From owner-chemistry@ccl.net Tue Aug 20 02:18:43 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.5/950822.1) id BAA03439; Tue, 20 Aug 1996 01:56:19 -0400 (EDT) Received: from goggins.bath.ac.uk for chpajt@bath.ac.uk by bedrock.ccl.net (8.7.5/950822.1) id BAA13574; Tue, 20 Aug 1996 01:56:19 -0400 (EDT) Received: from bath.ac.uk (actually host midge.bath.ac.uk) by goggins.bath.ac.uk with SMTP (PP); Tue, 20 Aug 1996 06:53:39 +0100 Date: Tue, 20 Aug 1996 06:53:34 +0100 (BST) From: A J Turner To: chemistry@ccl.net Subject: G: chelp & chelpg Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi! Can anyone shed some light on the difference between chelp and chlepg for esp fitting? Thanks in advance Alex ------------------------------------------------------------------- |Alexander J Turner |A.J.Turner@bath.ac.uk | |Post Graduate |http://www.bath.ac.uk/~chpajt/home.html| |School of Chemistry |+144 1225 8262826 ext 5137 | |University of Bath | | |Bath, Avon, U.K. |Field: QM/MM modeling | ------------------------------------------------------------------- From paul@heelisp.demon.co.uk Tue Aug 20 07:18:46 1996 Received: from relay-4.mail.demon.net for paul@heelisp.demon.co.uk by www.ccl.net (8.7.5/950822.1) id GAA04311; Tue, 20 Aug 1996 06:46:05 -0400 (EDT) Received: from post.demon.co.uk ([158.152.1.72]) by relay-4.mail.demon.net id ab15093; 20 Aug 96 10:41 GMT Received: from heelisp.demon.co.uk ([158.152.144.130]) by relay-3.mail.demon.net id aa17864; 20 Aug 96 11:41 +0100 Message-ID: Date: Tue, 20 Aug 1996 11:40:53 +0100 To: chemistry@www.ccl.net From: PAUL HEELIS Subject: adding hydrogens to pdb files MIME-Version: 1.0 X-Mailer: Turnpike Version 1.12 Dear all Anyone know of a program to add hydrogens to amino acids in a pdb file. preferably free. thanks in advance -- PAUL HEELIS From paul@heelisp.demon.co.uk Tue Aug 20 07:24:56 1996 Received: from relay-4.mail.demon.net for paul@heelisp.demon.co.uk by www.ccl.net (8.7.5/950822.1) id GAA04320; Tue, 20 Aug 1996 06:46:50 -0400 (EDT) Received: from post.demon.co.uk ([158.152.1.72]) by relay-4.mail.demon.net id aa15104; 20 Aug 96 10:41 GMT Received: from heelisp.demon.co.uk ([158.152.144.130]) by relay-3.mail.demon.net id aa17865; 20 Aug 96 11:41 +0100 Message-ID: Date: Tue, 20 Aug 1996 11:36:53 +0100 To: chemistry@www.ccl.net From: PAUL HEELIS Subject: pdb files MIME-Version: 1.0 X-Mailer: Turnpike Version 1.12 Dear All, anyone know of a program to put hydrogens on all the amino acids in a Pdb file?- preferably free. Thanks in advance. -- PAUL HEELIS From vvw@dialup.oar.net Tue Aug 20 09:18:51 1996 Received: from dialup.oar.net for vvw@dialup.oar.net by www.ccl.net (8.7.5/950822.1) id IAA04817; Tue, 20 Aug 1996 08:59:07 -0400 (EDT) Received: for vvw@dialup.oar.net by dialup.oar.net (8.6.10/931123.1402) id IAA28881; Tue, 20 Aug 1996 08:55:53 -0400 Date: Tue, 20 Aug 1996 08:55:50 -0400 (EDT) From: Vernon Walatka To: chemistry@www.ccl.net Subject: SMILES Summary Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII SMILES CODE FOR DESCRIBING MOLECULAR STRUCTURES I received about 20 responses to my request for information on Smiles Code. Most of the responses can be summarized as follows: 1. Smiles is an easy to use code for describing a chemical structure as a string of text. For simple molecules without rings, the text string is similar to the usual chemical structure, written as a line of text, with hydrogen atoms omitted. The Smiles code can be read as input by computer programs and chemical databases. 2. Excellent tutorials and information on Smiles Code can be obtained >from the web site: http://www.daylight.com 3. An excellent journal reference, with clearly explained rules for Smiles Code, is "SMILES, a Chemical Language and Information System. 