From S.R.Kilvington@soton.ac.uk Fri Mar 8 06:15:02 1996 Received: from beech.soton.ac.uk for S.R.Kilvington@soton.ac.uk by www.ccl.net (8.7.1/950822.1) id GAA08362; Fri, 8 Mar 1996 06:12:52 -0500 (EST) Received: from willow.soton.ac.uk (willow.soton.ac.uk [152.78.128.20]) by beech.soton.ac.uk (8.6.12/hub-8.5a) with ESMTP id LAA19761 for ; Fri, 8 Mar 1996 11:12:34 GMT Received: (from srk@localhost) by willow.soton.ac.uk (8.6.10/client-8.8) id LAA13565 for chemistry@www.ccl.net; Fri, 8 Mar 1996 11:10:24 GMT Message-Id: <199603081110.LAA13565@willow.soton.ac.uk> Subject: Marching Cubes ref To: chemistry@www.ccl.net Date: Fri, 8 Mar 1996 11:10:24 +0000 (GMT) From: "Simon Kilvington" X-Mailer: ELM [version 2.4 PL23] Content-Type: text Hia, does anyone have a reference for Lorensen and Cline's "Marching Cubes" paper? The ref. I have for it, Computers & Graphics 22 (1987) 163-169 doesn't seem to exist - I've searched the BIDS database and it's not in there - even searching for just "Lorensen" over the last 15 years doesn't give me a ref to the marching cubes paper. --- Simon Kilvington, srk@soton.ac.uk From grzesb@icm.edu.pl Fri Mar 8 09:15:03 1996 Received: from atol.icm.edu.pl for grzesb@icm.edu.pl by www.ccl.net (8.7.1/950822.1) id IAA09053; Fri, 8 Mar 1996 08:17:18 -0500 (EST) Received: from palma.icm.edu.pl (palma.icm.edu.pl [148.81.208.142]) by atol.icm.edu.pl (8.6.12/8.6.9) with ESMTP id OAA25561 for ; Fri, 8 Mar 1996 14:17:07 +0100 Received: from bryza.icm.edu.pl (bryza.icm.edu.pl [148.81.208.139]) by palma.icm.edu.pl (8.6.12/8.6.12) with ESMTP id OAA20151 for ; Fri, 8 Mar 1996 14:17:06 +0100 From: Grzegorz Bakalarski Received: (grzesb@localhost) by bryza.icm.edu.pl (8.7.2/8.6.12) id NAA17043 for chemistry@www.ccl.net; Fri, 8 Mar 1996 13:17:05 GMT Date: Fri, 8 Mar 1996 13:17:05 GMT Message-Id: <199603081317.NAA17043@bryza.icm.edu.pl> To: chemistry@www.ccl.net Subject: G94: IOp(5/32=...) IOp(5/38=...) Dear Netter, I have a problem with G94. It does not set properly specific options to overlay 5. One of our users found that for example setting iop(5/32=0) iop(5/38=0) does NOT work. I.e in route section written by a program they are set to different values. These two options select to use or not to use integral cutoffs during SCF. The user needs this options because he has a system with convergance problems ( weakly bound system). I tested the problem on water molecule. Following is input and output ++++++++++INPUT++++++++++++++ %chk=water.chk %mem=4000000 #p uhf/6-31g(d,p) geom=nocrowd units=au int=nosymm guess=core iop(3/22=0) iop(3/26=1) iop(3/27=16) iop(5/6=10) iop(5/32=0) iop(5/38=0) iop(9/9=10) pop=none title: water test 0 1 O H 1 Roh H 1 Roh 2 Ahh Roh=1.8 Ahh=105. +++++++++++++++++++++++++++++++ OUPUT ++++++++++++++++++++++++++++++ *************************************** Gussian 94: SGI-G94RevD.1 1-Feb-1996 5-Mar-1996 *************************************** %chk=water.chk %mem=4000000 ---------------------------------------------------------------------- #p uhf/6-31g(d,p) geom=nocrowd units=au int=nosymm guess=core iop(3/22 =0) iop(3/26=1) iop(3/27=16) iop(5/6=10) iop(5/32=0) iop(5/38=0) iop(9 /9=10) pop=none ---------------------------------------------------------------------- 1/20=1,38=1/1; 2/12=1,17=6,18=5/2; 3/5=1,6=6,7=101,11=2,25=1,26=1,27=16/1,2,3; 4/5=2,7=2/1; 5/5=2,6=10,32=1,38=4/2; 99/5=1,9=1/99; We use g94 Rev C3 and D1 on SGI, Dec Alpha, Sun Solaris and Cray Unicos YMP. I've also tested it with scf=NoSleazy and this also didn't work. Could you help us. Grzegorz Bakalarski ICM UW Poland grzesb@icm.edu.pl phone: +48-22-658-43-06 From ngo@interval.com Fri Mar 8 13:15:06 1996 Received: from fred.interval.com