From arthur@csb0.IPC.PKU.EDU.CN Fri Oct 17 00:31:09 1997 Received: from csb0.IPC.PKU.EDU.CN for arthur@csb0.IPC.PKU.EDU.CN by www.ccl.net (8.8.3/950822.1) id XAA26116; Thu, 16 Oct 1997 23:41:03 -0400 (EDT) Received: by csb0.IPC.PKU.EDU.CN (920330.SGI/940406.SGI.AUTO) for chemistry@www.ccl.net id AA20045; Fri, 17 Oct 97 11:40:17 -0700 Date: Fri, 17 Oct 1997 11:40:17 -0700 (PDT) From: Wang Arthur To: CCL mailing list Subject: Where to find GOLPE? Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear netters, We know GOLPE is a very useful procedure for optimizing PLS analysis. Our question is: How and where can we get a copy of GOLPE? Any clue will be surely appreciated. Best wishes, Arthur _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ Arthur Wang Doctoral Candidate _/ _/ Molecular Design Lab _/ _/ Institute of Physical Chemistry, Peking University _/ _/ Beijing 100871, P.R.China _/ _/ _/ _/ E-mail: arthur@ipc.pku.edu.cn _/ _/ Tel: 86-10-62751490 Fax: 86-10-62751725 _/ _/ WWW: http://www.ipc.pku.edu.cn/moldes/arthur/home.html _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ From wdi@TORVS.CCC.Uni-Erlangen.DE Fri Oct 17 05:31:13 1997 Received: from enar.organik.uni-erlangen.de for wdi@TORVS.CCC.Uni-Erlangen.DE by www.ccl.net (8.8.3/950822.1) id EAA27214; Fri, 17 Oct 1997 04:46:24 -0400 (EDT) Received: from wtewael (wtewael.organik.uni-erlangen.de) by enar.organik.uni-erlangen.de with SMTP id AA23521 for CHEMISTRY@www.ccl.net (5.65c/IDA-1.4.4/bs-02); Fri, 17 Oct 1997 10:46:37 +0100 Received: (from wdi@localhost) by wtewael (950413.SGI.8.6.12/950213.SGI.AUTOCF) id KAA19967; Fri, 17 Oct 1997 10:46:35 +0100 From: "Wolf-Dietrich Ihlenfeldt" Message-Id: <9710171046.ZM19965@eros.ccc.uni-erlangen.de> Date: Fri, 17 Oct 1997 10:46:34 +0100 In-Reply-To: Paul Beroza "CCL:2D chemical structure generation" (Oct 16, 17:06) References: <3.0.3.32.19971016170637.0095d530@leonardo.info.combichem.com> Reply-To: wdi@eros.ccc.uni-erlangen.de X-Phones: +49-9131-85-6579 X-Fax: +49-9131-85-6566 X-Mailer: Z-Mail (3.2.2 10apr95 MediaMail) To: Paul Beroza Subject: Re: CCL:2D chemical structure generation Cc: CHEMISTRY@www.ccl.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 8bit On Oct 16, 17:06, Paul Beroza wrote: > Subject: CCL:2D chemical structure generation > > Hi All, > > I have a molecule (several molecules actually) in an SD formatted file. > The connectivity and stereochemistry are correct, but the coordinates > are bogus. Is there a program out there that can generate reasonable > looking 2-D coordinates (preferably in SD format) for the compounds? > > Alternatively, is there a program that can convert a set of SMILES > strings in a file to reasonable looking 2-D structures in SD format > (with the proper stereochemistry)? > > Thanks for the help, > > Paul Beroza > CombiChem, Inc. > beroza@info.combichem.com > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: beroza@info.combichem.com > -- Original Sender From: Address: beroza@info.combichem.com > 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 > >-- End of excerpt from Paul Beroza Yes, there is. Please have a look at http://www2.organik.uni-erlangen.de/services/gif.html The underlying program can both input SMILES and SD, and output as SD (plus a whole bunch of other formats). Stereochemistry is fully supported. Feel free to send me a sample for conversion. -- 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 --- The three proven methods for ultimate success and fame: 1) Nakanu nara koroshite shimae hototogisu 2) Nakanu nara nakasete miseyou hototogisu 3) Nakanu nara naku made matou hototogisu From s.hogg@ic.ac.uk Fri Oct 17 06:31:13 1997 Received: from romeo.ic.ac.uk for s.hogg@ic.ac.uk by www.ccl.net (8.8.3/950822.1) id GAA27673; Fri, 17 Oct 1997 06:30:51 -0400 (EDT) Received: from judy.ic.ac.uk [155.198.5.5] by romeo.ic.ac.uk with esmtp (Exim 1.62 #1) id 0xM9fX-0007eB-00; Fri, 17 Oct 1997 11:30:11 +0100 