From chemistry-request@www.ccl.net Thu Nov 12 00:36:25 1998 Received: from hera.wku.edu (root@hera.wku.edu [161.6.20.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id AAA26332 Thu, 12 Nov 1998 00:36:24 -0500 (EST) Received: from adler by hera.wku.edu with local (Exim 1.82 #1) id 0zdpQc-0000B0-00; Wed, 11 Nov 1998 23:36:22 -0600 From: Allen Adler To: chemistry@www.ccl.net Subject: Re: are homology models useful for SBDD? Message-Id: Date: Wed, 11 Nov 1998 23:36:22 -0600 >Database docking into hosts has been successful in ligand discovery >(notably Kuntz's DOCK). This has traditionally used liganded enzyme xtl >structure as a starting point, with removal of the complexed ligand. >At the other extreme is an unliganded homology model of a receptor-bound >protein as a starting point. Sorry to barge in without a clue again, but I am just wondering whether the terminology "homology", as used above, has anything to do with the word "homology" as used in topology, homological algebra, Stokes' theorem, etc. If so, what are the relevant references to its use in chemistry? Allan Adler adler@hera.wku.edu From chemistry-request@www.ccl.net Thu Nov 12 06:53:42 1998 Received: from pobox.csc.fi (pobox.csc.fi [128.214.46.62]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id GAA27409 Thu, 12 Nov 1998 06:53:41 -0500 (EST) Received: from laaksonen.csc.fi (laaksonen.csc.fi [193.166.1.75]) by pobox.csc.fi (8.9.0.Beta5/8.9.0.Beta5/CSC/Rtrs-1.22) with ESMTP id NAA15216 for ; Thu, 12 Nov 1998 13:53:39 +0200 (EET) Date: Thu, 12 Nov 1998 13:51:36 +0200 (GTB Standard Time) From: Leif Laaksonen To: chemistry@www.ccl.net Subject: Format in which Peter Goodfords GRID files are written? Message-ID: X-X-Sender: laaksone@laaksonen.csc.fi MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I can't find the information about the binary format in which the GRID program by Peter Goodford is dumping out the contour (kont) information. If you have the information please do share it with me. The information is needed to process the files further. Thanks for your help. Regards, -leif laaksonen Ps. Please do answer me directly and not to the list. ------------------------------------------------------------------- Center for Scientific Computing | Phone: 358 9 4572378 P.O. Box 405 | Mobile: 358 400425203 FIN-02101 Espoo | Telefax: 358 9 4572302 FINLAND | Mail: Leif.Laaksonen@csc.fi -------- URL: http://laaksonen.csc.fi/leif.laaksonen.html --------- From chemistry-request@www.ccl.net Thu Nov 12 08:54:02 1998 Received: from ifi.unicamp.br (lua.ifi.unicamp.br [143.106.6.13]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id IAA28538 Thu, 12 Nov 1998 08:53:15 -0500 (EST) From: dasf@lua.ifi.unicamp.br Received: (from daemon@localhost) by ifi.unicamp.br (8.8.8/8.8.8) id LAA23231 for ; Thu, 12 Nov 1998 11:52:41 -0200 (BDB) Received: from nt-pos.ifi.unicamp.br(143.106.39.133), claiming to be "nt_pos" via SMTP by lua.ifi.unicamp.br, id smtpdaaxfla; Thu Nov 12 11:52:38 1998 Message-Id: <3.0.6.32.19981112115238.0091eaa0@lua.ifi.unicamp.br> X-Sender: dasf@lua.ifi.unicamp.br X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.6 (32) Date: Thu, 12 Nov 1998 11:52:38 -0200 To: chemistry@www.ccl.net Subject: Sp2 Hybridization and anisotropic properties of Graphite Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Hi, Does anybody knows the explanation of the highly anisotropic properties of the planar exagonal graphite latice of carbon and the quasi-metalic properties parallel to the carbon planes when we assume sp2 hybridization? Thanks in advance and please reply directly to me to not bother people in the list (dasf@ifi.unicamp.br). Demetrio From chemistry-request@www.ccl.net Thu Nov 12 09:47:38 1998 Received: from ifi.unicamp.br (lua.ifi.unicamp.br [143.106.6.13]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id JAA28864; Thu, 12 Nov 