for ngo@interval.com by www.ccl.net (8.7.1/950822.1) id MAA10871; Fri, 8 Mar 1996 12:17:37 -0500 (EST) Received: from interval.interval.com (interval.interval.com [192.203.7.10]) by fred.interval.com with ESMTP id JAA27607; Fri, 8 Mar 1996 09:17:23 -0800 Received: by interval.interval.com id JAA26777; Fri, 8 Mar 1996 09:17:19 -0800 Date: Fri, 8 Mar 1996 09:17:19 -0800 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: "Simon Kilvington" , chemistry@www.ccl.net From: ngo@interval.com (Tom Ngo) Subject: Re: CCL:Marching Cubes ref Cc: chemistry@www.ccl.net At 11:10 AM 3/8/96, Simon Kilvington wrote: > does anyone have a reference for Lorensen and Cline's "Marching >Cubes" paper? The ref. I have for it, > >Computers & Graphics 22 (1987) 163-169 > > doesn't seem to exist The reference is SIGGRAPH 1987, 163-169. The formal citation is: Computer Graphics 21(4), 163-169, 1987 (Until a couple of years ago, the book of proceedings for each annual SIGGRAPH conference was considered, from a citation perspective, to be just another issue in the volume of the journal Computer Graphics for that year. Interestingly, in the graphics community a SIGGRAPH publication is much more respected than a paper in one of the non-SIGGRAPH issues of Computer Graphics.) The confusion was widespread---hence the change. --Tom ============================================================================ Tom Ngo Voice: 415/842-6037 Interval Research Corporation FAX: 415/354-0872 1801-C Page Mill Rd ngo@interval.com Palo Alto, CA 94304-1216 USA http://www.interval.com/~ngo/ From netsci@awod.com Fri Mar 8 14:06:26 1996 Received: from sumter.awod.com for netsci@awod.com by www.ccl.net (8.7.1/950822.1) id NAA11115; Fri, 8 Mar 1996 13:11:17 -0500 (EST) Received: from [198.81.225.153] (chs0044.awod.com [198.81.225.153]) by sumter.awod.com (8.6.11/8.6.9) with SMTP id NAA28609; Fri, 8 Mar 1996 13:10:54 -0500 X-Sender: arichon@awod.com Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Fri, 8 Mar 1996 14:30:05 +0000 To: chemistry@www.ccl.net From: netsci@awod.com (Network Science) Subject: March Issue of NetSci Cc: netsci@awod.com Dear Netters: The March issue of NetSci is on-line at: http://www.awod.com/netsci/ The feature topic this month is Advances in the Use of Technology for Drug Discovery. In addition to the regular columns, featured articles this month include: Interpretative Neural Networks for QSAR, James H. Wikel*, Ernst R. Dow, and Michael Heathman, Eli Lilly Daylight CGI interface (DCGI) - a presentation from the Daylight Users Group Meeting, David Weininger, Daylight Chemical Information Systems The Impact of High Throughput Organic Synthesis on R&D in Bio-Based Industries, John P. Devlin, ARRT International Publishing Chemistry on the Internet, Steven M. Bachrach, Northern Illinois University; Peter Murray-Rust, Glaxo Wellcome; Henry S. Rzepa, Imperial College; and Benjamin J. Whitaker, University of Leeds Symmetrical Structures in Genetic Texts of Prokaryotes DNA Replication Origins, N. I. Akberova and A. Yu. Leontiev, Kazan State University (Note: This paper was scheduled to appear in the October, 1995 Issue on Bioinformatics. The editors apologize for the delay in posting this work). Software authors and distributors please note - The software section of NetSci is being significantly enhanced with the addition of a table which categorizes software by functionality and platform. A prototype is available for viewing. Please contact the editors of NetSci (netsci@awod.com) with specific information/changes/additions about your programs. Allen Richon & Merry Ambos From estiu@nahuel.biol.unlp.edu.ar Fri Mar 8 16:15:08 1996 Received: from