From mitchell_t%frgen.dnet@sb.com Mon Nov 22 09:28:48 1993 Received: from phinet.smithkline.com for mitchell_t%frgen.dnet@sb.com by www.ccl.net (8.6.1/930601.1506) id IAA25983; Mon, 22 Nov 1993 08:36:46 -0500 From: Received: by phinet.smithkline.com (5.57/ULTRIX-az-040392); id AA12909; Mon, 22 Nov 93 08:33:39 -0500 Date: Mon, 22 Nov 93 08:33:38 -0500 Message-Id: <9311221333.AA12909@phinet.smithkline.com> To: "chemistry@ccl.net"%INET.dnet@sb.com Subject: INET::"chemistry-request@ccl.net" Status: R Hi -- does anyone out there have any MM parameters for oxime ethers? i.e. >C==N--O--C- systems. I have found MM2 parameters for oximes (JOC 53(14) 3313-3316 (1988)), but this does not include the ethers, particularly the N--O torsional barrier height. Thanks in advance for any help .. .. .. Tim Mitchell ---------------------------------------------------------------------------- | _____ ____ || SmithKline Beecham Pharmaceuticals Ltd | | / ___\\\\ _ \ || Brockham Park | | | |___ \\|_| | || Tim Mitchell (Comp. Chem.) Betchworth | | \____ \ | _ < || Phone: (0)737 36 4535 Surrey | | ____| | | |_| | || Fax: (0)737 36 4539 RH3 7AJ | | \_____/ |____/ || E-Mail: mitchell_t%frgen.dnet@sb.com U.K. | ---------------------------------------------------------------------------- From RAINER.MALLON@physik.uni-ulm.de Mon Nov 22 10:29:00 1993 Received: from netway.rz.uni-ulm.de for RAINER.MALLON@physik.uni-ulm.de by www.ccl.net (8.6.1/930601.1506) id JAA26537; Mon, 22 Nov 1993 09:56:53 -0500 Received: by netway.rz.uni-ulm.de (5.57/UniUlm-12.1.93-kg) id AA02583; Mon, 22 Nov 93 15:56:36 +0100 Message-Id: <9311221456.AA02583@netway.rz.uni-ulm.de> Received: from CIP_PHYSIK/HG_MAIL by cipserv1.physik.uni-ulm.de (Mercury 1.1); Mon, 22 Nov 93 15:56:38 GMT+2 To: chemistry@ccl.net From: "RAINER MALLON" Date: Mon, 22 Nov 1993 15:56:08 MET-1 Subject: analyzing molecular systems Priority: normal X-Mailer: WinPMail v1.0 (R1) Status: R Dear Netters ! Thinking about analyzing a given molecular system the first step that has to be made is representing it, so that it can be dealt with. Systems I think would be pretty much interesting to analyze are : 1. single molecules a. small molecules b. periodical molecules c. single polymeric molecule 2. molecular systems a. molecular systems made up of molecules of only one type b. molecular crystals c. a single molecule in an environment of others d. molecules in solvations Setting up a single molecule should be pretty easy. Theres an origin of construction and a global or serveral local coordinate systems. But when it comes to the description of molecular systems - how are they set up ? How is an environment of molecules represented ? What way are molecules in solvation described ? Greetings, RaMa. +---------------------------------+------------------------------------------+ | Rainer "RaMa" Mallon | mallon@main01.rz.uni-ulm.de | | University of Ulm, Germany | rainer.mallon@physik.uni-ulm.de | | Department of Applied Physics | +49-731-502-2941 | +---------------------------------+------------------------------------------+ From longshot@chem.duke.edu Mon Nov 22 15:28:52 1993 Received: from duke.cs.duke.edu for longshot@chem.duke.edu by www.ccl.net (8.6.1/930601.1506) id PAA00742; Mon, 22 Nov 1993 15:25:36 -0500 Received: from london.chem.duke.edu by duke.cs.duke.edu (5.65/3.7G/4.1.3) id AA28313; Mon, 22 Nov 93 15:25:33 -0500 Received: from canada.chem.duke.edu by london.chem.duke.edu (5.64/1.19LP/4.1.1) id AA06424; Mon, 22 Nov 93 15:25:32 -0500 Received: by canada.chem.duke.edu (5.64/2.12L/4.1) id AA16725; Mon, 22 Nov 93 15:25:30 -0500 Date: Mon, 22 Nov 93 15:25:30 -0500 From: longshot@chem.duke.edu (Brad Isbister) Message-Id: <9311222025.AA16725@canada.chem.duke.edu> To: chemistry@ccl.net Subject: hydrophobic/hydrophilic surface areas Hi: Does anyone out there know of programs to calculate solvent-accessable polar and non-polar surface areas? Preferably code