1. Introduction to Methodology and Encoding Rules" by David Weininger J. Chem. Inf. Comput. Sci. 1988, Vol 28, pages 31-36 However, just as the chemical structure for a chemical compound can often be represented in many ways, the Smiles code is often not unique. A later paper describes a method for the unique generation of Smiles code. However that paper discusses computer algorithms and will not be of interest to a chemist who wants to know the basic encoding rules. The reference is "SMILES. 2. Algorithm for Generation of Unique SMILES Notation" David Weininger, Arthur Weininger, Joseph L. Weininger J. Chem. Inf. Comput. Sci. 1989, Vol 29, pages 97-101 SPECIFIC COMMENTS AND EXAMPLES OF SMILES CODE From: jsb2@camsoft.com Subject: Re: CCL:Smiles Code SMILES is a line notation for chemical structures. It was developed by Daylight and lots of information is available from their site (http://www.daylight.com). Basically, single bonds are implied by default, and hydrogens are implicit, so CCC is propane. Branches are shown by parentheses: CC(O)C is isopropanol. Double bonds are equals signs: CC=CC is 2-butene. Ring closures are shown by matching numbers: C1CCCCC1 is cyclohexane. The rules get more complicated, but that's the general idea. SMILES is a very compact way to store chemical structures in a textual form. CS ChemDraw Net is freely available from http://www.camsoft.com/chemfinder/download.html and will allow you to create SMILES strings for most any structure you can draw. You can use SMILES strings to search WWW databases such as the one at http://chemfinder.camsoft.com (and they of course have many other non-WWW uses as well) Jonathan Brecher CambridgeSoft Corporation jsb@camsoft.com From: Sjors Wurpel A SMILES string is a way of describing a chemical structure in a line of text. It can be created with e.g. CSC ChemDraw package (copy SMILES). It looks like this: trans-2-amino-cyclohexanol = [NH2]C1C([OH])CCCC1 From: "J. Eric Slone" SMILES is simplified molecular input line entry system... there is an on-line guide on the web. Examples are CC(=O)O for acetic acid and c1ccccc1 for benzene. From: Alan Shusterman SMILES is a language that was invented by David Weininger (DAYLIGHT Inc.). The language provides a simple means for writing complex molecular structures as a one-line code, and to have a computer recognize the code, e.g., the SMILES coding of most molecular formulas is not unique, but Weininger was able to find an efficient way to compare and recognize different SMILES for the same molecule, and to use this as a database key for information about the molecule. See: http://www.daylight.com OR e-mail: info@daylight.com Alan Shusterman Department of Chemistry Reed College Portland, OR 97202 From: "Gregory L. Durst - DowElanco R&D" SMILES stands for "Simplified Molecular Input Line Entry System", see the orig paper ... D. Weininger, "JCICS", vol28, (1988), 31-36. For more information contact: Daylight Chemical Information Systems phone: 714/367-9990 (Mission Viejo, CA) web url: http://www.daylight.com From: tj ODonnell SMILES is a line notation to represent chemical structures on computers. It was invented by Dave Weininger (now of Daylight, Inc.) and is used by lots of folks in molecular computing. Try looking at www.daylight.com for information. More specifically: http://www.daylight.com/dayhtml/smiles/ From: D.Winkler@chem.csiro.au (Dr. Dave Winkler) Subject: Re: CCL:Smiles Code SMILES is a very compact, very intuitive way of representing any molecular structure. There is a good tutorial on the Daylight page: http://www.daylight.com/dayhtml/smiles/ OTHER SUGGESTED SITES FOR INFORMATION AND TUTORIALS From: Wolf-Dietrich Ihlenfeldt Dr. Wolf-D. Ihlenfeldt Computer Chemistry Center, University of Erlangen-Nuernberg Naegelsbachstrasse 25, D-91052 Erlangen (Germany) Tel (+49)-(0)9131-85-6579 Fax (+49)-(0)9131-85-6566 http://www.daylight.com/dayhtml/smiles/smiles-intro.html http://schiele.organik.uni-erlangen.de/services/smiles.html From: Robert Fraczkiewicz http://schiele.organik.uni-erlangen.de/services/smiles.html From: Soaring Bear My chemistry web page has three links to SMILES tutorials on the web: http://fox.pomona.claremont.edu/chem/SMILES/index.html"> pomona - http://www.daylight.com/dayhtml/smiles/smiles-intro.html"> daylight - http://schiele.organik.uni-erlangen.de/services/smiles.html"> schiele - From: Bill Laidig http://fox.pomona.claremont.edu/chem/SMILES/index.html http://fox.pomona.claremont.edu/chem/SMILES/index.html Bill Laidig The Procter & Gamble Co. tel 513-627-2857 fax - 1233 Miami Valley Laboratories laidig@pg.com (preferred) P.O. Box 538707 wd_laidig@pg.com Cincinnati, OH 45253-8707 laidig@qtp.ufl.edu From: DOUGH@mdli.com I am sure you'll get lots of replies explaining what SMILES is - what might be more useful to you is a molecule file converter program called CONSYSTANT, >from Exographics, which can convert to and from about 30 different widely- used file formats, including SMILES. You can get more info by searching for Exographics on the Web, or contact ExoGraphics 144 Pinecliff Lake Dr West Milford, NJ 07480 (201) 728-0188 76070.726@compuserve.com >From Vernon Walatka (the author of this post) I generated Smiles code for the following three compounds. Titanium dioxide [Ti](=O)=O Aluminum hydroxide [Al](O)(O)O Zinc stearate CCCCCCCCCCCCCCCCCC(=O)(O-).[Zn+2].CCCCCCCCCCCCCCCCCC(=O)(O-) Note that the symbol "C" appears 18 times in each of the above two branches for zinc stearate. Vernon Walatka, Ph.D. Allen Research Center Quantum Chemical Company 11530 Northlake Drive Cincinnati, OH 45249 Voice (513) 530-4184 FAX (513) 530-4206 e-mail 62812142@eln.attmail.com (preferred) or vvw@dialup.oar.net From owner-chemistry@ccl.net Tue Aug 20 11:18:47 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.5/950822.1) id KAA05181; Tue, 20 Aug 1996 10:38:51 -0400 (EDT) Received: from mailgate.ci.tacoma.wa.us for cspires@ci.tacoma.wa.us by bedrock.ccl.net (8.7.5/950822.1) id KAA18104; Tue, 20 Aug 1996 10:38:52 -0400 (EDT) Received: from gw-smtp1.ci.tacoma.wa.us ([131.191.6.248]) by mailgate.ci.tacoma.wa.us (5.x/SMI-SVR4) id AA09643; Tue, 20 Aug 1996 07:39:11 -0700 Received: by gw-smtp1.ci.tacoma.wa.us with Microsoft Mail id <3219CDEF@gw-smtp1.ci.tacoma.wa.us>; Tue, 20 Aug 96 07:38:39 PDT From: "Spires, Caroline" To: "'smtp:chemistry@ccl.net'" Subject: Chemistry Date: Tue, 20 Aug 96 07:19:00 PDT Message-Id: <3219CDEF@gw-smtp1.ci.tacoma.wa.us> Encoding: 12 TEXT X-Mailer: Microsoft Mail V3.0 I am interested in information via email. Thank you Caroline Spires, Laboratory INTERNET: cspires@ci.tacoma.wa.us Mailing address: Caroline Spires 21007 90th Ave Court East Graham, WA 98338-9292 (206)847-9937 From jsb2@camsoft.com Tue Aug 20 11:35:58 1996 Received: from camsoft.com for jsb2@camsoft.com by www.ccl.net (8.7.5/950822.1) id KAA05067; Tue, 20 Aug 1996 10:19:07 -0400 (EDT) From: Date: Tue, 20 Aug 96 10:19:09 EDT Received: by camsoft.com (4.1/3.1.090690-Cambridge Scientific Computing) id AA04867; Tue, 20 Aug 96 10:19:09 EDT Message-Id: <9608201419.AA04867@camsoft.com> To: chemistry@www.ccl.net, paul@heelisp.demon.co.uk Subject: Re: CCL:pdb files >anyone know of a program to put hydrogens on all the amino >acids in a Pdb file?