From DAFNAN@vms.huji.ac.il Sun Apr 2 06:40:55 1995 Received: from VMS.HUJI.AC.IL for DAFNAN@vms.huji.ac.il by www.ccl.net (8.6.10/930601.1506) id GAA01082; Sun, 2 Apr 1995 06:22:11 -0400 Received: by HUJIVMS (HUyMail-V7b); Sun, 02 Apr 95 13:23:48 +0200 Received: by HUJIVMS (HUyMail-V7b); Sun, 02 Apr 95 11:01:51 +0200 Date: Sun, 2 Apr 95 10:56 +0200 Message-id: <02040095105631@HUJIVMS> From: To: chemistry@ccl.net MIME-version: 1.0 Content-type: Text/plain; charset=US-ASCII Content-Transfer-Encoding: 7BIT Subject: Summary of conformational analysis fortran program Dear Netters; Sorry for the time it took me to summarize the responses that I got concerning conformation analysis fortran programs, but better late than never. Once again, I thank the poeple who answered me. Best Wishes, Dafna Nathan. The original message was: >Subject: CCL:Conformation Analysis > > Dear CCL'ers; > > I'm looking for a Fortran program that compares the >similarity of two different conformations and gives their >RMS deviation. Does anybody out there know if there's a public >domain program of this kind, and what is its method for comparing >the conformations? > > Any help would be greatly appreciated. > > Sincerely, > Daffy Nathan > Hebrew University of Jerusalem, > Israel > ----------------------------------------------------------------- Date: Mon, 20 Mar 95 08:40:23 CST From: mliebman@amoco.com (Michael N. Liebman) Subject: Re: CCL:Conformation Analysis Are you comparing small molecules or proteins? the subject of structure comparison by superposition is not a simple anser of computing an rms. Michael N. Liebman, Ph. D. Director, Bioinformatics Vysis, Inc. 3100 Woodcreek Drive Downers Grove, Illinois 60515 (708) 271-7190 office (708) 271-7008 fax mliebman@amoco.com ------------------------------------------------------------------ Date: Mon, 20 Mar 95 09:36:29 -0500 From: carlos@extreme.bio.cornell.edu (Carlos Faerman) Subject: Re: CCL:Conformation Analysis Talk to Dr. Ron Elber. He is now at your University and has a code to do that (the name of the global code is MOIL but he has subroutines to analyze the RMS. Carlos ------------------------------------------------------------------- From: valery-g@DCL.CO.IL (Dr. Golender Valery) Subject: Conformer similarity Cc: valery@actcom.co.il Dear Daffy, I read your posting on CCl and want to inform you that our company, DCL Systems International located in Herzlia, is developing commercial software for drug design, molecular modeling and chemical databases. Our Apex-3D system integrated into InsightII of Biosym has a conformer clustering module that solves your problem. Hebrew University has Apex-3D licenses in the new computational class. Please let me know in what school and with whom are you working and I can help you to use the programm. Sincerely, Valery Golender, Ph.D. Director, Chemical Software DCL Systems International Ltd 20 Galgalei Haplada St. POB 544 Herzlia 46105 ISRAEL Tel: + 972-9-584-684 Fax: + 972-9-543-917 E-mail: valery-g@dcl.co.il, valery@actcom.co.il ----------------------------------------------------------------- From: kcousins@wiley.csusb.edu (Kimberley Cousins) Subject: conformers Date: Mon, 20 Mar 1995 17:42:06 -0800 (PST) You might check both the discussion and software archives on CCL. I believe that this topic has been discussed recently (within last six months). Kimberley Cousins Department of Chemistry California State University, San Bernardino 5500 University Parkway San Bernardino, CA 92407 (909)880-5391 kcousins@wiley.csusb.edu ---------------------------------------------------------------------- From: andrus@boc.ic.ee (Andrus Metsala) Subject: Re: CCL: Conformation Analysis Date: Tue, 21 Mar 95 15:59:43 estonia Dear Daffy Nathan: I am also interested in such kind of program. I would be greatly thankful if you could send me any information you probably will receive about this