From h.rzepa@ic.ac.uk Mon Sep 5 02:43:54 1994 Received: from judy.ic.ac.uk for h.rzepa@ic.ac.uk by www.ccl.net (8.6.9/930601.1506) id CAA26854; Mon, 5 Sep 1994 02:29:16 -0400 Received: from sg1.cc.ic.ac.uk by judy.ic.ac.uk with SMTP (PP) id <25967-0@judy.ic.ac.uk>; Mon, 5 Sep 1994 07:29:13 +0100 Received: from anxa07 by cscmgb.cc.ic.ac.uk (920330.SGI/4.0) id AA29925; Mon, 5 Sep 94 07:31:48 +0100 Message-Id: <9409050631.AA29925@cscmgb.cc.ic.ac.uk> X-Sender: rzepa@129.31.80.14 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Mon, 5 Sep 1994 07:32:16 +0000 To: CHEMISTRY@ccl.net From: h.rzepa@ic.ac.uk (Rzepa, Henry) (Rzepa, Henry) Subject: Mathematica and WWW We have implemented a MIME type for Mathematica notebooks; application/x-mathematica ma You can try it out on http://www.ch.ic.ac.uk/hm_second.html (the last example) Following discussions with WRI, it appears that this format may also be adopted by Wolfram Research Inc, and hence may be regarded as the de facto definition. Agreement would enable interesting notebooks to be defined as hyperlinks into WWW (and gopher) pages, and therefore incorporated into courses, electronically published research papers etc. There is one problem that needs solution. ma notebooks can have initialisation cells that may perform unsuspected functions on a users system, in contravention of the security guidelines. We also note that Mathematica <>, denoted by the suffix .m, also require much thought regarding the security implications. Does anyone have any interesting .ma notebook files relevant to chemistry that they may wish to offer the community in this form? Dr Henry Rzepa, Dept. Chemistry, Imperial College, London, SW7 2AY. Tel: +44 171 594 5809. Fax: +44 171 594 5804. E-mail: rzepa@ic.ac.uk http://www.ch.ic.ac.uk/rzepa.html. Sent via MacPPP/MacTCP using Eudora 2.02. From h.rzepa@ic.ac.uk Mon Sep 5 03:30:47 1994 Received: from punch.ic.ac.uk for h.rzepa@ic.ac.uk by www.ccl.net (8.6.9/930601.1506) id CAA26860; Mon, 5 Sep 1994 02:29:41 -0400 Received: from sg1.cc.ic.ac.uk by punch.ic.ac.uk with SMTP (PP) id <05978-0@punch.ic.ac.uk>; Mon, 5 Sep 1994 07:28:19 +0100 Received: from anxa07 by cscmgb.cc.ic.ac.uk (920330.SGI/4.0) id AA29936; Mon, 5 Sep 94 07:31:56 +0100 Message-Id: <9409050631.AA29936@cscmgb.cc.ic.ac.uk> X-Sender: rzepa@129.31.80.14 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Mon, 5 Sep 1994 07:32:23 +0000 To: CHEMISTRY@ccl.net From: h.rzepa@ic.ac.uk (Rzepa, Henry) (Rzepa, Henry) Subject: Call for new chemical MIME suggestions Cc: Murray-Rust Dr P , benw@chemistry.leeds.ac.uk CALL FOR CHEMICAL MIME TYPES Since the original proposal to create a chemical MIME type, I have had aproaches from several camps about defining new secondary chemical types. For example, the NMR community is discussing how time and frequency domain data may be defined in a standard way. A similar request came from the ESR community, and I have had a general request for MIME types related to "physical chemistry". We are seeking well defined data formats, ie those where a readily available definition is available in some form in the literature (as opposed to obscure technical manuals). If anyone know discussions about such formats that are underway, please let me know. Also, if anyone has used the "hierarchical data format", or HDF, which is already a MIME standard, do let me know how it has been applied to chemistry. The current status of the chemical MIME proposal is that the Internet draft expires in November. At this stage, if we wish to continue the process, a more formal Internet RFC will have to be presented to the Internet Engineering Task force. If this is accepted, it