From bennett@ubeclu.unibe.ch Mon Sep 23 05:30:53 1996 Received: from arwen.unibe.ch for bennett@ubeclu.unibe.ch by www.ccl.net (8.7.5/950822.1) id FAA14509; Mon, 23 Sep 1996 05:17:51 -0400 (EDT) Message-ID: Date: Mon, 23 Sep 96 11:17:26 +0100 From: "Frederick R. Bennett" Subject: Spin density with Molpro To: CHEMISTRY@www.ccl.net X-Mailer: VersaTerm Link v1.1 Hi, does anyone know how to calculate spin density at a given point in space with the molrpo properties package. I can generally calculate one electron properties given a density matrix, but not spin density. It should be there, but it is not documented. Ciao Fred =============================================================================== Frederick R. Bennett Papernet Address: Institut Fur anorganische, analytische und physikalische Chemie Freiestrasse 3 CH-3000 Bern 9 Switzerland Mouthnet Address: [41] (031) 631 4231 Faxnet Address [41] (031) 631 3994 Internet Address: bennett@ubeclu.unibe.ch =============================================================================== From owner-chemistry@ccl.net Mon Sep 23 08:30:56 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.5/950822.1) id IAA15118; Mon, 23 Sep 1996 08:00:36 -0400 (EDT) Received: from cbdcom.apgea.army.mil for grfamini@cbdcom.apgea.army.mil by bedrock.ccl.net (8.7.6/950822.1) id IAA08280; Mon, 23 Sep 1996 08:00:33 -0400 (EDT) Date: Mon, 23 Sep 96 7:52:14 EDT From: George R Famini To: chemistry@ccl.net cc: grfamini@cbdcom.apgea.army.mil Subject: COMP Schedule for SF Organization: International Programs Office Priority: Normal Message-ID: <9609230752.aa03684@cbdcom.apgea.army.mil> Sorry for the delay for getting this to everyone. Enclosed is the tentative agenda for the Division of Computers in Chemistry at the Spring 1997 meeting, to be held in San Francisco 13-17 April 1997. The Program Committee met in Orlando, and agreed to the agenda below. Please note, until the final program is submitted to ACS, the schedule is flexible, and may require some modification based on increased number of abstracts for a given symposium. However, we will endeavor to stay as close to this agenda as possible. I have also included the addresses for the organizers for SF (following the tentative agenda), as well as the proposed symposia for future meetings through 1998. In 1999, COMP will be celebrating its 25th anniversery, and I am very interested in doing "something" different for Anaheim (spring 1999). If anyone has ideas related to COMP's mission, history, and the history of computational chemistry, please contact me (and be prepared to assist!!!). I am also taking ideas for sympsia for 1999. George Famini COMP Program Chair San Francisco- COMP Tentative Program Symposium Sunday Monday Tuesday Wednesday Thursday Industrial Applications D D D Nucleic Acids D D Clusters and MPP D Inorganic Materials May be Cancelled. Will know soon Pharmacophores D D DFT P D D D Multivariate A Graduate and Undergraduate Education D Polymer D D D COMP CHEM Award Symposium A AI P Sci Mix E General Poster E General Oral D D = All Day (Morning and Afternoon); A = Morning Only; P = Afternoon Only; E = Evening American Chemical Society Computers in Chemistry Division San Francisco Meeting, April 13-18, 1997 Program Chair: George R. Famini, U.S. Army Edgewood Research, Development and Engineering Center, SCBRD-ASI, Aberdeen Proving Ground, MD 21010; Voice: (410)671-2552; Fax: (410)671-5373; email: grfamini@apgea.army.mil. Four (4) copies of 150-word abstract (Original on ACS Abstract Form) are due by October 25, 1996 to respective session or symposium chairpersons. Industrial Applications of Computational Chemistry - Dr. Rick Ross, PPG Industries, P.O. Box 9, Allison Park, PA 15101; Voice (412)492-5359; email: rickr@ppg.scripps.edu. Dr. Anne Chaka, Lubrizol. Molecular Modeling and Structure Determination of Nucleic Acids - Dr. Neocles B. Leontis, Department of Chemistry, Bowling Green State University, Bowling Green, OH 43403; voice: (419)372-8663; fax: (419)372-9809; email: neocles@rosalind.bgsu.edu. Computational Chemistry on Clusters, MPPs and Other Non-Traditional Computers -. Dr. Timothy G. Mattson, Intel Supercomputer Systems Division, 5200 N.E. Elam Young Parkway, Mail Stop C06-09, Hillsboro, OR 97124; voice: (503)531-5502; email: tgm@ssd.intel.com. Simulations of Inorganic and Organometalic Materials - Dr. Michael Sennett, Aviamed Corporation, Boston, MA, voice: (508)777-5410. (May be cancelled) Pharmacophore Identification - Dr. Yvonne Martin, Computer Assisted Molecular Design Project, D-47E, AP9A-LL, Abbott Laboratories, One Abbott Park Road, Abbott Park, IL 60064,voice: (708) 937-5362fax: 708 937-2625; email: MARTIN%cmda@randb.abbott.com. Recent Developments in Molecular Simulations Using Density Functional Theory - Dr. Jorge M. Seminario, Department of Chemistry, University of New Orleans, New Orleans, LA 70148, voice: fax: 504-286-6860; email: jsmcm@uno.edu Multivariate Models of