From parcom.ernet.in!gadre@parcom.ernet.in Fri Apr 7 01:57:26 1995 Received: from sangam.ncst.ernet.in for parcom.ernet.in!gadre@parcom.ernet.in by www.ccl.net (8.6.10/930601.1506) id BAA13234; Fri, 7 Apr 1995 01:45:31 -0400 Received: from parcom.UUCP (uucp@localhost) by sangam.ncst.ernet.in (8.6.8.1/8.6.6) with UUCP id LAA06350 for CHEMISTRY@ccl.net; Fri, 7 Apr 1995 11:14:36 +0530 Received: from parcom.UUCP by iucaa (4.1/SMI-4.1) id AA10549; Fri, 7 Apr 95 10:20:20+050 Received: from parcom by parcom.parcom.ernet.in (4.1/SMI-4.1) id AA15662; Fri Apr 7 10:04:44 1995 (GMT + 0530) Date: Fri Apr 7 10:04:44 1995 (GMT + 0530) From: gadre@parcom.ernet.in Message-Id: <9504070434.AA15662@parcom.parcom.ernet.in> To: CHEMISTRY@ccl.net Subject: anionic micellar molecules. Colleagues: I have a curiosity regarding anionic micellar molecules. Cosider, for instance, dodecane and dodecyl sulphate. Dodecyl sulphate has a polar "head" group and a hydrophobic "tail". There is a lot of discussion regrding the twisting of the molecule so that tere is cosiderable folding leading to head-tail interaction to some extent. However, there is no general discussion (at least in the limited sources I know) about the similarities and differences in the "hydrophobic" regions of these two molecules. Would they be rather similar or very different? Your reply will be graetly appreciated. If you have some references, please include them in the reply. I have some interesting results to share in case someone is interested. Shridhar Gadre 07.04.1995. From mcblab43@leonis.nus.sg Fri Apr 7 04:57:33 1995 Received: from sable.nus.sg for mcblab43@leonis.nus.sg by www.ccl.net (8.6.10/930601.1506) id EAA14649; Fri, 7 Apr 1995 04:47:32 -0400 Received: from leonis.nus.sg (mcblab43@leonis.nus.sg [137.132.1.18]) by sable.nus.sg (8.6.9/8.6.9) with ESMTP id QAA02411 for ; Fri, 7 Apr 1995 16:48:12 +0800 Received: (from mcblab43@localhost) by leonis.nus.sg (8.6.10/8.6.9/CNS-3.5) id QAA16088; Fri, 7 Apr 1995 16:41:32 +0800 Date: Fri, 7 Apr 1995 16:41:31 +0800 (SST) From: Raistlin Majere To: chemistry@ccl.net Subject: Packages for short peptide chains Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, A few weeks ago I posted the following question: Anyone knows if there are good packages that use genetic algorithms or simulated annealing to determine minimum structures of small molecules (ex: short peptide chains)? I will post a summary of relevant replies. Unfortunately I did not receive many replies. However, I would like to thank all those who have so kindly replied my question :) ***** Message 1 From: bernhard@F3.telekurs.ch (Bernhard Pabsch - Telekurs AG - FLCI) Hi, did you check out PEACS from the vanGunsteren (GROMOS) group? They also hold another new algorithm which uses a list of visited conformational places. Both are quite powerful new algorithms. Cheers Bernhard Anton Pabsch Tel: +41 (0) 1 279 23 02 ***** Message 2 From: jaeger@3dp.com (Ed Jaeger) In my previous position at Sterling Winthrop, I developed GA drivers to both SYBYL and MACROMODEL's BATCHMIN to do conformational analysis of small molecules. I unfortunately do not have access to either of these commercial modeling packages and hence I cannot provide you with any specific solution but I can say that it has been done. I look forward to other relevant responses. Ed Jaeger 3-Dimensional Pharmaceuticals, Inc. ph:610-458-6052 jaeger@3dp.com 665 Stockton Drive, Suite 104, Exton, PA 19341 fx:610-458-8249 ***** Message 3 From: polowin@hyper.hyper.com (Joel Polowin) > Anyone knows if there are good packages that use genetic algorithms or > simulated annealing to determine minimum structures of small molecules > (ex: short peptide chains)? I will post a summary of relevant replies. Our HyperChem software does simulated annealing; it also includes drawing functions specifically for contruction of peptide chains. The conformational search module of ChemPlus might also be useful for determining minimum structures of such molecules; it works by torsional variations. Regards, Joel ***** Message 4 From: hcj@mazda.wavefun.com (Harry C. Johnson) Spartan 4.0 from Wavefunction Inc. has four new conformational analysis methods, including a genetic algorithm and a Monte Carlo approach. For more information about Spartan, check out our web page at http://wavefun.com. -Harry Best Regards, Loh Chang Shiung, ~{B^UBP[~} Internet e-mail: mcblab43@leonis.nus.sg Centre for Natural Products Research, Contact no.: (65) 772 6872 National University of Singapore. (65) 772 7816 From teoulf@garm.teokem.lu.se Fri Apr 7 08:57:32 1995 Received: from garm.teokem.lu.se for teoulf@garm.teokem.lu.se by www.ccl.net (8.6.10/930601.1506) id IAA16829; Fri, 7 Apr 1995 08:54:34 -0400 Received: by garm.teokem.lu.se (AIX 3.2/UCB 5.64/4.03) id AA07364; Fri, 7 Apr 1995 