Received: from mtcmsa.mt.ic.ac.uk (root@mtcmsag1.mt.ic.ac.uk [155.198.96.22]) by judy.ic.ac.uk (8.7.5/8.7.5) with SMTP id LAA11102 for ; Fri, 17 Oct 1997 11:29:53 +0100 (BST) Received: from mtcse.mt.ic.ac.uk by mtcmsa.mt.ic.ac.uk (5.x/4.1) id AA14264; Fri, 17 Oct 1997 11:29:51 +0100 X-Received: from dialup-1-13.net.ic.ac.uk by mtcse.mt.ic.ac.uk; Fri, 17 Oct 1997 11:29:49 +0100 Message-Id: <3.0.3.32.19971017043951.006ece48@155.198.100.1> X-Sender: seth@155.198.100.1 X-Mailer: QUALCOMM Windows Eudora Pro Version 3.0.3 (32) Date: Fri, 17 Oct 1997 04:39:51 +0100 To: chemistry@www.ccl.net From: Simon Hogg Subject: Holographic Representation of Molecules - summary Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Well, thanks to those who replied, but I'm afraid the news isn't that good; Yes, holograms can be produced from 3-d file formats (pdb, xyz, povray scenes) but the mastering is expensive. One commercial service I contacted wanted 1000 USD for a master (10x20 cm) but after that it was about 20 cents per produced image. It will probably be cheaper if there is someone in your college who makes holograms (perhaps for medical imaging) Another option suggested was to use autostereograms (the 'dot' pictures) but guess that doesn't work for everybody - although it's more or less free. -- Simon Hogg, Imperial College, London, UK Tel. +44 171 589 5111 ext. 56721 Fax. +44 171 584 3194 Email: s.hogg@ic.ac.uk Glass-List: glass-list@ic.ac.uk From morreale@chem.iupui.edu Fri Oct 17 08:31:15 1997 Received: from plato.chem.iupui.edu for morreale@chem.iupui.edu by www.ccl.net (8.8.3/950822.1) id IAA28029; Fri, 17 Oct 1997 08:00:05 -0400 (EDT) Received: from localhost by plato.chem.iupui.edu (940816.SGI.8.6.9/MSU-2.04) id MAA15787; Fri, 17 Oct 1997 12:22:43 GMT Date: Fri, 17 Oct 1997 07:22:43 -0500 (EST) From: Antonio Morreale To: chemistry@www.ccl.net Subject: Drug desing and de novo design Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi all, I have couple questions regarding drug design: 1. (I posted this one before, but due to mail problems, I'm not sure it was in the list). I'm looking for some information about drug design for undergraduets. I refer to some kind of simple exercises that show basic techniques in this field. Any information, like books, papers, WWW pages or personal experience will be greatly apreciated. 2. This question is related with my PhD project in de novo desig. I want to buy some software, or get some free one, to begin with, so I'll apreciate so much personal experiences with this kind of program, which are more friendly to work with, which are available, which one I should avoid... Thank you very much in advance. Antonio Morreale. morreale@chem.iupui.edu From PEARLMAN@VAX.PHR.UTEXAS.EDU Fri Oct 17 09:31:20 1997 Received: from VAX.PHR.UTEXAS.EDU for PEARLMAN@VAX.PHR.UTEXAS.EDU by www.ccl.net (8.8.3/950822.1) id JAA28453; Fri, 17 Oct 1997 09:26:17 -0400 (EDT) From: Date: Fri, 17 Oct 1997 8:26:18 -0500 (CDT) To: CHEMISTRY@www.ccl.net CC: PEARLMAN@VAX.PHR.UTEXAS.EDU Message-Id: <971017082618.1fd15@VAX.PHR.UTEXAS.EDU> Subject: LAST CALL -- Chemical Diversity at Dallas ACS Meeting Hello -- This is the FINAL CALL for abstracts for the "Diverse Perspectives of Chemical Diversity" symposium scheduled for March 31 and April 1 of the ACS Meeting in Dallas next spring. Topics will include: - chemistry-space metrics (including fingerprints) - metric validation - diversity-related algorithms - use of diversity software for library design, pro's and con's - use of diversity software for other diversity-related tasks, pro's and con's In keeping with recent tradition, the symposium program will be a mix of invited and contributed papers. If you would like to present a 30-minute talk at this symposium, please send me an abstract **IMMEDIATELY** . I look forward to hearing from you! -- Bob Pearlman Robert S. Pearlman, Ph.D Coulter R. Sublett Regents Chair in Pharmacy and