Chemical Processes - Dr. Karen Rappaport, Hoechst-Celanese, 86 Morris Ave, Summitt, NJ 07901; voice: (908)522-7868; fax: (908)522-3913; email: kdr1@sumhcc1.hcc.com. Computational Chemistry in Graduate and Undergraduate Education- Dr. Angelo R. Rossi, IBM Research Division, T. J. Watson Research Center,Yorktown Heights, New York 10598: voice: 914-945-3834; Fax: 914-945- 2141; e-mail: rossi@watson.ibm. Artificial Intelligence in Chemistry - Dr. Daniel Dolota, Department of Chemistry, University of Ohio W Polymer Modeling - Wayne L. Mattice, Polymer Science, University of Akron, Akron, OH 44325-3909; voice: (216) 972- 5128; fax: (216) 972-5396; wlm@frank.polymer.uakron.edu. General Computational Chemistry - Poster and/or Oral Sessions - Dr. George R. Famini, US Army Edgewood Research, Development and Engineering Center, SCBRD-ASI, APG, MD 21010; voice: 410)671-2552; Fax: (410)671-5373; email: grfamini@apgea.army.mil. American Chemical Society Computers in Chemistry Division Las Vegas Meeting, September 7-11, 1997 Program Chair: George R. Famini, U.S. Army Edgewood Research, Development and Engineering Center, SCBRD-ASI, Aberdeen Proving Ground, MD 21010; Voice: (410)671-2552; Fax: (410)671-5373; email: grfamini@apgea.army.mil. Four (4) copies of 150-word abstract (Original on ACS Abstract Form) are due by April 19, 1997 to respective session or symposium chairperson. Computational Tools for Rational Drug Design - Dr. Abby Parrill, Chemistry Department, Artificial Intelligence in Chemistry Laboratory, The University of Arizona, email: abby@mercury.aichem.arizona.edu, and Dr. M. Rami Reddy, Gensia Inc., 9390 Towne Centre Drive, SanDiego, CA 92121; voice: (619)-622-3851; fax: (619)-622-4184; email: reddy@gensia.com Combined Quantum Mechanical/Molecular Mechanical Methods - Dr. Jiali Gao, Department of Chemistry, SUNY Buffalo, Buffalo, NY, email: jaili@tams.chem.buffalo.edu; Mark A. Thompson, Molecular Science Research Center,Pacific Northwest Laboratory, PO Box 999, Mail Stop K1-96 Richland, WA., 99352 , voice: 509-375-6734 FAX : 509-375-6631;email: d3f012@pnlg.pnl.gov Structure Based Drug Design: Chemistry and Biology - Dr. Tomi Sawyer, Parke Davis Pharmaceutical Research, 2800 Plymouth Rd., Ann Arbor, MI 48105, phone (313)998-2811; fax: (313)998-2782; email: sawhert@aa.wl.com. New Methods in Computational Chemistry - Dr. Herschel Weintraub, RW Johnson Co. 1000 Route 202,Raritan, NJ 08869; phone: (908)704-5835; fax: (908)725-4264; email: weintraubh@alloy.bitnet. Multidimensional Data Visualization - Dr. Frank K. Brown, Oxford Molecular Group, Chapel Hill, NC 27516; Voice: (919)-968-8815; Fax: (919)962-6401; email: fbrown@oxmol.com. Solvation Models: Applications and Theory - Dr. John McKelvey, Research Labs, Eastman-Kodak Co., Rochester, NY, 14650; Voice: (716)477-3335; email: mckelvey@Kodak.com. Internet for the Practicing Chemist - Dr. Jan Labonowski, Ohio Supercomputer Center, 1224 Kinnear Rd, Columbus, OH 43212; Phone: 614-292-9279; FAX: 614-292-7168; e-mail: jkl@ccl.net. Electrostatic Effects in Chemistry - Dr. Donald Truhlar, Department of Chemistry, University of Minnesota, Minneapolis, MN 55455; phone: (612)624- 7555; fax: (612)624-9390; email: mf12101@sc.msc.edu: Dr. Christopher Cramer, Department of Chemistry, University of Minnesota, Minneapolis, MN 55455; phone: (612) (612)624-0859; fax: (612)626-9390; email: cramer@maroon.tc.umn.edu. General Computational Chemistry - Poster and/or Oral Sessions and Electronic Posters- Dr. George R. Famini, US Army Edgewood Research, Development and Engineering Center, SCBRD-ASI, APG, MD 21010; voice: 410)671-2552; Fax: (410)671-2014; email: grfamini@apgea.army.mil. American Chemical Society Computers in Chemistry Division Dallas Meeting, March 29 - April 2, 1998 Program Chair: George R. Famini, U.S. Army Edgewood Research, Development and Engineering Center, SCBRD-ASI, Aberdeen Proving Ground, MD 21010; Voice: (410)671-2552; Fax: (410)671-5373; email: grfamini@apgea.army.mil. Four (4) copies of 150-word abstract (Original on ACS Abstract Form) are due by October 20, 1997 to respective session or symposium chairperson. Computational Reaction Mechanisms - Dr. Timothy Clark, Chemie-Centrum des Institus fur Organische Chemie, Friedrich-Alesander-UniversitaetErlhangen- Nuernberg, Naegelsbachstrasse 25, D-91052 Erlangen, GERMANY; phone: +49-9131-852948; fax: +49-9131- 856565; email: clark@organik.uni-erlangen.de. Compuational Chemisty on Organophosphorus Compounds - Dr. William E. White, U.S. Army Edgewood Research, Development and Engineering Center, SCBRD-ASI, Aberdeen Proving Ground, MD 21010; Voice: (410)671-3058; Fax: (410)671-1912; email: wewhite@apgea.army.mil. QSAR and Related Techniques - Dr. Curt Breneman,Department of Chemistry, Rensellaer Polytechnic University, Cogswell Lab, 110 8th St, Troy, NY, phone: (518)276-2678; fax: )518)276-4045; email: brenec@rpi.edu. Activity Prediction and Database Searching: A Synergistic Approach - Dr. Ajay Shah, Biosym Corporation, 9685, Scranton Road, San Diego, CA 92121- 3752 ; fax: (619) 458-0136; email: avs@biosym.com. Computational Methods in Catalysis - Dr. Donald Truhlar, Department of Chemistry, University of Minnesota, Minneapolis, MN 55455; phone: (612)624- 7555; fax: (612)624-9390; email: mf12101@sc.msc.edu Diverse Perspectives in Chemical Diversity - Dr. Robert Pearlman, College of Pharmacy, University of Texas, Austin, Texas 78712, voice: 512-471-3383, FAX: 512-471-7474, email: pearlman@vax.phr.utexas.edu. Three Dimensional Descriptors - Dr. James Devillers, Centre de Traitement de lInformation Sciengifique, 21 rue de la Banniere, 69003 Lyon, FRANCE, phone: 33-78-62- 84-99, fax: 33-78-62-99-12. Linear Scaling Quantum Mechnical Methods - Dr. Kenneth M. Merz Jr., Associate Professor of Chemistry, 152 Davey Laboratory, Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802: Phone: (814) 865-3623; Fax: (814) 863-8403 Email: merz@retina.chem.psu.edu Laboratory Automation and Instrumentation - Dr. Karen Rappaport, Hoechst-Celanese, 86 Morris Ave, Summitt, NJ 07901; voice: (908)522-7868; fax: (908)522- 3913; email: kdr1@sumhcc1.hcc.com. General Computational Chemistry - Poster and/or Oral Sessions - Dr. George R. Famini, US Army Edgewood Research, Development and Engineering Center, SCBRD-ASI, APG, MD 21010; voice: 410)671- 2552; Fax: (410)671-2014; email: grfamini@apgea.army.mil. American Chemical Society Computers in Chemistry Division Boston Meeting, 23-27 August, 1998 Program Chair: George R. Famini, U.S. Army Edgewood Research, Development and Engineering Center, SCBRD-ASI, Aberdeen Proving Ground, MD 21010; Voice: (410)671-2552; Fax: (410)671-5373; email: grfamini@apgea.army.mil. Four (4) copies of 150-word abstract (Original on ACS Abstract Form) are due by April 19, 1998 to respective session or symposium chairpersons. De Novo Drug Design - Dr. Mark A. Murcko, Vertex Pharmaceuticals Inc., 40 Alston St., Cambridge, MA 02139; voice: 617-576-3111; fax: 617-576-2109; email: markm@portal.vpharm.com. Computational Chemistry and Transition Metals - Dr. Michelle Francl, Department of Chemistry, Bryn Mawr University. Computational Chemistry and the Classroom - Dr. Jeffry D. Madura, Department of Chemistry, University of South Alabama, Mobile, AL 36688; Phone: (334) 460-7430; FAX: (334) 460-7359; e-mail: jmadura@jaguar1.usouthal.edu Molecular Mechanics Parameters and Parameterization - Dr. Thomas Halgren, Merck and Co. Molecular Simulations with Extended Lagrangians - Dr. Joel S. Bader,CuraGen Corp., 322 E. Main St.,Branford, CT 06405,voice: (203)481- 104x236; fax: (203)481-1106;email: jsbader@curagen.com; Dr. Steven Rick, National Cancer Institute, Bldg 430, Frederick, MD. 21702-1201, voice: (301) 846-5549; fax: (301) 846-5762; email: rick@ncifcrf.gov. Combinatorial Chemistry - Dr. David Spellmeyer, Chiron Corporation, Emeryville, CA 94608; voice: (510)601-3313; fax: (510)601-3360; email: davids@chiremv.chiron.co Building the Bridge Between Computational Chemistry and Process Modeling - Dr. Rick Ross, PPG Industries, P.O. Box 9, Allison Park, PA 15101; Voice (412)492-5359; email: rickr@ppg.scripps.edu. General Computational Chemistry - Poster and/or Oral Sessions - Dr. George R. Famini, US Army Edgewood Research, Development and Engineering Center, SCBRD-ASI, APG, MD 21010; voice: (410)671-2552; Fax: (410)671-5373; email: grfamini@apgea.army.mil. 23-Apr-96 From mao@csb0.IPC.PKU.EDU.CN Mon Sep 23 11:31:00 1996 Received: from csb0.IPC.PKU.EDU.CN for mao@csb0.IPC.PKU.EDU.CN by www.ccl.net (8.7.5/950822.1) id KAA16106; Mon, 23 Sep 1996 10:55:14 -0400 (EDT) Received: by csb0.IPC.PKU.EDU.CN (920330.SGI/940406.SGI.AUTO) for CHEMISTRY@www.ccl.net id AA18742; Mon, 23 Sep 96 22:52:07 -0700 Date: Mon, 23 Sep 1996 22:52:06 -0700 (PDT) From: Fenglou Mao To: "CHEMISTRY@www.ccl.net" Subject: G94 released software Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear netters: I will compute some problems, I want to use the software G94.But I can't find it in my SGI computer. Do someone know where I can get the software released? Please tell me the FTP server's name or address. I will be very grateful for your help. Best wishs. Sincerely Yours, FengLou Mao ******************************* ADD:Mr. FengLou Mao Peking University BeiJing P.R.China Tel:86-10-62751490 Fax:86-10-62751725 From owner-chemistry@ccl.net Mon Sep 23 12:31:00 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.5/950822.1) id LAA17851; Mon, 23 Sep 1996 11:39:28 -0400 (EDT) Received: from mallard.duc.auburn.edu for newhoir@duc.auburn.edu by bedrock.ccl.net (8.7.6/950822.1) id LAA14791; Mon, 23 Sep 1996 11:39:25 -0400 (EDT) Received: by mallard.duc.auburn.edu (SMI-8.6/SMI-SVR4) id KAA24320; Mon, 23 Sep 1996 10:39:22 -0500 Date: Mon, 23 Sep 1996 10:39:22 -0500 From: newhoir@duc.auburn.edu (Irene Newhouse) Message-Id: <199609231539.KAA24320@mallard.duc.auburn.edu> To: chemistry@ccl.net Subject: CCL:G: Structures