14:56:14 +0200 Date: Fri, 7 Apr 1995 14:56:14 +0200 From: teoulf@garm.teokem.lu.se (Ulf Ryde) Message-Id: <9504071256.AA07364@garm.teokem.lu.se> To: chemistry@ccl.net Subject: Calculate EPR g and A parameters Hi! Is there any quantum chemical programs available that can calulate the electron spin resonace g and A parameters of small (transition metal) complexes? Ab initio methods is preferred, but all hints (and references) are welcome. Ulf Ryde Dep. Theoretical Chemistry University of Lund POB 124 S-221 00 Lund Sweden teoulf@garm.teokem.lu.se From shubin@email.unc.edu Fri Apr 7 12:57:35 1995 Received: from email.unc.edu for shubin@email.unc.edu by www.ccl.net (8.6.10/930601.1506) id MAA22429; Fri, 7 Apr 1995 12:50:53 -0400 Received: by email.unc.edu (AIX 3.2/UCB 5.64/4.03) id AA130609; Fri, 7 Apr 1995 12:50:53 -0400 Date: Fri, 7 Apr 1995 12:50:53 -0400 (EDT) From: Shubin Liu To: chemistry@ccl.net Cc: chemistry@ccl.net Subject: CCL: Does optimized structure depend on the input? In-Reply-To: <9504071256.AA07364@garm.teokem.lu.se> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all CCLers: Recently I come up with a question that using Gaussian 92, does the optimized geometrical structure depend on the initial input? Since the result is a local minimum, the answer seems yes. But how to avoid this local minimum to obtain a global minimum? Please give me a reply if you have an idea. Thank you! Shubin ............................................................................. Shubin Liu Department of Chemistry Email: shubin@email.unc.edu University of North Carolina sliu@mulliken.chem.unc.edu Chapel Hill, NC 27599-3290 Tel : (919) 962-0150(O) USA (919) 914-6923(H) ............................................................................. From stevens@jordan.uchicago.edu Fri Apr 7 14:12:36 1995 Received: from jordan.uchicago.edu for stevens@jordan.uchicago.edu by www.ccl.net (8.6.10/930601.1506) id OAA23734; Fri, 7 Apr 1995 14:03:01 -0400 Received: by jordan.uchicago.edu (AIX 3.2/UCB 5.64/4.03) id AA26769; Fri, 7 Apr 1995 12:59:32 -0500 Date: Fri, 7 Apr 1995 12:59:32 -0500 From: stevens@jordan.uchicago.edu (Jonathan Stevens) Message-Id: <9504071759.AA26769@jordan.uchicago.edu> To: CHEMISTRY@ccl.net Subject: HONDO manual or docs Cc: finley@kff1.uchicago.edu, freed@sar2.uchicago.edu Does anyone know where I can find a manual or documentation for HONDO 8? Thanks in advance, Jonathan Stevens From neville@chaos.chm.nau.edu Fri Apr 7 16:42:41 1995 Received: from NAUVAX.UCC.NAU.EDU for neville@chaos.chm.nau.edu by www.ccl.net (8.6.10/930601.1506) id QAA26566; Fri, 7 Apr 1995 16:39:45 -0400 Received: from chaos.chm.nau.edu by NAUVAX.UCC.NAU.EDU (PMDF V4.3-8 #2384) id <01HP25B11FBK0002E3@NAUVAX.UCC.NAU.EDU>; Fri, 07 Apr 1995 13:38:15 -0700 (MST) Received: by chaos.chm.nau.edu (931110.SGI/930416.SGI) for @nauvax.ucc.nau.edu:CHEMISTRY@ccl.net id AA08327; Fri, 7 Apr 95 15:01:23 -0700 Date: Fri, 07 Apr 1995 15:01:23 -0700 From: Todd Neville Subject: Graduate CompChem Programs To: CHEMISTRY@ccl.net Message-id: <9504071501.ZM8325@chaos.chm.nau.edu> MIME-version: 1.0 X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7BIT To CCL: I am currently an undergraduate ACS major involved in a search of graduate school programs. For the last two years I have been involved in research in computational chemistry (Spartan) and would like to continue this course. However, I am having difficulty locating programs which fit my intrests. The "Chemical Sciences Graduate School Finder" and the "ACS Directory of Graduate Research" both lack any listing for computational chemistry whatsoever. Specifically, I am looking for a program in computer aided drug design, preferrably one which utilizes Homology modeling (Homology, Profiles 3D, Caveat, Protien Design, etc.), Pharmacophore identification (Apex, C2 QSAR+ & HipHop, etc.), and/or receptor structure based (de Novo) ligand design (Ludi, Caveat, etc.). It has been my experience that most of this research has been done in the private sector with only limited applications in academics. Does anyone have any suggestions on how to locate individuals in the academic sector involved in these pursuits? Responses can be sent directly to me at "neville@chaos.chm.nau.edu". I will summarize to any who request it. Thank you. -Todd Neville -- ##### (o o) **************************oooO***(__)***Oooo**************************** * * * It's all ball bearings these days anyway - Fletch * * * * Todd Neville (602) 556-0276 home * * neville@chaos.chm.nau.edu (602) 773-5241 digital pager * * http://chaos.chm.nau.edu:80/~neville/ * * * * tgn@dana.ucc.nau.edu * * tgn2@nauvax.ucc.nau.edu * * * * Northern Arizona University * * Computational Chemistry & WWW server Admin. * ************************************************************************