for Sun workstations. Free or commercial, either is acceptable. Please e-mail replies, I will summarize. Thanks! Brad Isbister longshot@canada.chem.duke.edu Duke University Department of Chemistry Durham, NC 27705 From sverdlik@trinity.tc.cornell.edu Mon Nov 22 16:28:52 1993 Received: from trinity.tc.cornell.edu for sverdlik@trinity.tc.cornell.edu by www.ccl.net (8.6.1/930601.1506) id PAA01059; Mon, 22 Nov 1993 15:35:32 -0500 Received: by trinity.tc.cornell.edu (AIX 3.2/UCB 5.64/4.03) id AA52375; Mon, 22 Nov 1993 15:35:29 -0500 Message-Id: <9311222035.AA52375@trinity.tc.cornell.edu> To: chemistry@ccl.net Cc: Edward Nicolescu , Daniel Sverdlik Subject: MOPAC7 port to an RS/6000 From: Daniel Ira Sverdlik Reply-To: Daniel Ira Sverdlik Date: Mon, 22 Nov 93 15:35:29 -0500 Sender: sverdlik@trinity.tc.cornell.edu We are porting MOPAC7, from QCPE. to an RS/6000. When the code is executed on the provided test data, we get a segmentation fault. Any help in determining why we get the segmentation fault would be appreciated. In doing the port, a number of changes were necessitated: 1. In subroutine ef.f, flush was replaced by fflush. The common block FLUSH was renamed to FLUSHCOMMON. It was necessary to add the LOGICAL variable LIMSCF. The compilation line for mopac.exe has been accordingly modified by adding the -lc library. 2, In subroutine iter.f, the open statement was changed from OPEN(UNIT=6,FILE=GETNAM('FOR006'),ACCESS='APPEND') to OPEN(UNIT=6,FILE=GETNAM('FOR006'),STATUS='UNKNOWN') 3. In subroutine readmo.f, the calls to fdate and etime were replaced with calls to fdate_ and etime_. 4. The dimensions for ALLZ and ALLC in setupg.f had to be modified to (6,6,2). The common block is now COMMON/STO6G/ALLC(6,6,2),ALLZ(6,6,2). From raman@bioc01.uthscsa.edu Mon Nov 22 17:25:05 1993 Received: from thorin.uthscsa.edu for raman@bioc01.uthscsa.edu by www.ccl.net (8.6.1/930601.1506) id QAA02391; Mon, 22 Nov 1993 16:51:03 -0500 Received: from bioc01.uthscsa.edu by thorin.uthscsa.edu with SMTP; Mon, 22 Nov 1993 15:51:48 -0600 (CST) Received: by bioc01.uthscsa.edu (4.1/SMI-4.1) id AA02903; Mon, 22 Nov 93 15:51:27 CST From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Message-Id: <9311222151.AA02903@bioc01.uthscsa.edu> Subject: Re: hydrophobic/hydrophilic surface areas To: longshot@chem.duke.edu (Brad Isbister) Date: Mon, 22 Nov 1993 15:51:21 -0600 (CST) Cc: chemistry@ccl.net In-Reply-To: <9311222025.AA16725@canada.chem.duke.edu> from "Brad Isbister" at Nov 22, 93 03:25:30 pm X-Mailer: ELM [version 2.4 PL3] Content-Type: text Content-Length: 1681 Hi > > Does anyone out there know of programs to calculate solvent-accessable polar and non-polar surface areas? Preferably code for Sun workstations. Free or commercial, either is acceptable. The program you need is called ACCESS and is very popular for doing exactly what you are asking, in the protein folding area. I am going to assume that you are working on protein structure. ACCESS and the related program VOLUME were written by Fred Richards and colleagues at Yale U. You can obtain them by writing to Art Perlo at: perlo@hhvms8.csb.yale.edu OR perlo@csb.yale.edu This of course is Fortran code and an adaptation of the Richmond algorithm (in C) is available from Scott Presnell, UCSF. GRASP from Tony Nicholls (Columbia U) and MSP package from Mike Connolly are also capable of doing this. While ACCESS and the Presnell code are free, there is a nominal fee for licensing GRASP and MSP. Cheers -raman -- C.S.Raman raman@bioc01.uthscsa.edu - Internet UNIX Programming & Administration 70412.2354@compuserve.com - CIS SPARC & SGI Systems raman@hermes.chpc.utexas.edu - CHPC Department of Biochemistry c.raman@launchpad.unc.edu UTHSCSA 7703 Floyd Curl Dr. (210) 567-6623 [Tel] San Antonio, TX 78284-7760 (210) 567-6595 [Fax] ****************************************************************************** If a man's wit be wandering, let him study