problem. Sincerely, ________________________________________________________________________ Andrus Metsala Phone: (3722)526510 Institute of Chemistry Fax: (3722)536371 Estonian Academy of E-Mail: andrus@boc.ic.ee Sciences Akadeemia tee 15 EE0026 Tallinn Estonia _________________________________________________________________________ From aiba@ir.phys.chem.ethz.ch Sun Apr 2 10:25:58 1995 Received: from bernina.ethz.ch for aiba@ir.phys.chem.ethz.ch by www.ccl.net (8.6.10/930601.1506) id KAA01886; Sun, 2 Apr 1995 10:25:21 -0400 Received: from volta (actually volta.ethz.ch) by bernina.ethz.ch with SMTP inbound; Sun, 2 Apr 1995 16:24:39 +0200 Date: Sun, 2 Apr 1995 16:24:08 +0200 Message-Id: <95040216240799@ir.phys.chem.ethz.ch> From: aiba@ir.phys.chem.ethz.ch (Ayaz Bakasov, Phys. Chem., ETH Zurich) To: chemistry@ccl.net Subject: compl. wave funct.; physicist&chemists X-VMS-To: smtp%"chemistry@ccl.net" X-VMS-Cc: AIBA On 2-APR-1995 Joe Landman wrote quite few things in response to my posting of 31-Mar-1995 about complex wave functions. Many issues were touched upon in his response, not only the complex wave functions in quantum chemistry. I am grateful to him for his response. I'll nevertheless try to push the discussion back to complex wave functions. However, a preliminary remark is in order. I am a theoretical physicist, with almost 9 years of postdoctoral experience, worked in statistical physics, quantum optics and quantum field theory, including high energy physics, in Moscow State University, in Joint Institute for Nuclear Research (Dubna, Russia, 1984-1990); in International Centre for Theoretical Physics (Trieste, Italy, 1990-1993); in Swiss Federal Institute of Technology (Zuerich, Switzerland, 1993->) Currently, I am working on parity violation effects in large (bio-)molecules - the effects which might be determined by electroweak interaction mediated by very massive Z_0 bosons. That's how a theoretical physicist (from high energy) MIGHT get into chemistry. Our paper summarizing the two years work within this project must reach a journal soon. Joe Landman assumed that my posting is a posting from a chemist (why?) - and he acted correspondingly. I think there is NO need to passionately defend physicists from a physicist or from a chemist; no one has any ground to think that he is inherently closer to physicists than others and can alone express the opinion of the whole of community of physicists. Just people have different PERSONAL OPINIONS. Yes, I cited textbooks, but my message was in response to posting where there was an EXPLICIT request to put references on. Then was there a need to write: "There is no need to haul out the bible (Landau and Lifschitz).." ?! Indeed, Joe Landman missed the beginning of discussion as he puts it himself: "Now I didnt see the beginning of this thread.." So, it's instrustive to look back. It's also meaningful to notice that I have put the words "fundamental physics" in quotation marks - I do NOT divide physics into fundamental and non-fundamental as perhaps seemed to Joe Landman. I also think that one should NOT to be discouraged even if one has "been told several times by "more energetic" colleagues that I work with the uninteresting dirt left over after all the interesting physics occurs... :-( " It's upto those "colleagues". Joe Landman, just go ahead with your own work and I sincerely wish you success. Now, let me please return to complex wave functions in quantum chemistry. The following statement by Joe Landman is either incomplete or wrong: > It is well known (or it should be by those > who use QM) that stationary states are real valued. They generally are NOT. Once more, the static electric potential is NOT the only one which is present in atom or molecule. If the citations of general character from Landau and Lifschitz are not sufficient let us consider the example - hydrogen atom. Two terms, as I wrote before must be included (apart from few others like Fermi