from pot. scan checkpoints Could someone please let me know how to extract desired structures from the checkpoint files generated in a potential surface scan with Gaussian94? Thanks! Irene Newhouse From jochen@sunserver1.rz.uni-duesseldorf.de Mon Sep 23 12:39:12 1996 Received: from sirene.rz.uni-duesseldorf.de for jochen@sunserver1.rz.uni-duesseldorf.de by www.ccl.net (8.7.5/950822.1) id MAA18914; Mon, 23 Sep 1996 12:18:35 -0400 (EDT) Received: from sunserver1.rz.uni-duesseldorf.de by sirene.rz.uni-duesseldorf.de with SMTP (PP) id <15513-0@sirene.rz.uni-duesseldorf.de>; Mon, 23 Sep 1996 18:17:44 +0000 Received: from localhost by sunserver1.rz.uni-duesseldorf.de (SMI-8.6/SMI-SVR4) id SAA25530; Mon, 23 Sep 1996 18:17:14 +0200 Date: Mon, 23 Sep 1996 18:17:14 +0200 (MET DST) From: jochen X-Sender: jochen@sunserver1 To: Computational Chemistry List Subject: Summary: geometry optimizations of isotopic substituted molecules Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters, Some days ago I asked the following question: > recently a friend came up with the problem of geometry optimization of > deuterated species. He is expecting slighthly different geometries for > the different isotopic species that are not only originated in the > zero point vibrations. > Packages like GAMESS and gaussian only use isotopic information in > frequency calculations. Are there any other packages that use this > information in geometry optimizations. The answers are: 1.) From: Jan Hrusak Bin Chemiker und aufgewachsen mit Massenspektrometrie, also habe enormes interesse an den isotopenmarkierten verbindungen. ZPVE ist recht OK obwohl auch eine geometrie- optimiereung mit einschluss dieser nicht trivial ist. Aber der elektronische anteil bleibt unberuecksichtigt. Wie gesagt bin ich nicht in der teilchenphysik sehr bewandert aber es hat mich schon immer fasziniert dass das H anderes IP hat wie D. Da es aber ein zweitelchenproblem ist laesst sich es wohl loesen in dem man die korrekte reduzierte masse einsetzt. Interssant in diesem zusammenhang ist auch dass das IP von H im nicht-BO fall nicht genau 0.5 Hartree ist, sondern muss den faktor Me+MH/MeMH korigiert werden. Fur groesere systeme als H wird es noch schwieriger. Ich glaube nicht, dass das angesprochen problem fuer andere systeme als H2+, HD+ und D2+ im moment zu loesen ist. ---------------------------------------------------------------------------- 2.) From FREDHAG@VM.CC.PURDUE.edu Mon Sep 9 13:58:09 1996 First, I don't know your answer. But the reason GAMESS and Gaussian do not include isotopic discrimination is because most (if not all) of the levels of theory in the packages only include e-e, e-n, and n-n interactions through nuclear charge, i.e., not including nuclear mass effects. I believe from my advanced courses, that these effects are much smaller than ZPE effects that you can take into consideration, perhaps even smaller in effect than the accuracy of the rest of the Hamiltonian. ---------------------------------------------------------------------------- 3.) From zuilhof@chem.chem.rochester.edu Mon Sep 9 18:28:25 1996 Dear Jochen, Due to the Born-Opperheimer approximation used in most quentum chemical packages, the geometry of isotopically subsituted compounds will be identical to the parent species. However, sometimes the variations in bond lengths that do in fact occur in nature due to isotopic subsitutions do in fact influence experiments. We bumped into such a phenomenon while studying the ESR properties of isotopically substituted pyrenes, and rationalized the experimental data using the differences in bond length between C-H and C-D bonds. This was confirmed by quantum chemical computations, in which we fixed the C-D bond length to be a certain fraction shorter than the optimized C-H bond length, and re-optimized the whole system again with this fixation of the C-D bond length. Reference: Perturbation of spin density distribution due to deuterium substitution Zuilhof, H; Lodder, G.; Van Mill, R.P.; Mulder, P.P.J.; Kage, D.E.; Reiter, R.C.; Stevenson, C.D. - J. Phys. Chem. 1995, 99, 3461-3464. ---------------------------------------------------------------------------- 4.) From: schrecke@zinc.chem.ucalgary.ca this is an interesting question: please summarize! ---------------------------------------------------------------------------- 5.) From: Jens Spanget-Larsen There are subtle differences in the electronic structures of atomic hydrogen and deuterium. Due to the increased mass of the deuterium nucleus, the reduced mass of the electron-nuclear two-body system is slightly larger for deuterium than for hydrogen. This means that the electronic energy is slightly more negative, corresponding to slightly larger ionization energy, and the orbital wavefunction is slightly more contracted for deuterium. I would guess that the equilibrium structures for the diatomic molecules corresponds to a slightly shorter bond length for