Director, Laboratory for Molecular Graphics and Theoretical Modeling College of Pharmacy University of Texas Austin, Texas 78712 512-471-3383 (voice) 512-471-7474 (FAX) pearlman@vax.phr.utexas.edu From sps@dou.dk Fri Oct 17 10:31:15 1997 Received: from gamma.dou.dk for sps@dou.dk by www.ccl.net (8.8.3/950822.1) id KAA28632; Fri, 17 Oct 1997 10:00:07 -0400 (EDT) Received: from localhost (sps@localhost) by gamma.dou.dk (8.8.6/8.8.4) with SMTP id PAA26445 for ; Fri, 17 Oct 1997 15:59:55 +0200 (METDST) Date: Fri, 17 Oct 1997 15:59:55 +0200 (METDST) From: "Stephan P.A. Sauer" Reply-To: "Stephan P.A. Sauer" To: CHEMISTRY@www.ccl.net Subject: CCL:geometry of Anthracene Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I am looking for experimentally or theoretically determined bondlengths and bondangles of C10H14 anthracene. Stephan -------------------------------------------------------------------------------- Stephan P. A. Sauer Assistant Professor | Department of Physical Chemistry | Tel : +45-35320268 H. C. {\O}rsted Institute | Fax : +45-35320299 University of Copenhagen | E-mail : sps@dou.dk Universitetsparken 5 | http://ithaka.ki.ku.dk/~sps DK-2100 Copenhagen {\O}, Denmark | -------------------------------------------------------------------------------- From jsb2@camsoft.com Fri Oct 17 10:35:05 1997 Received: from camsoft.com for jsb2@camsoft.com by www.ccl.net (8.8.3/950822.1) id KAA28752; Fri, 17 Oct 1997 10:26:32 -0400 (EDT) From: Date: Fri, 17 Oct 97 10:26:33 EDT Received: by camsoft.com (4.1/3.1.090690-CambridgeSoft Corp.) id AA08322; Fri, 17 Oct 97 10:26:33 EDT Message-Id: <9710171426.AA08322@camsoft.com> To: CHEMISTRY@www.ccl.net, beroza@info.combichem.com Subject: Re: CCL:2D chemical structure generation >I have a molecule (several molecules actually) in an SD formatted file. >The connectivity and stereochemistry are correct, but the coordinates >are bogus. Is there a program out there that can generate reasonable >looking 2-D coordinates (preferably in SD format) for the compounds? ChemOffice Ultra for Windows will do this. We ran the public NCI SD file (127,000 compounds with connectivity but no coordinates) overnight. No particular problems, except for some highly-bridged polycycles which aren't going to look particularly good in two dimensions without lots of subjective human attention. >Alternatively, is there a program that can convert a set of SMILES >strings in a file to reasonable looking 2-D structures in SD format >(with the proper stereochemistry)? ChemOffice Ultra will do this as well. Jonathan Brecher CambridgeSoft Corporation jsb@camsoft.com From jochen@pc1.uni-duesseldorf.de Fri Oct 17 11:31:24 1997 Received: from sirene.rz.uni-duesseldorf.de for jochen@pc1.uni-duesseldorf.de by www.ccl.net (8.8.3/950822.1) id KAA28904; Fri, 17 Oct 1997 10:42:02 -0400 (EDT) Received: from bacchus.pc1.uni-duesseldorf.de by sirene.rz.uni-duesseldorf.de with SMTP (PP); Fri, 17 Oct 1997 16:41:29 +0200 Received: by bacchus.pc1.uni-duesseldorf.de (5.65v3.2/1.1.10.5/06Jan97-0309PM) id AA04460; Fri, 17 Oct 1997 16:41:28 +0200 Date: Fri, 17 Oct 1997 16:41:28 +0200 From: Jochen Kuepper Message-Id: <9710171441.AA04460@bacchus.pc1.uni-duesseldorf.de> To: chemistry@www.ccl.net, s.hogg@ic.ac.uk Subject: Re: CCL:Holographic Representation of Molecules - summary Reply-To: jochen@uni-duesseldorf.de MIME-version: 1.0 Content-type: text/plain; charset="ISO-8859-1" Content-transfer-encoding: quoted-printable Content-Md5: bxNqSjqj/mHPALLWwC7/zw== Simon Hogg wrote: :> Another option suggested was to use autostereograms (the 'dot' = pictures) :> but guess that doesn't work for everybody - although it's more or = less free. Any program available that makes printable files from a structure ? (Preferably color Postscript output, best it would run on one or another Unix.) Jochen ----------------------------------------------------------------------- Jochen K=FCpper Heinrich-Heine-Universit=E4t