would then become the formal standard definition for the carriage of chemical information on the Internet. Of course, further additions to this standard could be subsequently proposed, but anyone wishing to be on the "first" boat that leaves should strive to meet the above deadline. The other alternative is that a second revised Internet draft replaces the expired one, but this would only make sense if significant changes had transpired to the first one. Dr Henry Rzepa, Dept. Chemistry, Imperial College, London, SW7 2AY. Tel: +44 171 594 5809. Fax: +44 171 594 5804. E-mail: rzepa@ic.ac.uk http://www.ch.ic.ac.uk/rzepa.html. Sent via MacPPP/MacTCP using Eudora 2.02. From nbbienia@cyf-kr.edu.pl Mon Sep 5 04:43:54 1994 Received: from nms.cyf-kr.edu.pl for nbbienia@cyf-kr.edu.pl by www.ccl.net (8.6.9/930601.1506) id EAA27759; Mon, 5 Sep 1994 04:38:59 -0400 Received: from lfs.cyf-kr.edu.pl by nms.cyf-kr.edu.pl (4.1/SMI-4.1) id AA12674; Mon, 5 Sep 94 10:39:04 +0200 Received: by lfs.cyf-kr.edu.pl (4.1/SMI-4.1) id AA13235; Mon, 5 Sep 94 10:35:42 +0200 Date: Mon, 5 Sep 1994 10:35:41 +0200 (MET DST) From: Leslaw Bieniasz Subject: Chemical Kinetic Programs (fwd) To: chemistry@ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Krako'w, 5.09.94 Dear Netters, I am trying to collect the literature concerning the development of general purpose software designed for chemical kinetic modelling. I would welcome any information, references to published materials, papers, conference proceedings, etc. on existing scientific or commercial programs for (widely understood) homogeneous and heterogeneous kinetics, including special applications like, for example, atmospheric chemistry. Any indication of works on related subjects, such as the design of reaction compilers, user- interfaces, coupled PDE/ODE solving, algebraic-differential solvers, solvers for reaction-diffusion problems, etc. will also be appreciated. Thanks in advance, Leszek (email: nbbienia@cyf-kr.edu.pl) From ADAMSL@CSOVAX.PORTSMOUTH.AC.UK Mon Sep 5 05:43:55 1994 Received: from sun2.nsfnet-relay.ac.uk for ADAMSL@CSOVAX.PORTSMOUTH.AC.UK by www.ccl.net (8.6.9/930601.1506) id FAA27981; Mon, 5 Sep 1994 05:14:52 -0400 From: Message-Id: <199409050914.FAA27981@www.ccl.net> Via: uk.ac.portsmouth.csovax; Mon, 5 Sep 1994 10:14:41 +0100 Date: Mon, 5 Sep 94 10:11 GMT To: CHEMISTRY Subject: Docking molecules using Sybyl Please could someone offer some advice on the use of Sybyl Dock? The molecule I am trying to dock contains an aromatic system, which is puckered when I try to dock it into a strand of DNA with 10 base pairs. This appears to be due to the atomic positions being minimised with respect to steric and electrostatic factors, but ignoring the energy of the ligand itself. The energy of the overall system is lowered, but the energy of the ligand is increased. The manual does not appear to give any suggestions as far as molecules of this size are concerned. Lesley Adams Centre for Molecular Design University of Portsmouth U.K. From dufner@ws01.pc.chemie.th-darmstadt.de Mon Sep 5 06:43:57 1994 Received: from rs2.hrz.th-darmstadt.de for dufner@ws01.pc.chemie.th-darmstadt.de by www.ccl.net (8.6.9/930601.1506) id GAA28500; Mon, 5 Sep 1994 06:33:28 -0400 Received: from ws01.pc.chemie.th-darmstadt.de by rs2.hrz.th-darmstadt.de with SMTP id AA09702 (5.65c/IDA-1.4.4 for <@rs2.hrz.th-darmstadt.de:chemistry@ccl.net>); Mon, 5 Sep 1994 12:33:22 +0200 Received: by ws01.pc.chemie.th-darmstadt.de (940406.SGI/931108.SGI.AUTO.ANONFTP) for @rs2.hrz.th-darmstadt.de:chemistry@ccl.net id AA05712; Mon, 5 Sep 94 12:33:21 +0200 Date: Mon, 5 Sep 94 12:33:21 +0200 From: dufner@ws01.pc.chemie.th-darmstadt.de (Hagen Dufner) Message-Id: <9409051033.AA05712@ws01.pc.chemie.th-darmstadt.de> To: chemistry@ccl.net Subject: force-field parameters Hi folks, I' m looking for force-field parameters for inorganic phosphate (PO4) and calcium (Ca). Any help is appreciated. # #+----------------------------------------------+ #| Hagen Dufner | #| Technische Hochschule Darmstadt | #| Physikalische Chemie I | #| Petersenstr. 