di-deuterium, D-D, than for di-hydrogen, H-H. However, I have not looked up the literature for experimental data (Gmelin?). In any case, the difference should be really small. Factors due to the different zero point energy levels are probably more significant, and I have not heard of any computational package that treats the electronic systems of H and D differently. ---------------------------------------------------------------------------- Thanks to everybody who responded, Jochen +-----------------------------------------------------------------------+ | Jochen Kuepper | | | | Heinrich-Heine-Universitaet Duesseldorf jochen@uni-duesseldorf.de | | Institut fuer Physikalische Chemie I | | Universitaetsstrasse 26.43.02.29 phone ++49-211-8113681 | | 40225 Duesseldorf fax ++49-211-8115195 | | Germany | | | +-----------------------------------------------------------------------+ From zfeng@mdh.bim.anl.gov Mon Sep 23 13:31:00 1996 Received: from mdh.bim.anl.gov for zfeng@mdh.bim.anl.gov by www.ccl.net (8.7.5/950822.1) id MAA19063; Mon, 23 Sep 1996 12:32:45 -0400 (EDT) Received: from pyp.bim.anl.gov (pyp.bim.anl.gov [146.139.36.45]) by mdh.bim.anl.gov (8.6.11/8.6.11) with ESMTP id QAA18836 for ; Mon, 23 Sep 1996 16:32:45 GMT Received: from pyp.bim.anl.gov (localhost [127.0.0.1]) by pyp.bim.anl.gov (8.6.11/8.6.11) with SMTP id QAA00698 for ; Mon, 23 Sep 1996 16:32:43 GMT Message-Id: <199609231632.QAA00698@pyp.bim.anl.gov> Date: Mon, 23 Sep 96 11:32:43 -0500 Sender: zfeng@mdh.bim.anl.gov From: Zhou Feng X-Mailer: Mozilla 1.12IS (X11; I; IRIX 5.3 IP22) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: (no subject) X-URL: http://www.ccl.net/ccl/welcome.text.html#3 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Hi: I am looking for a reasonably accurate implicit solvation energy program which can do some simple energy minimization or low temperature MD to predict the energies of a biomoleular system, there are moderate conformational changes which has to be predicted along with the energies. IS there anyone who can give me some suggestions? We have CHARMM & Delphi, but we need to do some dynamics with the implicit solvent model. Feng Zhou Argonne National Lab. From iok@tpci.eie.ariadne-t.gr Mon Sep 23 13:37:24 1996 Received: from tpci.eie.ariadne-t.gr for iok@tpci.eie.ariadne-t.gr by www.ccl.net (8.7.5/950822.1) id NAA22056; Mon, 23 Sep 1996 13:11:22 -0400 (EDT) Message-Id: <199609231711.NAA22056@www.ccl.net> Received: by tpci.eie.ariadne-t.gr (16.8/16.2) id AA02033; Mon, 23 Sep 96 20:25:45 +0300 From: plucky Subject: Yet another version of RasMol.NS To: CHEMISTRY@www.ccl.net Date: Mon, 23 Sep 96 20:25:44 EET Mailer: Elm [revision: 70.30] Dear All, Another port of RasMol for NextStep is out. Version number is 1.2. Ftp it from 143.233.144.10==apollon.servicenet.ariadne-t.gr If someone is kind enough please put it (if you know how) to CCL so that people can get it faster than they could if there were to log here. Our line is slow. So please check CCL as well. Some things are better in this version. Feedback is something I would appreciate. This version is close to 2.6 by Sayle but not quite. It has plenty of buttons to play with. Adjust cylinder (of bond) radius, sphere radius (also sphere radius is different by some linear function for different Z), unitcell line width. If you see my code you get the picture how to fudge the porting code. That is about it for the time being. I apologize for the taken bandwidth. Have a nice day all of you. -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= -=-=-=-=-=-=-=-= Ioannis Koutselas (to be Ph.D.) ------------------------------- ---------------- Dept of Theoretical and Physical Chemistry National Hellenic Research Foundation Vassileos Constantine 48, 11635 Athens, Hellas (or Greece) From smb@smb.chem.niu.edu Mon Sep 23 14:31:05 1996 Received: from mp.cs.niu.edu for smb@smb.chem.niu.edu by www.ccl.net (8.7.5/950822.1) id NAA23078; Mon, 23 Sep 1996 13:33:25 -0400 (EDT) Received: from cz2.chem.niu.edu by mp.cs.niu.edu with SMTP id AA21140 (5.67b/IDA-1.5 for <@mp.cs.niu.edu.chem.niu.edu:CHEMISTRY@www.ccl.net>); Mon, 23 Sep 1996 12:33:23 -0500 Received: from cz.chem.niu.edu by cz2.chem.niu.edu via SMTP (920330.SGI/890607.SGI) (for @mp.cs.niu.edu.chem.niu.edu:CHEMISTRY@www.ccl.net) id AA24128; Mon, 23 Sep 96 10:59:56 -0500 Received: from smb.chem.niu.edu by cz.chem.niu.edu via SMTP (920330.SGI/890607.SGI) (for @cz2.chem.niu.edu:CHEMISTRY@www.ccl.net) id AA08955; Mon, 23 Sep 96 10:59:55 -0500 Received: by smb.chem.niu.edu (940816.SGI.8.6.9/940406.SGI) for CHEMISTRY@www.ccl.net id LAA18154; Mon, 23 Sep 1996 11:08:26 -0500 Date: Mon, 23 Sep 1996 11:08:26 -0500 From: smb@smb.chem.niu.edu (Steven Bachrach) Message-Id: <199609231608.LAA18154@smb.chem.niu.edu> To: CHEMISTRY@www.ccl.net Subject: Re: CCL:COMP Schedule for SF George should have noted that all current information on the Programs for the Computers in Chemistry Division are available at