biol.unlp.edu.ar for estiu@nahuel.biol.unlp.edu.ar by www.ccl.net (8.7.1/950822.1) id PAA12382; Fri, 8 Mar 1996 15:56:22 -0500 (EST) Received: from aitor.biol.unlp.edu.ar (aitor.biol.unlp.edu.ar [163.10.7.4]) by biol.unlp.edu.ar (8.6.9/8.6.9) with SMTP id RAA20387 for ; Fri, 8 Mar 1996 17:34:38 -0300 Date: Fri, 8 Mar 1996 17:34:38 -0300 Message-Id: <199603082034.RAA20387@biol.unlp.edu.ar> X-Sender: estiu@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: estiu@nahuel.biol.unlp.edu.ar (Estiu, Guillermina) Subject: summary:GABA Dear CCL readers, Here is a summary of my recent posting regarding references of recent publications of calculations on GABA . Thanks for those responding > A Study on GABA, Glutamate, and their analogues with the Molecular Orbital Method. M.Tsuda. Mie Medical Journal 1992; 42 (1) 7-19 A study of GABA and its analogues using the molecular orbital method. M.Tsuda et.al. J.Molecular Structure (Theochem), 280 (1993) 261-272 3- and 5-isoxazolol zwitterions: an ab initio molecular orbital study relating to GABA agonism and antagonism. T.Boulanger et.al. J.theor.biol (1987) 127,479-489 Ab initio electronic structure calculations of molecular similarity: a case study of 4-aminobutyric acid and its agonists. J.Cioslowski et al. Croatica Chemica Acta CCACAA 66 (1) 113-121 (1993). Michael Ramek and Michaela Flock, Ab-initio SCF investigation of gamma-aminobutyric acid, Amino Acids 8, 271-289 (1995) M. Ramek, Ab initio SCF investigatio of the intramolecular hydrogen bonding in d-aminopentanoic acid, Structural Chemistry 6, 15-24 (1995). >> Guillermina Estiu >> estiu@nahuel.biol.unlp.edu.ar >> > From frederik@hydra.acs.uci.edu Fri Mar 8 16:22:10 1996 Received: from hydra.acs.uci.edu for frederik@hydra.acs.uci.edu by www.ccl.net (8.7.1/950822.1) id PAA12318; Fri, 8 Mar 1996 15:26:46 -0500 (EST) Received: from vega.acs.uci.edu (vega.acs.uci.edu [128.200.16.36]) by hydra.acs.uci.edu (8.7.1/8.7.1) with SMTP id MAA03316; Fri, 8 Mar 1996 12:26:40 -0800 (PST) Received: from localhost by vega.acs.uci.edu (5.x) id AA26567; Fri, 8 Mar 1996 12:26:36 -0800 To: Gregory Rechtsteiner Cc: chemistry@www.ccl.net Subject: Re: CCL:rods and cones info. In-Reply-To: Your message of Thu, 07 Mar 1996 18:56:32 -0800. Date: Fri, 08 Mar 1996 12:26:31 -0800 Message-Id: <26566.826316791@vega.acs.uci.edu> From: "Donald M. Frederick" > Hello: > > I am sorry if this may seem a bit off topic, but I am in need > on finding the following: > > 1. a supplier of pigments found in the rods (rhodopsin only) and cones > of the eye (human). > > [ Red, Blue and Green sensitive pigments in cones: 11-cis retinene bound > [ to various opsins (protein portions). 11-cis retinene is the chromophore > [ in each and I would assume that the protein portion that the pigments > [ are bound to influence the lambda max of each. It may be possible to just > [ buy 11-cis retinene, but it would give us less info. > > 2. If anyone has studied these pigments and has computational and/or > experimental spectra (UV-Vis) it would also be beneficial. > > Thank you very much for your time and information, > > gregory a rechtsteiner > > -- > Pepperdine University > Natural Science Division > grechtst@pepvax.pepperdine.edu > grechtst@pacificnet.net > http://pacificnet.net/~grechtst > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: grechtst@pepvax.pepperdine.edu > -- Original Sender From: Address: grechtst@pepperdine.edu > 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 > March 1996 Journal of the Optical Society of America, series A, is a special issue devoted to the study of the retina. Might want to contact some of the authors. ------------------------------------------------------------------------ Donald Frederick | Office of Academic Computing frederik@uci.edu | University of California, Irvine oac@uci.edu | Irvine, CA 92717-2225 (714) 824-3200 | FAX (714) 824-2069 http://www.oac.uci.edu/indiv/frederik/ ----------------------------------------------------------------------- From nauss@ucmod2.che.uc.edu Fri Mar 8 16:25:11 1996 Received: from ucmod2.che.uc.edu for nauss@ucmod2.che.uc.edu by www.ccl.net (8.7.1/950822.1) id QAA12419; Fri, 8 Mar 1996 16:03:26 -0500 (EST) Received: by ucmod2.che.uc.edu (951211.SGI.8.6.12.PATCH1042/940406.SGI.AUTO) id QAA09997; Fri, 8 Mar 1996 16:03:33 -0500 From: nauss@ucmod2.che.uc.edu (Jeffrey L. Nauss) Message-Id: <9603081603.ZM9995@ucmod2.che.uc.edu> Date: Fri, 8 Mar 1996 16:03:22 -0500 Reply-To: Jeffrey.Nauss@UC.Edu Organization: Dept. Chemistry, University of Cincinnati X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@www.ccl.net, DIBUG@sunsite.icm.edu.pl Subject: CFF91 and Carbohydrates - Summary X-Zm-Priority: Low Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Sometime ago, I posed the following question: > The tutorial for InsightII optimizes an ligand for lysozyme using > the CFF91 forcefield. Has this forcefield been optimized for > carbohydrates now. If so, is there are reference available > supporting the use of CFF91 with carbohydrates? The quick answer is no. Neither CFF91 nor its successor CFF93 are parameterized for carbohydrates. CFF95, however, is reported to be parameterized for them. Unfortunately, CFF95 is only available as a separate purchase. I will let you call your own Biosym/MSI sales representative for the price. The use of CFF91 in the insightII 95.0 tutorial was strictly for demonstration purposes. An edited version of the individual replies is included below. The complete mail messages are available at http://www.che.uc.edu/~nauss/cff91_carbohydrates.html Jeff Nauss *************************************************************************** From: "Dr. James Brown" The answer is no, CFF91 was no parameterized against carbohydrates. From: marvin@biosym.COM (Marvin Waldman) The new CFF95 forcefield available from Biosym/MSI has parameters for carbohydrates (as well as peptides, nucleic acids, organics, metal ions, ...). CFF95 is available as a separately sold product from Biosym/MSI. Please contact your local sales representative for information on how to purchase this product.... Cff91 deals with carbohydrates by recognizing the oxygens and carbons using either alcohol or ether type parameters for which it is well parameterized. The cff95 forcefield is specifically parameterized for carbohydrates with special atom types assigned for this functional group. This (together with the functional form which includes important cross terms such as bond-torsion) enables cff95 to give a highly accurate representation of the conformational energetics of carbohydrates, in particular the anomeric effect is well treated which is not the case for cff91. From: David Renouf Biosym have informed me that CFF95 is the version that has these parameters and that CFF95 has to be purchased in addition to the supplied forcefields. -- Jeff Nauss *********************************************************************** * UU UU Jeffrey L. Nauss, PhD * * UU UU Director, Molecular Modeling Services * * UU UU Department of Chemistry * * UU UU CCCCCCC University of Cincinnati * * UU UU CCCCCCCC Cincinnati, OH 45221-0172 * * UUUU CC * * CC Telephone: 513-556-0148 Fax: 513-556-9239 * * CC * * CCCCCCCC e-mail: Jeffrey.Nauss@UC.Edu * * CCCCCCC URL http://www.che.uc.edu/~nauss * ***********************************************************************