20 | #| 64287 Darmstadt, Germany | #| Phone: (+int) 6151 165397 | #| Fax: (+int) 6151 164298 | #| Network : | #+----------------------------------------------+ From heelisp@newi.ac.uk Mon Sep 5 09:43:57 1994 Received: from dylan.newi.ac.uk for heelisp@newi.ac.uk by www.ccl.net (8.6.9/930601.1506) id JAA29474; Mon, 5 Sep 1994 09:13:46 -0400 Received: by dylan.newi.ac.uk (5.57/25-eef) id AA16463; Mon, 5 Sep 94 14:14:25 GMT From: Paul F Heelis Message-Id: <9409051414.AA16463@dylan.newi.ac.uk> To: chemistry@ccl.net Subject: ENTROPY CALCS AND SIMULATING HYDRATION WITH MOPAC/PM3 Date: Mon, 5 Sep 94 14:13:22 GMT Re: Entropy calaculations with PM3 As a newcomer to semi-empirical MO calcs, can anyone help with 2 basic questions. 1. I believe that MOPAC/PM3 can calculate entropies as well as enthalpies. I need to know how to do it and are the results meaningful. I know that the enthalpy calcs are pretty good, but I have no idea about entropy. Is it a waste of time to try and calculate free energy changes from delta H and delta S? 2. How can I simulate hydration of the structures? I am using Chem-x on a MAC Quadra, which has MOPAC 6.43. I would really appreciate any help you can give to a novice. Paul Heelis North East Wales Institute UK Heelisp@NEWI.AC.UK From ren@chvsmw.chem.ncsu.edu Mon Sep 5 16:44:04 1994 Received: from chvsmw for ren@chvsmw.chem.ncsu.edu by www.ccl.net (8.6.9/930601.1506) id QAA05176; Mon, 5 Sep 1994 16:20:36 -0400 From: Message-Id: <199409052020.QAA05176@www.ccl.net> Date: Mon, 5 Sep 1994 16:22:04 -0400 To: chemistry@ccl.net Subject: DF programs for solids ? X-VMS-To: SMTP%"chemistry@ccl.net" Dear Netters, Are there any Density Functional Method programs available to calculate band structures of solids (for instance, 1-D, 2-D or 3-D periodical crystals)? Thanks for your help. I'll post a summary of responses. REN@CHVZMW.CHEM.NCSU.EDU From wtwinter@mailbox.syr.edu Mon Sep 5 17:44:03 1994 Received: from SUVM.SYR.EDU for wtwinter@mailbox.syr.edu by www.ccl.net (8.6.9/930601.1506) id QAA05801; Mon, 5 Sep 1994 16:58:12 -0400 Received: from gamera.syr.edu by SUVM.SYR.EDU (IBM VM SMTP V2R2) with TCP; Mon, 05 Sep 94 10:01:22 LCL Received: by gamera.syr.edu (5.0/Spike-2.0) id AA00464; Mon, 5 Sep 1994 09:55:39 +0500 Date: Mon, 5 Sep 1994 09:55:38 -0400 (EDT) From: "William T. Winter" Subject: Re: CCL:Routine TRED2 To: chemistry@ccl.net In-Reply-To: <9409021645.AA09777@iris120.biosym.com> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII content-length: 834 There are so many versions of this procedure in use it is difficult to to be certain which one is under discussion. Early versions of the Fortran codes for tred2 found in the EISPACK routines had a machine dependent variable MACHEP whose correct value was dependent upon the precision with which real numbers were stored. Failure to correctly define the value of MACHEP certainly led to errors. Current versions of TRED2 no longer have this variable. Instead they utilize machine independent methods of assessing the precision. =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Dr. William T. Winter Phone: (315)470-6876 315 Baker Lab FAX: (315)470-6856 SUNY-ESF Internet: wtwinter@mailbox.syr.edu Syracuse, NY 13210-2786