the division's we page: http://hackberry.chem.niu.edu/COMP Steve Steven Bachrach Department of Chemistry Northern Illinois University DeKalb, Il 60115 Phone: (815)753-6863 smb@smb.chem.niu.edu Fax: (815)753-4802 From shenkin@still3.chem.columbia.edu Mon Sep 23 14:38:11 1996 Received: from mailhub.cc.columbia.edu for shenkin@still3.chem.columbia.edu by www.ccl.net (8.7.5/950822.1) id OAA23555; Mon, 23 Sep 1996 14:23:08 -0400 (EDT) Received: from still3.chem.columbia.edu (still3.chem.columbia.edu [128.59.112.36]) by mailhub.cc.columbia.edu (8.7.5/8.7.3) with SMTP id OAA02651; Mon, 23 Sep 1996 14:23:08 -0400 (EDT) Received: by still3.chem.columbia.edu (950413.SGI.8.6.12/930416.SGI.AUTO) id OAA15190; Mon, 23 Sep 1996 14:23:07 -0400 From: "Peter Shenkin" Message-Id: <9609231423.ZM15188@still3.chem.columbia.edu> Date: Mon, 23 Sep 1996 14:23:06 -0400 In-Reply-To: zfeng@enzyme.bim.anl.gov (Zhou Feng) "Re: CCL: Implicit Solvation" (Sep 23, 1:22pm) References: <9609231822.AA18028@enzyme.bim.anl.gov> X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: zfeng@enzyme.bim.anl.gov (Zhou Feng), zfeng@mdh.bim.anl.gov Subject: Re: CCL: Implicit Solvation Cc: CHEMISTRY@www.ccl.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii On Sep 23, 1:22pm, Zhou Feng wrote: > Subject: Re: CCL: Implicit Solvation > It does almost everything, I see from Web site. Leaps buildings in a single bound.... :-) -P. -- ****** ********** In Memoriam, Bill Monroe, 1911 - 1996 ****************** * Peter S. Shenkin, Chemistry, Columbia U., 3000 Broadway, Mail Code 3153,* ** NY, NY 10027; shenkin@columbia.edu; (212)854-5143; FAX: 678-9039 *** MacroModel WWW page: http://www.cc.columbia.edu/cu/chemistry/mmod/mmod.html From shenkin@still3.chem.columbia.edu Mon Sep 23 14:42:35 1996 Received: from mailhub.cc.columbia.edu for shenkin@still3.chem.columbia.edu by www.ccl.net (8.7.5/950822.1) id OAA23535; Mon, 23 Sep 1996 14:18:17 -0400 (EDT) Received: from still3.chem.columbia.edu (still3.chem.columbia.edu [128.59.112.36]) by mailhub.cc.columbia.edu (8.7.5/8.7.3) with SMTP id OAA00757; Mon, 23 Sep 1996 14:18:17 -0400 (EDT) Received: by still3.chem.columbia.edu (950413.SGI.8.6.12/930416.SGI.AUTO) id OAA15150; Mon, 23 Sep 1996 14:18:15 -0400 From: "Peter Shenkin" Message-Id: <9609231418.ZM15148@still3.chem.columbia.edu> Date: Mon, 23 Sep 1996 14:18:15 -0400 In-Reply-To: Zhou Feng "CCL:(no subject)" (Sep 23, 11:32am) References: <199609231632.QAA00698@pyp.bim.anl.gov> X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: Zhou Feng Subject: Re: CCL: Implicit Solvation Cc: CHEMISTRY@www.ccl.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii On Sep 23, 11:32am, Zhou Feng wrote: > Subject: CCL:(no subject) > Hi: > > I am looking for a reasonably accurate implicit solvation energy program which > can do some simple energy minimization or low temperature MD to predict the > energies of a biomoleular system, there are moderate conformational changes > which has to be predicted along with the energies. IS there anyone who can give > me some suggestions? We have CHARMM & Delphi, but we need to do some dynamics > with the implicit solvent model. MacroModel/BatchMin has GB/SA solvation, which will probably do what you need. See the URL below for info. on cost and availability, and also for literature references to GB/SA. -P. -- ****** ********** In Memoriam, Bill Monroe, 1911 - 1996 ****************** * Peter S. Shenkin, Chemistry, Columbia U., 3000 Broadway, Mail Code 3153,* ** NY, NY 10027; shenkin@columbia.edu; (212)854-5143; FAX: 678-9039 *** MacroModel WWW page: http://www.cc.columbia.edu/cu/chemistry/mmod/mmod.html From korkin@qtp.ufl.edu Mon Sep 23 14:47:17 1996 Received: from qtp.ufl.edu for korkin@qtp.ufl.edu by www.ccl.net (8.7.5/950822.1) id NAA23234; Mon, 23 Sep 1996 13:46:55 -0400 (EDT) Received: from white7.qtp.ufl.edu by qtp.ufl.edu (SMI-8.6/SMI-SVR4) id NAA14694; Mon, 23 Sep 1996 13:43:39 -0400 From: "Anatoli Korkin" Received: by white7.qtp.ufl.edu (SMI-8.6/4.11) id MAA14280; Mon, 23 Sep 1996 12:45:20 -0500 Date: Mon, 23 Sep 1996 12:45:20 -0500 Message-Id: <199609231745.MAA14280@white7.qtp.ufl.edu> To: mao@csb0.IPC.PKU.EDU.CN Subject: Re: CCL:G:G94 released software Cc: CHEMISTRY@www.ccl.net, info@gaussian.