- preferably free. Chem3D Pro will do this, but is not free. Chem3D Net is freely available from http://www.camsoft.com and will do this, and will let you view the hydrogenated structure onscreen, but will not allow you to save the changes. This is a question that comes up periodically. You chould check the CCL archives, probably in the 2-3 months ago range. There are a number of other programs that can do this. I definitely remember a discussion that Macromodel can, but I don't remember the others offhand. Jonathan Brecher CambridgeSoft Corporation jsb@camsoft.com From cynder@juno.com Tue Aug 20 13:18:47 1996 Received: from x8.boston.juno.com for cynder@juno.com by www.ccl.net (8.7.5/950822.1) id MAA05719; Tue, 20 Aug 1996 12:47:39 -0400 (EDT) Received: (from cynder@juno.com) by x8.boston.juno.com (queuemail) id MAA04313; Tue, 20 Aug 1996 12:47:20 EDT To: jsb2@camsoft.com Cc: chemistry@www.ccl.net, paul@heelisp.demon.co.uk Date: Thu, 15 Aug 1996 11:45:13 PST Subject: Re: CCL:pdb files Message-ID: <19960815.114515.8055.2.Cynder@juno.com> References: <9608201419.AA04867@camsoft.com> X-Mailer: Juno 1.00 X-Juno-Line-Breaks: 0-3,5-7,9 From: cynder@juno.com (Kyle Martin) On Tue, 20 Aug 96 10:19:09 EDT writes: >Chem3D Net is freely available from http://www.camsoft.com and will do >this, and will let you view the hydrogenated structure onscreen, but will >not allow you to save the changes. hmm..I don't know about any other web browsers, but with Netscape and America Online, you may save any images. From Mike.Turpin@unilever.com Tue Aug 20 13:26:09 1996 Received: from gatekeeper.homecare.com for Mike.Turpin@unilever.com by www.ccl.net (8.7.5/950822.1) id NAA05857; Tue, 20 Aug 1996 13:08:55 -0400 (EDT) Received: from x500mhub.lo.u1388.unilever.com by gatekeeper.homecare.com (5.65v3.2/1.1.8.2/24Jan95-0439PM) id AA23855; Tue, 20 Aug 1996 18:08:17 +0100 X400-Received: by /c=GB/admd=telemail/prmd=Unilever/; Relayed; 20 Aug 1996 18:05:18 +0100 X400-Received: by mta MTAandromeda in /c=GB/admd=telemail/prmd=Unilever/; Relayed; 20 Aug 1996 18:05:18 +0100 X400-Mts-Identifier: [/c=GB/admd=telemail/prmd=Unilever/; 02D433219F04E019-MTAandromeda] Content-Identifier: 02D433219F04E019 Content-Return: Allowed X400-Content-Type: P2-1988 ( 22 ) Conversion: Allowed Original-Encoded-Information-Types: IA5-Text Priority: normal Disclose-Recipients: Prohibited Alternate-Recipient: Allowed X400-Originator: Mike.Turpin@unilever.com X400-Recipients: non-disclosure; Message-Id: <02D433219F04E019*/c=gb/admd=telemail/prmd=unilever/o=unilever/ou=andromeda/ou=ccmail/s=Turpin/g=Mike/@MHS> Date: 20 Aug 1996 18:05:18 +0100 From: "Mike Turpin" To: "ah45952@ggr.co.uk Anne Hersey glaxo" Anne Hersey glaxo , (Return requested), "ahw1@cus.cam.ac.uk" (Return requested), "ai-sales@aiware.com" (Return requested), "aprice@vishnu.msicam.co.uk" (Return requested), "atiller@vishnu.msicam.co.uk" (Return requested), "brian_h_warrington%notes@sbphrd.com" (Return requested), "c.j.scott@pac.soton.ac.uk" (Return requested), "charlton@hxsgi2.zeneca.co.uk" (Return requested), "CHEMISTRY-REQUEST@www.ccl.net" (Return requested), "CHEMISTRY@www.ccl.net" (Return requested), "clive@msi.com" (Return requested), "d.t.clark@daresbury.ac.uk" (Return requested), "davel@chmqst.demon.co.uk" (Return requested), "davis_am@fisonspharm.co.uk" (Return requested), "debay5f9@ibmmail.com" (Return requested), "dhk@ReactionDesign.com" (Return requested), "dkitson@msicam.co.uk" (Return requested), "erich@biosym.fr" (Return requested), "evers@zx.basf-ag.de" (Return requested), "fleusen@msicam.co.uk" (Return requested), "fordm@biol.port.ac.uk" (Return requested), "fraaije@chem.rug.nl" (Return requested), "gerhard@msicam.co.uk" (Return requested), "ian.wakeling@bbsrc.ac.uk" (Return requested), "jmnewsa@biosym.com" (Return requested), "JohnKendirck@wilton.ici.co.uk" (Return requested), "js@qc.ag-berlin.mpg.de" (Return requested), "K.MCEWEN@UK.AC.BBK.PHYSICS" (Return requested), "lissa@biosym.com" (Return requested), "liz@oxmat.co.uk" (Return requested), "m.cates@ed.ac.uk" (Return requested), "m.f.guest@dl.ac.uk" (Return requested), "m.p.allen@bristol.ac.uk" (Return