the Mathematics -Francis Bacon ****************************************************************************** From rovshan@atlas.chemistry.uakron.edu Mon Nov 22 18:28:53 1993 Received: from dax.cc.uakron.edu for rovshan@atlas.chemistry.uakron.edu by www.ccl.net (8.6.1/930601.1506) id SAA03612; Mon, 22 Nov 1993 18:23:32 -0500 Received: from atlas.chemistry.uakron.edu by dax.cc.uakron.edu (5.65/Ultrix4.3) id AA00870; Mon, 22 Nov 1993 18:23:16 -0500 Received: from cronus.chemistry.uakron.edu by atlas.chemistry.uakron.edu (4.1/SMI-4.1) id AA05325; Mon, 22 Nov 93 18:26:36 EST Date: Mon, 22 Nov 93 18:26:36 EST From: rovshan@atlas.chemistry.uakron.edu (Rovshan G. Sadygov) Message-Id: <9311222326.AA05325@atlas.chemistry.uakron.edu> To: CHEMISTRY@ccl.net Subject: Excimer Calculations Hi, Does anyone out there know of programs to calculate excimers? I have tried Argus and MOPAC5. They do not seem to give satisfactory results for the problem. Preferably code for Sun workstations and written on C. Thanks Rovshan G Sadygov From cmartin@rainbow.uchicago.edu Mon Nov 22 22:49:50 1993 Received: from midway.uchicago.edu for cmartin@rainbow.uchicago.edu by www.ccl.net (8.6.4/930601.1506) id WAA05565; Mon, 22 Nov 1993 22:43:40 -0500 Received: from rainbow.uchicago.edu by midway.uchicago.edu for CHEMISTRY@ccl.net Mon, 22 Nov 93 21:43:33 CST Received: by rainbow.uchicago.edu (920330.SGI/920502.SGI) for @midway.uchicago.edu:CHEMISTRY@ccl.net id AA20520; Mon, 22 Nov 93 23:07:54 -0600 From: cmartin@rainbow.uchicago.edu (Charles Martin) Message-Id: <9311230507.AA20520@rainbow.uchicago.edu> Subject: Re: Excimer Calculations To: rovshan@atlas.chemistry.uakron.edu (Rovshan G. Sadygov) Date: Mon, 22 Nov 1993 23:07:53 -0600 (CST) Cc: CHEMISTRY@ccl.net In-Reply-To: <9311222326.AA05325@atlas.chemistry.uakron.edu> from "Rovshan G. Sadygov" at Nov 22, 93 06:26:36 pm X-Mailer: ELM [version 2.4 PL22] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 2060 > Netters, > Rovshan G Sadygov asks: > > Does anyone out there know of programs to calculate excimers? I have tried > Argus and MOPAC5. They do not seem to give satisfactory results for the > problem. Preferably code for Sun workstations and written on C. > I am just curious what the problem is? Some old calculations have been performed to model the excimer bond. See "Mechanism and Theory in Organic Chemistry," Lowry and Richardson, Chapter 12 Photochemistry, which references 1a) Th. F\"orster, Angwew. Chem. Int. Ed., vol 8, page 333, (1969) 1b)B. Stevens in Advances in Photochemistry, vol 8 W. A. Noyes, G. S. Hammond, and J. N. Pitts, Jr. Eds, Wiley NY 1971, page 161 1c) M. Gordan and W. R. Ware, Eds, "The Expliex" Academic Press NY 1975 2) E.A. Chandross and C. J. Dempster, JACS vol 92, page 3586 (1970) 3) A.S. Cherkasov and T.M. Vember, Optics and Spectroscopy, vol 6, page 319 (1959) Lowry and Richardson claim that Quantum Mechanical calculations (I don't know what kind) give good esitmate of the theoretical position of the excimer flourescence band (I don't now how "good" good is) if the calculations account for charge resonance and excitatiojn resonance. That is, if the excimer takes the form: A*A <-> AA* <-> A+A- <-> A-A+ Is this along the lines of what you are looking for? On the other hand, many excimer fluorescence intensity depend on concentration. If you are trying to model concentration dependence, take a look at some work by Peter Rosky (Texas at Austin?) He has some been looking at some similar problems with excited atoms in solution. Hope this helps Chuck ================================================================== Charles H. Martin email: chm6@quads.uchicago.edu U.S. snail: c/o Freed Group The James Franck Institute and The Department of Chemistry The University of Chicago 5640 South Ellis Avenue Chicago, Illinois 60637 Work: (312) 702-3457 Fax: (312) 702-5863 ==================================================================