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Content-MD5: phYNOhTGmGXgoIrRxO2LXg== > > > Dear netters: > I will compute some problems, I want to use the software G94.But I > can't find it in my SGI computer. Do someone know where I can get the > software released? Please tell me the FTP server's name or address. > I will be very grateful for your help. > Best wishs. > > Sincerely Yours, > > FengLou Mao > ******************************* > ADD:Mr. FengLou Mao > Peking University > BeiJing > P.R.China > Tel:86-10-62751490 > Fax:86-10-62751725 > > > Hi! If you a son of MAO, you might get it free :-) ... but it is worth to contact info@gaussian.com anyway. AK > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: mao@csb0.IPC.PKU.EDU.CN > -- Original Sender From: Address: mao@csb0.IPC.PKU.EDU.CN > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > From zfeng@enzyme.bim.anl.gov Mon Sep 23 15:31:01 1996 Received: from enzyme.bim.anl.gov for zfeng@enzyme.bim.anl.gov by www.ccl.net (8.7.5/950822.1) id OAA23796; Mon, 23 Sep 1996 14:45:53 -0400 (EDT) Received: by enzyme.bim.anl.gov (AIX 3.2/UCB 5.64/4.03) id AA18071; Mon, 23 Sep 1996 13:46:59 -0500 Date: Mon, 23 Sep 1996 13:46:59 -0500 From: zfeng@enzyme.bim.anl.gov (Zhou Feng) Message-Id: <9609231846.AA18071@enzyme.bim.anl.gov> To: chemistry@www.ccl.net, robert@pauli.utmb.edu, zfeng@mdh.BIM.ANL.GOV Subject: Re: CCL:(no subject) Dear RObert: We are working on RNA systems. DOes Fantom provide accurate solvation energy potential for ribozymes as well? How does it calculate solvent effects? If it works well for RNAs, it would be very interesting for us. Feng From robert@pauli.utmb.edu Mon Sep 23 15:36:29 1996 Received: from nmr.utmb.edu for robert@pauli.utmb.edu by www.ccl.net (8.7.5/950822.1) id OAA23663; Mon, 23 Sep 1996 14:36:52 -0400 (EDT) Received: from pauli.utmb.edu by nmr.utmb.edu via SMTP (931110.SGI/930416.SGI.AUTO) for chemistry@www.ccl.net id AA22065; Mon, 23 Sep 96 13:41:54 -0600 Received: (from robert@localhost) by pauli.utmb.edu (950413.SGI.8.6.12/950213.SGI.AUTOCF) id NAA10063; Mon, 23 Sep 1996 13:36:11 -0500 From: "Robert Fraczkiewicz" Message-Id: <9609231336.ZM10061@pauli.utmb.edu> Date: Mon, 23 Sep 1996 13:36:11 -0500 In-Reply-To: Zhou Feng "CCL:(no subject)" (Sep 23, 11:32am) References: <199609231632.QAA00698@pyp.bim.anl.gov> X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: Zhou Feng , chemistry@www.ccl.net Subject: Re: CCL:(no subject) Cc: werner@nmr.utmb.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii On Sep 23, 11:32am, Zhou Feng wrote: > Subject: CCL:(no subject) > Hi: > > I am looking for a reasonably accurate implicit solvation energy program which > can do some simple energy minimization or low temperature MD to predict the > energies of a biomoleular system, there are moderate conformational changes > which has to be predicted along with the energies. IS there anyone who can give > me some suggestions? We have CHARMM & Delphi, but we need to do some dynamics > with the implicit solvent model. > > Feng Zhou > Argonne National Lab. An excellent program FANTOM written by Werner Braun and co-workers can do that. Please, refer to the following web page for information: http://www.hbcg.utmb.edu/faculty/braun/fm_home.html FANTOM is free of charge for academic users. Regards, Robert Fraczkiewicz, University of Texas Medical Branch From MAR@ecs.umass.edu Mon Sep 23 15:41:18 1996 Received: from ecs.umass.edu for MAR@ecs.umass.edu by www.ccl.net (8.7.5/950822.1) id OAA23773; Mon, 23 Sep 1996 14:44:34 -0400 (EDT) Received: from ECS.UMASS.EDU by ECS.UMASS.EDU (PMDF V5.0-7 #6523) id <01I9TLFMGAS08WWBMS@ECS.UMASS.EDU> for chemistry@www.ccl.net; Mon, 23 Sep 1996 14:44:04 -0500 Date: Mon, 23 Sep 1996 14:44:04 -0500 From: Perry Mar Subject: Summary: Becke 1988 exchange potential To: chemistry@www.ccl.net Message-id: <01I9TLFMHWNM8WWBMS@ECS.UMASS.EDU> X-VMS-To: IN%"chemistry@www.ccl.net" MIME-version: 1.0 Content-transfer-encoding: 7BIT Here is a summary of the answers I have received to my query about the Becke 1988 nonlocal exchange potential. Thanks to everyone who responded. I posted the following query on September 12, 1996. > I am seeking the formulas for the Becke 1988 nonlocal exchange > potential for the nonlocal exchange energy functional proposed in > the paper > > Becke, A. D., "Density-Functional Exchange-Energy Approximation > with Correct Asymptotic Behavior," Phys. Rev. A, 38(6), 3098-3100 > (1988). To summarize the answer, this potential has been published in Fan, Liangyou and Ziegler, Tom, "The Influence of Self-Consistency on Nonlocal Density Functional Calculations," J. Chem. Phys., 94(9), 6057--6063 (1991). An asymptotic form of the potential is given in Engel, E., Chevary, J. A., Macdonald, L. D., and Vosko, S. H., "Asymptotic Properties of the Exchange Energy Density and the Exchange Potential of Finite Systems: Relevance for Generalized Gradient Approximations," Z. Phys. D, 23, 7-14 (1992). A form for spherically symmetric systems is given in Gritsenko, O. V., Cordero, N. A., Rubio, A., Balbas, L. C., and Alonso, J. A., "Weighted-Density Exchange and Local-Density Coulomb Correlation Energy Functionals for Finite Systems: Application to Atoms," Phys. Rev. A, 48(6), 4197-4212 (1993). A summary of the responses I received follows. ***************************************************************** From Liang Lou at liang@wavefun.com: 12-SEP-1996 18:20:59.72 From: IN%"liang@wavefun.com" To: IN%"MAR@ecs.umass.edu" "Perry Mar" CC: Subj: RE: CCL:Becke 1988 nonlocal exchange potential One paper in a series published by Ziegler's group at Calgary L. Fan and T. Ziegler, JCP 6057 (1991) contains