requested), "Mike_Stapleton@msicam.co.uk" (Return requested), "mischa@basel.sgi.com" (Return requested), "ms@com.sgi.basel" (Return requested), "N.Quirke@bangor.ac.uk" (Return requested), "nilesh@ri.ac.uk" (Return requested), "p.harvey01@ic.ac.uk" (Return requested), "p.j.durham@Daresbury.ac.uk" (Return requested), "p.sherwood@dl.ac.uk" (Return requested), "pcoulter@msicam.co.uk" (Return requested), "richard@ri.ac.uk" (Return requested), "rzepa@ic.ac.uk" (Return requested), "sally@biofocus.u-net.com" (Return requested), "sbriggs@beilstein.com" (Return requested), "schreieck@zx.basf-ag.de" (Return requested), "snaith@mcmaster.ca" (Return requested), "t_r_jones@ecc-jkh.ccmail.compuserve.com" (Return requested), "v.sokhan@ic.ac.uk" (Return requested), "w.smith@daresbury.ac.uk" (Return requested), "wakeling@bbsrc.ac.uk" (Return requested), "mike.turpin@unilever.com" (Return requested) Subject: New Internet Address for Mike Turpin Mime-Version: 1.0 Please note that my new e-mail address is mike.turpin@unilever.com The previous address will only be available for a few weeks. regards Mike Turpin From irikura@ENH.NIST.GOV Tue Aug 20 15:18:49 1996 Received: from ENH.NIST.GOV for irikura@ENH.NIST.GOV by www.ccl.net (8.7.5/950822.1) id OAA08634; Tue, 20 Aug 1996 14:52:58 -0400 (EDT) Received: from h178075 (bratsche.nist.gov) by ENH.NIST.GOV (PMDF V5.0-5 #10952) id <01I8I3Y9KNLS00T08W@ENH.NIST.GOV> for chemistry@www.ccl.net; Tue, 20 Aug 1996 14:54:13 -0400 (EDT) Date: Tue, 20 Aug 1996 14:53:09 -0400 From: Karl Irikura Subject: ACS/Orlando, Panel Discussion: "Computational Thermochemistry" X-Sender: irikura@enh.nist.gov To: chemistry@www.ccl.net Message-id: <01I8I3Y9LZTU00T08W@ENH.NIST.GOV> MIME-version: 1.0 X-Mailer: Windows Eudora Version 2.1.1 Content-type: text/plain; charset="us-ascii" Content-transfer-encoding: 7BIT > Panel Discussion on Computational Thermochemistry > > (Symposium on Computational Thermochemistry) > > Tuesday, August 27, 10-noon Omni-Rosen Hotel, Salon 15 (level 2) > > >Topic areas will include: > > Thermochemical data needs in industry, academia, military, etc. > Bottlenecks in generating data > Experimental verification needs > Suggestions for techniques development (user friendliness, etc.) > Condensed phase data (vaporization heats, sublimation heats,...) > Common, consensus test data set for model verification > >Panel Members: > > Dr. David Frurip (Discussion Leader) > The Dow Chemical Co. > > Dr. Joseph Golab > Amoco Corp. > > Prof. Klavs Jensen > Massachusetts Institute of Technology > > Maj. Walter Lauderdale, Ph.D. > Wright-Patterson AFB > > Dr. George Thomson > Design Institute for Physical Property Research (DIPPR) > > >This panel discussion offers a unique opportunity for both the users of >thermochemical data and the researchers who are developing the techniques to >discuss, in an open forum, how to work toward common goals which are mutually >beneficial. > >If you are involved with the development of new computational methods, >you should come away from this discussion with a clearer picture of the actual >thermochemical needs in both the industrial and academic areas. These needs >may be data on particular classes of compounds or they may be technique-related. > >If you are a user of thermochemical data, this is your opportunity to advertise >your concerns, needs, and experiences to a broad audience. We hope to arrive >at a consensus list of reasonable ideas which can be translated into tangible >action items. > ---------------------------------------------- Dr. Karl K. Irikura Physical and Chemical Properties Division National Institute of Standards and Technology Gaithersburg, MD 20899 voice: 301-975-2510 fax: 301-975-3670 e-mail: irikura@enh.nist.gov ----------------------------------------------