1998 09:47:34 -0500 (EST) From: dasf@lua.ifi.unicamp.br Received: (from daemon@localhost) by ifi.unicamp.br (8.8.8/8.8.8) id MAA20718; Thu, 12 Nov 1998 12:47:02 -0200 (BDB) Received: from nt-pos.ifi.unicamp.br(143.106.39.133), claiming to be "nt_pos" via SMTP by lua.ifi.unicamp.br, id smtpdaazCda; Thu Nov 12 12:46:55 1998 Message-Id: <3.0.6.32.19981112124655.0090ead0@lua.ifi.unicamp.br> X-Sender: dasf@lua.ifi.unicamp.br X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.6 (32) Date: Thu, 12 Nov 1998 12:46:55 -0200 To: chemistry@www.ccl.net Subject: Sp2 Hybridization and anisotropic properties of Graphite Cc: CHEMISTRY@www.ccl.net Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Hi, Does anybody knows the explanation of the highly anisotropic properties of the planar exagonal graphite latice of carbon and the quasi-metalic properties parallel to the carbon planes when we assume sp2 hybridization? Thanks in advance and please reply directly to me to not bother people in the list (dasf@ifi.unicamp.br). Demetrio From chemistry-request@www.ccl.net Thu Nov 12 10:44:03 1998 Received: from chrs1.chem.lsu.edu (chrs1.chem.lsu.edu [130.39.132.111]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id KAA29521 Thu, 12 Nov 1998 10:44:03 -0500 (EST) Received: from localhost by chrs1.chem.lsu.edu (AIX 4.1/UCB 5.64/4.03) id AA31042; Thu, 12 Nov 1998 09:46:04 -0600 Date: Thu, 12 Nov 1998 09:46:04 -0600 (CST) From: Chris Harwell To: ccl Subject: Advice on predicting enantiomeric selectivity with comp chem Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL'ers, A coleague asked me to solicit the expertise of this list. He is an analytical chemist working with chiral separations, and is just getting started using molecular modeling, initially using sybyl. The question: what would be the best predictive method for determining the interaction between two different enantiomers and a chiral surfactant. They uses capillary electrophoresis to perform enantiomeric separations using surfactants. The surfactants are polymerized amino acid bases. They suspect hydrophobic/hydrophilic and electrostatic effects cause the separations. They do notice temperature effects where the order of separation may even reverse. 1) What methods (molecular mechanics, monte carlo, semi-empirical, force-field, other?) would be able to identify this type of difference in a practical amount of time? 2) If you know of any literature references or similar topics which could be searched in the literature your recommendations would be greatly appreciated! Thank you very much! Sincerely, Chris Harwell charwel@chrs1.chem.lsu.edu From chemistry-request@www.ccl.net Thu Nov 12 10:56:18 1998 Received: from theory.tc.cornell.edu (THEORY.TC.CORNELL.EDU [128.84.30.174]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA29686 Thu, 12 Nov 1998 10:56:18 -0500 (EST) Received: from tc.cornell.edu (r670-73-1.sc98.org [147.73.73.1]) by theory.tc.cornell.edu (8.8.4/8.8.3/CTC-1.0) with ESMTP id KAA21144 for ; Thu, 12 Nov 1998 10:56:18 -0500 Message-ID: <364B0604.B6E8C2D8@tc.cornell.edu> Date: Thu, 12 Nov 1998 11:00:04 -0500 From: Richard Gillilan X-Mailer: Mozilla 4.07 [en] (WinNT; I) MIME-Version: 1.0 To: "chemistry@www.ccl.net" Subject: multipole in ionic solution Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit It seems like it should be possible to derive a single multipole expansion for a set of point charges in ionic solution from the non-linear Poission Boltzman equation. This surely must have been done long ago. Anyone have a reference for this? ps. I'm not interested in numerical PB solvers, just the analytic solution if it exists. Thanks Richard Gillilan Cornell Theory Center From chemistry-request@www.ccl.net Thu Nov 12 11:27:31 1998 Received: from hartree.chem.kuleuven.ac.be (hartree.quantchem.kuleuven.ac.be [134.58.49.