysis, and analysis of large databases of molecules. Other projects have included modeling of electron impact on materials, design of laser pulses for control of chemical motion, and the use of genetic algorithms for protein structure prediction. PROPOSED DAILY SCHEDULES Wednesday Overview of Molecular Modeling: Introduction to classical mechanics; force fields; minimization; dynamics; conformation searching; docking; free energy perturbation methods; case study: modeling thermolysin inhibitors polarization; screening; embedded atom method for metals Computer lab session: Introduction to building molecules; calculating energies; conformations; visualization tools; dynamics and minimization Thursday Quantum Chemistry: Molecular Schr=9Adinger equation, Born-Oppenheimer approximation; Hartree-Fock; basis sets; analytical derivatives; electron correlation; accuracy of thermodynamic and electronic properties; general introduction to using QC programs; QC literature; QC resources on the Internet; QC software; case study: chemical properties of environmental carcinogens Computer lab session: Introduction to ab initio quantum chemical software and computational experiments on hydrogen peroxide, disilyne, and hydrogen fluoride dimers =46riday Modeling Solvation Effects: Importance of solvation effects; Born model; self-consistent reaction fields; polarizable continuum models; case study: protonation states of phosphoramide mustard anticancer drugs Protein homology modeling: Need to predict structure from sequence; overview of information available; meaning of homology, low vs. high; high homology models; threading; multiple sequence alignment Computer lab session: Mini-research project using computational chemistry software Saturday Miscellaneous Modeling Topics: Commercially available modeling software; optimization methods; parallel computers Computer lab session: Mini-research project using computational chemistry software REGISTRATION FORM Cornell Theory Center Introduction to Computer-aided Molecular Design Workshop July 10-13, 1996 Cornell University, Ithaca, NY Registration deadline: May 28, 1996 To apply, complete the registration form and return with payment. Priority will be given to registrations received by May 28, 1996. Payment may be sent separately for registrations that are submitted electronically. However, the registration will not be acted upon until the payment arrives. Refunds will be made to those applicants not accepted to the workshop. Refunds cannot be made after applicant is accepted. Return registration form to: Jeanne Butler, 427 Rhodes Hall, Cornell Theory Center, Ithaca, NY 14853-3801, or jeanne@tc.cornell.edu. WORKSHOP REGISTRATION FEES Academic/Government: $100 CPP Member: $250 Corporate: $400 Name: _________________________________________ Company/Institution: _________________________________________ Address: _________________________________________ Email address: _________________________________________ Telephone: _________________________________________ Academic discipline or Corporate Area of Interest: _______________________________ Status (check all that apply): __Corporate Participant __Corporate Research Institute (CRI) Member __Undergraduate Student __Graduate Student __Post-doctoral __Faculty __Smart Node Consultant __Smart Node Advisor __Smart Node Associate __CTC Collaborator (explain): __Other (explain): Do you currently have an allocation at CTC? __Yes __No __Pending If you have an allocation, or an allocation pending, please indicate: Principal Investigator: _________________________________________ If you have an allocation, please indicate: Account number: _________________________________________ Your Userid: _________________________________________ Social Security #:_________________________________________ (for new supercomputer accounts) (Submission of social security numbers is voluntary and will not affect eligibility for access to the Center's facilities. However, they are an integral part of the National Science Foundation's information system and assist in managing the Supercomputer Centers program. SSN solicited under NSF Act of 1950, as amended.) Indicate which of the following best describes you (optional): __African American __Caucasian __Asian American __Hispanic American __Native American or Alaskan Native __Other (please specify): =46or technical information about this course, contact Michael E. Colvin Center for Computational Engineering Sandia National Laboratories Livermore, CA 94551 mecolv@california.sandia.gov Cyrus Umrigar Computational Science & Engineering Research Group Cornell Theory Center Ithaca, NY 14853-3801 cyrus@tc.cornell.edu Information also available at: http://www.tc.cornell.edu/Events/comp.chem.html All trade names referenced are trademarks or registered trademarks of their respective companies.