D=FCsseldorf = jochen@uni-duesseldorf.de Institut f=FCr Physikalische Chemie I Universit=E4tsstrasse 1, Geb 26.43.02.19 phone ++49-211-8113681 40225 D=FCsseldorf fax ++49-211-8115195 Germany http://www-public.rz.uni-duesseldorf.de/~jochen ----------------------------------------------------------------------- From elewars@alchemy.chem.utoronto.ca Fri Oct 17 15:31:20 1997 Received: from alchemy.chem.utoronto.ca for elewars@alchemy.chem.utoronto.ca by www.ccl.net (8.8.3/950822.1) id PAA01019; Fri, 17 Oct 1997 15:06:31 -0400 (EDT) Received: (from elewars@localhost) by alchemy.chem.utoronto.ca (8.7.4/8.7.3) id PAA02822 for chemistry@www.ccl.net; Fri, 17 Oct 1997 15:06:30 -0400 (EDT) Date: Fri, 17 Oct 1997 15:06:30 -0400 (EDT) From: "E. Lewars" Message-Id: <199710171906.PAA02822@alchemy.chem.utoronto.ca> To: chemistry@www.ccl.net Subject: EXTENDED HUCKEL--COMMENT AND THANKS Frid, 1997 Oct 17 >From E. Lewars To: CCL Subj: Extended Huckel Method Thanks to all who responded to my question (below) about the extended Hueckel method as popularized by Roald Hoffmann. The answers (below) all agree that the overlap matrix is calculated and used to obtain an orthogonalizing matrix-- i.e the S matrix is _not_ taken as a unit matrix. Two points may not be generally realized: (1) Because the overlap _integrals_ S are used to calculate the Fock matrix elements (1/2KS(I + I')), it does _not_ follow that the overlap _matrix_ must be used, and in fact (2) There _is_ an extended Hueckel-type method that simply sets the overlap matrix equal to the unit matrix: S. L. Dixon and P. C. Jurs, "Fast geometry optimization using a modified extended Hueckel method...", J. Comp Chem 15 (7), 733-746 (1994). With several modifications to the Fock elements it is said to match or surpass AM1 geometries. Thanks again, E. Lewars ================ ================ Hello, Regarding the extended Hueckel method as implemented by Roald Hoffmann: I know that the overlap integrals are calculated and used to construct the Fock matrix elements (which are proportional to these integrals in the EHM). My question is: in Hoffmann's implementation are the overlap integrals used to calculate an orthogonalizing matrix to convert (e.g. by Loewdin orthogonalization) the matrix equation FC = SCe into standard eigenvalue form F'C' = C'e i.e F' = C'eC'^-1 as in ab initio calculations, OR is it simply pretended, as in simple Hueckel theory, that S=I ? I read Hoffmann's 1963 paper in J Chem Phys, but this point does not seem to be explicity made clear. Maybe I missed it. Thanks E. Lewars ================ ====================== Message 1: >From sasha@chem.uit.no Wed Oct 15 11:40:35 EDT 1997 Date: Wed, 15 Oct 1997 17:41:53 +0200 (MDT) >From: "Alexander Bagatur'yants" To: "E. Lewars" Subject: Re: CCL:EXTENDED HUECKEL AND ORTHOGONALIZATION Dear Dr. Lewars Certainly all overlap integrals are taken into account, which is the essence of EHT. Best wishes =========================================================== # Prof. Alexander A. Bagatur'yants # # Photochemistry Center, Russian Academy of Sciences, # # ul. Novatorov 7a, Moscow, 117421, Russia # # Phone: (007)-(095)-433-5325 h. (007)-(095)-936-2588 o. # # Fax: (007)-(095)-936-1255; e-mail: sasha@mx.icp.rssi.ru # #---------------------------------------------------------# # Till November 20, 1997 # # Department of Chemistry, Faculty of Science, # line 1 [h for help]# University of Tromsoe, 9037 Tromsoe, Norway, # # Phone: +47-776-44078; e-mail: sasha@chem.uit.no # =========================================================== Message 2 >From wall@phys.chem.ethz.ch Wed Oct 15 12:42:13 EDT 1997 Date: Wed, 15 Oct 1997 18:42:03 +0200 (CEST) >From: Ernst-Udo Wallenborn To: "E. Lewars" Subject: CCL:EXTENDED HUECKEL AND ORTHOGONALIZATION Hi there, well S is real and symmetric, hence it can be diagonalised. Its eigenvalues are usually <>0, so S^-1 exists. Thus, HC = SCe is multiplied to the left by S^-1 S^-1H