contact interaction) to get just satisfactory agreement with experiment: the spin-orbit term and hypefine interaction term. Then the degeneracy is lifted and and the stationary states of hydrogen are necessarily COMPLEX wave functions. Otherwise one gets no agreement with experiment even within hundreds MHz. The point is, sorry for repeating myself, that those terms are large enough on the present experimental and computational accuracy scale. Even for molecules. I know it from my own work and from my own calculations. What I am forced to do is to make the perturbation theory "by hand", running my own code ON TOP of output of G92. This code refines the wave function, including into solution the spin-orbit interaction. The wave function gets COMPLEX after that. The ONLY thing I wish is that this ROUTINE procedure was done by G92 itself, as well as by any other ab initio package. I repeat - I am convinced that the compex wave functions are the NEAREST future of computational chemistry. Sincerely, Ayaz Bakasov. From kamal@univ-orleans.fr Sun Apr 2 13:26:00 1995 Received: from centre.univ-orleans.fr for kamal@univ-orleans.fr by www.ccl.net (8.6.10/930601.1506) id NAA03033; Sun, 2 Apr 1995 13:11:28 -0400 Received: from mailhost.univ-orleans.fr ([193.49.81.2]) by centre.univ-orleans.fr (8.6.9/8.6.9) with SMTP id TAA11345 for ; Sun, 2 Apr 1995 19:16:58 +0200 LD?Resent-Date: Sun, 2 Apr 1995 19:16:58 +0200 Message-Id: <199504021716.TAA11345@centre.univ-orleans.fr> X-Sender: kamal@mailhost.univ-orleans.fr X-Mailer: Windows Eudora Version 1.4.4 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Sun, 02 Apr 1995 18:01:03 +0100 To: chemistry@ccl.net From: kamal@univ-orleans.fr (Kamal Azzaoui) Subject: GROMOS PARAMETERS Hi Netters I try to make MD on glucose (beta and alpha conformers) in a water box using GROMOS force field. I am looking for anlge parameters of O-C-OH where C is the anomeric carbon. Does any one can help me ? Thanks in advance Kamal ******************************************************************** Kamal AZZAOUI LCBA Universite d'Orleans France Tel 38-41-70-42 email : kamal@centre.univ-orleans.fr ******************************************************************** From DAFNAN@vms.huji.ac.il Sun Apr 2 13:41:00 1995 Received: from VMS.HUJI.AC.IL for DAFNAN@vms.huji.ac.il by www.ccl.net (8.6.10/930601.1506) id NAA03457; Sun, 2 Apr 1995 13:30:21 -0400 Received: by HUJIVMS (HUyMail-V7b); Sun, 02 Apr 95 20:30:23 +0200 Received: by HUJIVMS (HUyMail-V7b); Sun, 02 Apr 95 11:01:51 +0200 Date: Sun, 2 Apr 95 10:56 +0200 Message-id: <02040095105631@HUJIVMS> From: To: chemistry@ccl.net MIME-version: 1.0 Content-type: Text/plain; charset=US-ASCII Content-Transfer-Encoding: 7BIT Subject: Summary of conformational analysis fortran program Dear Netters; Sorry for the time it took me to summarize the responses that I got concerning conformation analysis fortran programs, but better late than never. Once again, I thank the poeple who answered me. Best Wishes, Dafna Nathan. The original message was: >Subject: CCL:Conformation Analysis > > Dear CCL'ers; > > I'm looking for a Fortran program that compares the >similarity of two different conformations and gives their >RMS deviation. Does anybody out there know if there's a public >domain program of this kind, and what is its method for comparing >the conformations? > > Any help would be greatly appreciated. > > Sincerely, > Daffy Nathan > Hebrew University of Jerusalem, > Israel > ----------------------------------------------------------------- Date: Mon, 20 Mar 95 08:40:23 CST From: mliebman@amoco.com (Michael N. Liebman) Subject: Re: CCL:Conformation Analysis Are you comparing small molecules or proteins? the subject of structure comparison by superposition is not a simple anser of computing an rms. Michael N. Liebman, Ph. D. Director, Bioinformatics Vysis, Inc. 3100 Woodcreek Drive Downers Grove, Illinois 60515 (708) 271-7190 office (708) 271-7008 fax mliebman@amoco.com ------------------------------------------------------------------ Date: Mon, 20 Mar 95 09:36:29 -0500 From: carlos@extreme.bio.cornell.edu (Carlos Faerman) Subject: Re: CCL:Conformation Analysis Talk to Dr. Ron Elber. He is now at your University and has a code to do that (the name of the global code is MOIL but he has subroutines to analyze the RMS. Carlos ------------------------------------------------------------------- From: valery-g@DCL.CO.IL (Dr. Golender Valery) Subject: Conformer similarity Cc: valery@actcom.co.il Dear Daffy, I read your posting on CCl and want to inform you that our company, DCL Systems International located in Herzlia, is developing commercial software for drug design, molecular modeling and chemical databases. Our Apex-3D system integrated into InsightII of Biosym has a conformer clustering module that solves your problem. Hebrew University has Apex-3D licenses in the new computational class. Please let me know in what school and with whom are you working and I can help you to use the programm. Sincerely, Valery Golender, Ph.D. Director, Chemical Software DCL Systems International Ltd 20 Galgalei Haplada St. POB 544 Herzlia 46105 ISRAEL Tel: + 972-9-584-684 Fax: + 972-9-543-917 E-mail: valery-g@dcl.co.il, valery@actcom.co.il ----------------------------------------------------------------- From: kcousins@wiley.csusb.edu (Kimberley Cousins) Subject: conformers Date: Mon, 20 Mar 1995 17:42:06 -0800 (PST) You might check both the discussion and software archives on CCL. I believe that this topic has been discussed recently (within last six months). Kimberley Cousins Department of Chemistry California State University, San Bernardino 5500 University Parkway San Bernardino, CA 92407 (909)880-5391 kcousins@wiley.csusb.edu ---------------------------------------------------------------------- From: andrus@boc.ic.ee (Andrus Metsala) Subject: Re: CCL: Conformation Analysis Date: Tue, 21 Mar 95 15:59:43 estonia Dear Daffy Nathan: I am also interested in such kind of program. I would be greatly thankful if you could send me any information you probably will receive about this problem. Sincerely, ________________________________________________________________________ Andrus Metsala Phone: (3722)526510 Institute of Chemistry Fax: (3722)536371 Estonian Academy of E-Mail: andrus@boc.ic.ee Sciences Akadeemia tee 15 EE0026 Tallinn Estonia _________________________________________________________________________ From SCABANIS@KENTVM.KENT.EDU Sun Apr 2 14:41:01 1995 Received: from phem3 for SCABANIS@KENTVM.KENT.EDU by www.ccl.net (8.6.10/930601.1506) id OAA04188; Sun, 2 Apr 1995 14:35:07 -0400 Received: from KENTVM.KENT.EDU (MAILER@KENTVM) by phem3.acs.ohio-state.edu (PMDF V4.2-13 #5888) id <01HOV5QAWIZK98NYAP@phem3.acs.ohio-state.edu>; Sun, 2 Apr 1995 13:35:00 EST Received: from KENTVM.KENT.EDU (NJE origin SCABANIS@KENTVM) by KENTVM.KENT.EDU (LMail V1.2a/1.8a) with BSMTP id 9017; Sun, 2 Apr 1995 14:34:05 -0400 Date: Sun, 02 Apr 1995 14:17:30 -0400 (EDT) From: Steve Cabaniss Subject: Fall ACS Symposium To: Computational Chemistry List Message-id: <01HOV5QAWIZM98NYAP@phem3.acs.ohio-state.edu> Content-transfer-encoding: 7BIT Final call for papers for Fall ACS (Chicago) Symposium Molecular Modeling and Environmental Computational Chemistry Applications of molecular modeling and computational chemistry to environmental problems, including organic pollutants, trace metals, aqueous, terrestrial and atmospheric systems, structure and function, reaction mechanisms, property prediction and database design, toxicology Please submit abstracts on ACS abstract forms by April 15. The division of environmental chemistry also requests 4-page extended abstracts suitable for photo-reproduction and distribution in the division's pre-conference abstract book. Organizers- Steve Cabaniss, Dept. Chemistry, Kent State University, Kent, OH 44242, (216) 