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id LAA00059 Thu, 12 Nov 1998 11:27:26 -0500 (EST) Received: from localhost (steven@localhost) by hartree.chem.kuleuven.ac.be (8.9.0/8.9.0) with ESMTP id SAA64436 for ; Thu, 12 Nov 1998 18:39:03 +0100 Date: Thu, 12 Nov 1998 18:39:02 +0100 (NFT) From: Steven Creve To: Computational Chemistry List Subject: CCL:G9x:disk space CCSD(T) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Is there any simple rule to estimate the *actual* amount of disk space required by a CCSD(T) calculation with TRAN=full, i.e. a full MO transformation? steven -------------------------------------------------------------------------- Steven Creve steven.creve@chem.kuleuven.ac.be Labo Quantumchemie Celestijnenlaan 200F 3001-HEVERLEE tel: (32) (16) 32 73 93 BELGIUM fax: (32) (16) 32 79 92 From chemistry-request@www.ccl.net Wed Nov 11 04:18:58 1998 Received: from comsig.nibsc.ac.uk (comsig.nibsc.ac.uk [193.62.43.13]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id EAA20707 Wed, 11 Nov 1998 04:18:57 -0500 (EST) Received: from nibsc.ac.uk (dlinmf.nibsc.ac.uk [193.62.42.144]) by comsig.nibsc.ac.uk (980427.SGI.8.8.8/970903.SGI.AUTOCF) via ESMTP id JAA02408; Wed, 11 Nov 1998 09:18:07 GMT Message-ID: <36495658.DAE43DB4@nibsc.ac.uk> Date: Wed, 11 Nov 1998 09:18:16 +0000 From: Mark Forster Organization: NIBSC X-Mailer: Mozilla 4.05 [en] (Win95; I) MIME-Version: 1.0 To: juan andres ramirez CC: CHEMISTRY@www.ccl.net Subject: Re: CCL:Help on software!!!! References: <19981106221257.21482.qmail@hotmail.com> Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear Juan The European Bioinformatics Institute (EBI) web page is at http://www.ebi.ac.uk. But a search of the archives there shows no program named MINTAL. But the codes described on the page http://www.ebi.ac.uk/biocat/Metabolic_regulation.html may be useful to you. juan andres ramirez wrote: > Dear CCler´s > > I am an undergraduate chemistry student trying to finish my thesis. > I am looking for a program that allows me to calculate equilibrium > compositions if I fix the initial feed composition, the possible > reactions and the temperature and pressure conditions. > I have found in my research articles a program named MINTAL developed in > the E.B.I. but I have no clue on how to get it if anyone here in the > list knows about this or any other program of this kind I would > certainly be very grateful. > > Thanking your response > > Juan Andres Ramirez > > Universidad Nacional de Colombia > Facultad de Ciencias > Departamento de Quimica > Laboratorio de Combustibles > > ______________________________________________________ > Get Your Private, Free Email at http://www.hotmail.com > > --- > Administrivia: This message is automatically appended by the mail exploder: > 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 > --- -- Dr Mark J Forster Ph.D. Principal Scientist Informatics Laboratory National Institute for Biological Standards and Control Blanche Lane, South Mimms, Hertfordshire EN6 3QG, United Kingdom. Tel 01707 654753 FAX 01707 646730 E-mail mforster@nibsc.ac.uk From larry@melanie.ucd.ie Thu Nov 12 05:57:17 1998 Return-Path: Received: from hermes.ucd.ie (hermes.ucd.ie [137.43.1.49]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id FAA27316 Thu, 12 Nov 1998 05:56:57 -0500 (EST) Received: from melanie.ucd.ie by hermes.ucd.ie (PMDF V5.1-10 #U3251) with SMTP id <0F2B0058T2DLKK@hermes.ucd.ie> for chemistry-request@www.ccl.net; Thu, 12 Nov 1998 10:56:10 +0000 (GMT) Received: by melanie.ucd.ie (1.37.109.4/0.0) id AA09829; Thu, 12 Nov 1998 10:48:49 +0000 (GMT) Date: Thu, 12 Nov 1998 10:48:49 +0000 (GMT) From: larry@melanie.ucd.ie (Larry Cuffe) Subject: ECP with DFT To: chemistry@www.ccl.net Message-id: <9811121048.AA09829@melanie.ucd.ie> Mailer: Elm [revision: 70.85] I'm trying to study complexes of Mo. using DFT. Does it make sense to use an ECP