specifically the expansion you are seeking for. Regards, Liang Lou *********************** From Richard Hall at R.Hall@mcc.ac.uk: 13-SEP-1996 03:56:18.07 From: IN%"mbdtsrh@afs.mcc.ac.uk" "mbdtsrh" To: IN%"mar@ecs.umass.edu" CC: Subj: becke functional I'm not *exactly* sure if this is the functional you require, but a paper by Johnson Gill and Pople gives the formula for a number of functionals and their first derivatives. The reference is B.G.Johnson, P.M.W.Gill and J.A.Pople, J.Chem.Phys. 98 p.5612 (1993) hope this helps. regards, Richard -- ------------------------------------------------------------------------ Richard Hall 1) Computational Chemistry Support email: R.Hall@mcc.ac.uk Manchester Computing tel: (0161) 275 7179 University of Manchester Manchester, UK, M13 9PL 2) Department of Chemistry email: Richard.Hall@man.ac.uk University of Manchester tel: (0161) 275 4686 Manchester, UK, M13 9PL ------------------------------------------------------------------------ *********************** From Reinaldo at pis_diez@nahuel.biol.unlp.edu.ar: 13-SEP-1996 11:16:20.75 From: IN%"pis_diez@nahuel.biol.unlp.edu.ar" To: IN%"MAR@ecs.umass.edu" "Perry Mar" CC: Subj: RE: CCL:Becke 1988 nonlocal exchange potential Try E Engel, JA Chevary, LD MacDonald and SH Vosko, Z Phys D 23 (1992) 7 and OV Gritsenko, NA Cordero, A Rubio, LC Balbas and JA Alonso, PRA 48 (1993) 4197. REgards, Reinaldo ***************************************************************** Sincerely, Perry Mar Department of Chemical Engineering E-mail: mar@ecs.umass.edu University of Massachusetts Phone: (413) 545-0770 Amherst, MA 01003-3110, USA Fax: (413) 545-1647 From chpajt@bath.ac.uk Mon Sep 23 16:31:03 1996 Received: from goggins.bath.ac.uk for chpajt@bath.ac.uk by www.ccl.net (8.7.5/950822.1) id QAA24534; Mon, 23 Sep 1996 16:06:59 -0400 (EDT) Received: from bath.ac.uk (actually host midge.bath.ac.uk) by goggins.bath.ac.uk with SMTP (PP); Mon, 23 Sep 1996 21:06:47 +0100 Date: Mon, 23 Sep 1996 21:06:43 +0100 (BST) From: A J Turner To: jochen cc: Computational Chemistry List Subject: Re: CCL:G:Summary: geometry optimizations of isotopic substituted molecules In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi! I am sorry not to have replied firt time around. Clearly the anharmon nature of the c-d vibration will make the c-d bond shorter when temp > 0 K. The best way of truely finding this owuld be to get the mean bond length from a dynamics trajectory. Is is easly done - but the cost is prohibitive for large theory or large molecules. If you are looking at super computers and three heavies I guess MP2 is well within reach. Hope it helps Alex ------------------------------------------------------------------- |Alexander J Turner |A.J.Turner@bath.ac.uk | |Post Graduate |http://www.bath.ac.uk/~chpajt/home.html| |School of Chemistry |+144 1225 8262826 ext 5137 | |University of Bath | | |Bath, Avon, U.K. |Field: QM/MM modeling | ------------------------------------------------------------------- From rok@UDel.Edu Mon Sep 23 17:31:03 1996 Received: from copland.udel.edu for rok@UDel.Edu by www.ccl.net (8.7.5/950822.1) id QAA24786; Mon, 23 Sep 1996 16:35:38 -0400 (EDT) Received: from chopin.udel.edu (chopin.udel.edu [128.175.13.17]) by copland.udel.edu (8.7.6/8.7.3) with SMTP id QAA20951 for ; Mon, 23 Sep 1996 16:35:26 -0400 (EDT) Date: Mon, 23 Sep 1996 16:35:25 -0400 (EDT) From: Robert Konecny To: CHEMISTRY@www.ccl.net Subject: g94 CASSCF Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear ccl, I would like to find a conical intersection between singlet and triplet states using CASSCF in g94. What keyword do I use to specify a triplet as the "state of interest" in CASSCF? NRoot=3 (or 4) just gives me excited singlets. This is the route card I've used: CASSCF(4,4,NRoot=3,Slater) Gen Pop=NaturalOrb Opt=Conical SCF=Conven Guess=Read So how do I tell g94 to search for a conical intersection between singlet (ground) state and triplet (excited) state? Thanks in advance, Robert rok@udel.edu From feblm@csd.uwm.edu Mon Sep 23 22:31:05 1996 Received: from batch1.csd.uwm.edu for feblm@csd.uwm.edu by www.ccl.net (8.7.5/950822.1) id WAA29062; Mon, 23 Sep 1996 22:10:32 -0400 (EDT) Received: from alpha1.csd.uwm.edu (feblm@alpha1.csd.uwm.edu [129.89.169.1]) by batch1.csd.uwm.edu (8.7.6/8.6.8) with ESMTP id VAA08477 for ; Mon, 23 Sep 1996 21:10:32 -0500 (CDT) Received: (feblm@localhost) by alpha1.csd.uwm.edu (8.7.6/8.6.8) id VAA21266; Mon, 23 Sep 1996 21:10:32 -0500 (CDT) Date: Mon, 23 Sep 1996 21:10:31 -0500 (CDT) From: Patricia M Fulmer To: CHEMISTRY@www.ccl.net Cc: feblm@alpha1.csd.uwm.edu Subject: FAD in MOPAC Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Friends, Suppose I would like a quick estimate of the partial charges on flavin adenine dinucleotide (FAD) using MOPAC. What keywords would you recomend? This poor molecule disociates with words like PM3 PULAY MMOK T=7200 XYZ Will post replys to the list. Thanks in advance.