C = Ce voila. =============== Message 3: >From adrian@aer.nist.gov Wed Oct 15 13:38:24 EDT 1997 >From: "Adrian Roitberg" Date: Wed, 15 Oct 1997 13:37:42 -0400 To: "E. Lewars" Subject: Re: CCL:EXTENDED HUECKEL AND ORTHOGONALIZATION Hi, MY experience with Hoffman's ICON program (QCPE) is that the S matrix is indeed computed. In fact, the H matrix is computed as : H_ij = K/2 S_ij * (H_ii + H_jj) and then solve for HC = SHe as you said. Icon takes care of orbital type (s, p) and distances to compute the S matrix. Adrian E. Roitberg ======================================================================== NIST | Phone: (301) 975-4469. Building 222, A-353 | Fax (301) 975-5449 Gaithersburg, MD 20899 | E-mail : adrian@nist.gov ============================================================================================ Message 4: >From sichelj@UMoncton.ca Wed Oct 15 14:02:43 EDT 1997 Date: Wed, 15 Oct 1997 15:04:26 -0300 (ADT) >From: "J. Sichel" Subject: Re: CCL:EXTENDED HUECKEL AND ORTHOGONALIZATION To: "E. Lewars" Cc: chemistry@www.ccl.net Yes, Hoffmann's EH method uses explicit Lowdin orthogonalization; I remember working through a copy of his computer code as a graduate student in 1964! As for his 1963 JCP paper, he does say (p.1399) that "the complete set of Eq.(2) [the secular equations] is solved with _two_ matrix diagonalizations." If S = 1 were assumed, only one diagonalization would be required. John Sichel Dept de chimie et biochimie Universite de Moncton, NB, Canada ============== Message 5 x-sender: rkanters@facstaff.richmond.edu >From: Ren=?ISO-8859-1?Q?=e9_Kanters?= To: "E. Lewars" Dear Dr. Lewars, The overlap matrix is calculated explicitely. It has to, otherwise it would be just Huckel and not Extended Huckel, as you pointed out yourself. Rene P.F. Kanters, Ph.D. Chemistry Project Specialist Chemistry Department University of Richmond VA 23173 phone: (804) 287 6873 www: http://www.science.richmond.edu/~kanters email: rkanter@richmond.edu ===== Message 6 Subject: Re: CCL:EXTENDED HUECKEL AND ORTHOGONALIZATION To: elewars@alchemy.chem.utoronto.ca (E. Lewars) Date: Thu, 16 Oct 1997 09:31:50 +0930 (CST) All EHM programs solve FC = SCe exactly. The best way is to use the Choleski decoimposition, I believe. Cheers, Brian. -- Associate Professor Brian Salter-Duke (Brian Duke) School of Mathematical and Physical Sciences, Northern Territory University, Darwin, NT 0909, Australia. Phone (61) (0)8-89466702 e-mail: b_duke@lacebark.ntu.edu.au or b_duke@quoll.ntu.edu.au ============= From mikha001@maroon.tc.umn.edu Fri Oct 17 17:31:20 1997 Received: from mhub2.tc.umn.edu for mikha001@maroon.tc.umn.edu by www.ccl.net (8.8.3/950822.1) id RAA02244; Fri, 17 Oct 1997 17:28:38 -0400 (EDT) Received: from maroon.tc.umn.edu by mhub2.tc.umn.edu; Fri, 17 Oct 97 16:28:27 -0500 Received: from localhost by maroon.tc.umn.edu; Fri, 17 Oct 97 16:28:27 -0500 Date: Fri, 17 Oct 1997 16:28:26 -0500 (CDT) From: Dmitri V Mikhailov To: CHEMISTRY@www.ccl.net Subject: surface docking Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello netters, I am trying to do MM calculations for interactions between a protein and a surface. I would like to construct different atomic level models for the surface and "dock" a protein to them. Could anyone point me to a reference in a literature or existing software that could handle such a relatively big system (~40000 atoms) and estimate the "most favorable" position of a protein on atomic surfaces. I am quite new to this area of surface simulations, so any advise will be greatly appreciated. Thank you. Regards, Dmitri Mikhailov Ph.D. student ***************************************************** Univ. of Minnesota Medical School Department of Biochemistry 312 Church St, BSBE 5-258 Minneapolis MN 55455 tel. (612) 625-8611 fax. (612) 624-5121 e-mail: mikha001@maroon.tc.umn.edu WWW : http://tyr.med.umn.edu/~dimitri/ *****************************************************