basis set with DFT (b3lyp) and if so has anyone any sugestions for basis set of about 6-311G* quality larry From jkl@ccl.net Thu Nov 12 14:20:46 1998 From: Jan Labanowski Date: Thu, 12 Nov 1998 14:20:44 -0500 (EST) Message-Id: <199811121920.OAA27158@krakow.ccl.net> To: jkl@ccl.net Subject: Chemical Java Applet available at http://www.chemaxon.com/marvin/ Dear CCL, I looked at a nice site which has free Java Applets useful for sketching and displaying (and more) chemical structures on the Web. It is free for free Internet sites, and some of you may want to use it. Check it out: http://www.chemaxon.com/marvin/ It comes with good documentation and examples of usage within Web HTML and JavaScript pages, as well as CGI scripts. Read also the docs, and view the pages source, since they are quite useful. Jan jkl@ccl.net Jan Labanowski jkl@ccl.net From chemistry-request@www.ccl.net Thu Nov 12 15:45:13 1998 Received: from sumter.awod.com ([208.140.99.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id PAA02537 Thu, 12 Nov 1998 15:45:12 -0500 (EST) Received: from [208.140.98.204] (wa0204.tnt1-56k.awod.com [208.140.98.204]) by sumter.awod.com (8.8.7/8.8.8) with SMTP id PAA12794; Thu, 12 Nov 1998 15:45:11 -0500 (EST) (envelope-from netsci@awod.com) X-Sender: arichon@208.140.99.1 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 12 Nov 1998 15:50:59 +0100 To: chemistry@www.ccl.net From: netsci@awod.com (Network Science) Subject: Final Call for Student Poster Abstracts to Charleston Conference March 15 - 17, 1999 -- Wild Dunes Resort This is the final call for poster abstracts for The 1999 Charleston Conference Student Stipend Award. Network Science Corporation (e-mail: editors@netsci.org) is sponsoring travel awards to advanced graduate students and postdoctoral fellows which will promote participation in The Charleston Conference. Stipends will be granted to two students based on the innovative nature of their research and its potential application to drug discovery. These awards will include a waiver of the conference registration fee as well as travel expenses up to a maximum of $700 per awardee. Receipients of the Network Science Student Stipend will present their posters as a part of the Monday evening Poster Session. Students who wish to submit an abstract for consideration by the Conference Organizing Committee should complete the form on the NetSci web site (http://www.netsci.org) by Friday, November 20, 1998. Awards will be announced on the NetSci website on December 1, 1998. From chemistry-request@www.ccl.net Thu Nov 12 20:25:19 1998 Received: from smaug.wrq.com (smaug.wrq.com [150.215.17.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id UAA03997 Thu, 12 Nov 1998 20:25:18 -0500 (EST) Received: from ursula.wrq.com (root@ursula.wrq.com [150.215.11.58]) by smaug.wrq.com (8.8.6 (PHNE_14041)/8.8.6) with ESMTP id RAA29677 for ; Thu, 12 Nov 1998 17:25:19 -0800 (PST) Received: from biggeek ([150.215.151.125] (may be forged)) by ursula.wrq.com with SMTP (8.8.6 (PHNE_14041)/8.7.3) id RAA13138 for ; Thu, 12 Nov 1998 17:25:18 -0800 (PST) Received: by biggeek with Microsoft Mail id <01BE0E61.6AE60A70@biggeek>; Thu, 12 Nov 1998 17:25:18 -0800 Message-ID: <01BE0E61.6AE60A70@biggeek> From: Mark Alan Thompson To: "'chemistry@www.ccl.net'" Subject: ArgusLab status Date: Thu, 12 Nov 1998 17:25:17 -0800 MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Apologies for the great inconvenience if you have been trying to access the ArgusLab website, or send email to me. The website has been disabled temporarily while the University updates my status. I will try to get this re-enabled as quickly as possible. Mark Thompson ************************************************* Mark Thompson WRQ Inc. 1500 Dexter Ave. N. Seattle, WA. 98109 web: www.wrq.com email: markt@wrq.com *************************************************