672-3731, FAX (216) 672-3816, SCabanis@KentVM.Kent.Edu Krish Namboodiri, National Environmental Supercomputing Center, Martin Marietta Technical Services, 135 Washington Ave., Bay City, MI 48708 nke@nesc.epa.gov (517) 894-7661 Sam Traina, School of Geophysical Sciences, Ohio State University, 2021 Coffey Rd., Columbus, OH 43210 (614) 292-9037 STraina@Magnus.ACS.Ohio-State.Edu In addition to research presentations, an introductory tutorial session and a concluding panel discussion are planned. The former will introduce novices to computational methods. The latter will examine potential developments, emphasizing current needs in environmental science and future capabilities of computational methods. Suggested questions for the panel discussion should be directed to the organizers by April 15. From longshot@chem.duke.edu Sun Apr 2 17:11:03 1995 Received: from duke.cs.duke.edu for longshot@chem.duke.edu by www.ccl.net (8.6.10/930601.1506) id QAA05066; Sun, 2 Apr 1995 16:58:21 -0400 Received: from london.chem.duke.edu by duke.cs.duke.edu (5.65/3.10G/4.1.3) id AA12893; Sun, 2 Apr 95 16:58:19 -0400 Received: from canada.chem.duke.edu by london.chem.duke.edu (5.64/1.19LP/4.1.1) id AA17234; Sun, 2 Apr 95 16:58:17 -0400 Received: by canada.chem.duke.edu (5.64/2.12L/4.1) id AA17190; Sun, 2 Apr 95 16:58:17 -0400 Date: Sun, 2 Apr 95 16:58:17 -0400 From: longshot@chem.duke.edu (Brad Isbister) Message-Id: <9504022058.AA17190@canada.chem.duke.edu> To: chemistry@ccl.net Subject: GROMOS PARAMETERS for carbohydrates Kamal Azzaoui is looking for parameters to use in carbohydrate MD. I have done similar studies using AMBER 4.0 and have used the parameters from SW Homans, Biochemistry, v29, 9110-9118 (1990). They should at least provide a starting point. You can also look at JW Brady, JACS, v111, 5155-5165 (1988) for an early paper on Glucose MD in water. -Brad ---------------------------------------------------------------------------- Brad Isbister Duke University E.J. Toone group Department of Chemistry longshot@chem.duke.edu DukeChem Home Page http://www.chem.duke.edu/~longshot http://www.chem.duke.edu/ From steve@carbo.chem.binghamton.edu Sun Apr 2 20:41:20 1995 Received: from carbo.chem.binghamton.edu for steve@carbo.chem.binghamton.edu by www.ccl.net (8.6.10/930601.1506) id TAA05759; Sun, 2 Apr 1995 19:18:12 -0400 Received: by carbo.chem.binghamton.edu (931110.SGI/931108.SGI.ANONFTP) for chemistry@ccl.net id AA10338; Sun, 2 Apr 95 19:04:42 -0400 Date: Sun, 2 Apr 1995 19:00:00 -0400 (EDT) From: Steven Schafer Subject: Q:Free Energy Perturbation To: chemistry@ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Can anyone recomend any good introductory books or articles on the topic of Free Energy Perturbation Theory? Thanks in advance, Steven Schafer S.U.N.Y. Binghamton Chemistry Department http://chemiris.chem.binghamton.edu:8080 Binghamton, New York USA From afj@chem.ucla.edu Sun Apr 2 22:11:07 1995 Received: from krypton.chem.ucla.edu for afj@chem.ucla.edu by www.ccl.net (8.6.10/930601.1506) id WAA06890; Sun, 2 Apr 1995 22:08:37 -0400 Received: (from afj@localhost) by krypton.chem.ucla.edu (8.6.9/8.6.9) id TAA24029; Sun, 2 Apr 1995 19:06:36 -0700 Date: Sun, 2 Apr 1995 19:06:36 -0700 From: Andy Jacobson Message-Id: <199504030206.TAA24029@krypton.chem.ucla.edu> To: CHEMISTRY@ccl.net, choic@gusun.acc.georgetown.edu Subject: Re: CCL:f2c ?? Here's the info on the f2c ftp site. Best of luck, -A.J. Theftp site has moved to ftp://netlib.att.com/netlib/f2c so you should now use ftp netlib.att.com name: anonymous password: binary cd netlib/f2c If you have trouble getting through, send email to ehg@research.att.com. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Andy Jacobson Dept. Pharmacology / Div. Nuclear Medicine and Biophysics CHS B2-086 UCLA School of Medicine Phone:310-641-1600x102 Los Angeles, CA 90024-6948 Fax: 310-641-1676 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~