From acklin@chbs.CIBA.COM Wed Apr 5 05:41:53 1995 Received: from chsun.eunet.ch for acklin@chbs.CIBA.COM by www.ccl.net (8.6.10/930601.1506) id FAA07932; Wed, 5 Apr 1995 05:31:57 -0400 Received: from Ciba-GW.CHBS.CIBA.COM by chsun.eunet.ch (8.6.10/1.34) id LAA02486; Wed, 5 Apr 1995 11:32:49 +0200 Received: from Central.CHBS.CIBA.COM by Ciba-GW.CHBS.CIBA.COM (4.1/Ciba2.0-R1.0) id AA25916; Wed, 5 Apr 95 11:32:01 +0200 Received: from camm1.ph.chbs by Central.CHBS.CIBA.COM id AA17899; Wed, 5 Apr 1995 11:31:37 +0200 (5.65c8/Ciba2.0-C1.1) Received: by camm1.ph.chbs (931110.SGI/930416.SGI/camm.ph.chbs-1.0) for @cgchm.is.chbs:chemistry@ccl.net id AA10780; Wed, 5 Apr 95 11:35:03 +0200 From: "Dr.Pierre Acklin" Message-Id: <9504051135.ZM10778@camm1.ph.chbs> Date: Wed, 5 Apr 1995 11:35:03 +0000 X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: chemistry@ccl.net Subject: clogP summary Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 Netters, five days ago I asked the following question; > are there some kind of programs available to calculate logP, delta logP, > solvation values preferably on PC or Mac available to an affordable price. > I'd like to thank all of you who answered my request and post the summary to the net. Pierre ***************************************************************************** Summary ****************************************************************************** Hi - There was a similar question a while ago - I still have the summary. I'll mail it on to you and hope it is useful. Best wishes David David E. Clark | Proteus Molecular Design Ltd., | Tel: 01625-500555 Lyme Green Business Park, | Fax: 01625-500666 Macclesfield, Cheshire, | Email: D.E.Clark@proteus.co.uk SK11 0JL, UK | Date: Fri, 26 Aug 94 09:47:47 EST From: pballester Hello, Thanks to everybody who responded to my question regarding logP calculation software. Here i is a summary of replies I got to my question. ****************************ANSWERS****************************************** >From riusal@redvax1.dgsca.unam.mx Thu Aug 25 22:51:09 1994 I have used Hyperchem and chemplus to do LogP calculation of organic compounds and the agreement is quite good. Chemplus is a program that runs under Hyperchem Autodesk use to market Hyperchem but now is market directly from Hypercube from Canada. With my best regars Carlos ============================================================ >From dec@proteus.co.uk Fri Aug 26 07:39:56 1994 Dear Pau I'm not sure if there is a corresponding program available but there was recently a good article on the subject : @article{Klop94 , author = "Klopman, G., Li, J.-Y., Wang, S. and Dimayuga, M. ", title = "Computer Automated log P Calculations Based on an Extended Group Contr ibution Approach ", journal = "Journal of Chemical Information and Computer Sciences ", year = "1994 ", volume = "34 ", pages = "752--781 ", } Best wishes David E. Clark ============================================================= Hello Pau, A good commercial PC program for calculating log P is available from CheMicro Ltd Hegedus Gy. u. 6. H-1136 Budapest Hungary phone: (+36-1)-131 3847 fax: (+36-1)-132 9330 best wishes Tamas ***************************************************************************** Tamas E. Gunda phone: (+36-52) 316666 ext 2479 Research Group of Antibiotics fax : (+36-52) 310936 L. Kossuth University e-mail: tamasgunda@tigris.klte.hu POBox 36 tamasgunda@huklte51.bitnet H-4010 Debrecen Hungary ***************************************************************************** ============================================================= >From HODGKINE@prince.mm.wyeth.com Fri Aug 26 03:14:48 1994 From: Hodgkin, Ed Date: Fri, Aug 26, 1994 8:43 AM Subject: LogP To: pau@cubist.com Pau I'm also interested in logP calculation. Can you post a summary of replies to the CCL please? Edward Hodgkin Wyeth Research (UK) Ltd hodgkine@prince.mm.wyeth.com ============================================================= Hello Pau, A good commercial PC program for calculating log P is available from CheMicro Ltd Hegedus Gy. u. 6. H-1136 Budapest Hungary phone: (+36-1)-131 3847 fax: (+36-1)-132 9330 best wishes Tamas ***************************************************************************** Tamas E. Gunda phone: (+36-52) 316666 ext 2479 Research Group of Antibiotics fax : (+36-52) 310936 L. Kossuth University e-mail: tamasgunda@tigris.klte.hu POBox 36 tamasgunda@huklte51.bitnet H-4010 Debrecen Hungary ***************************************************************************** ============================================================= Dear Dr. Ballester; CompuDrug Chemistry, Ltd. markets a pretty good Windows-based programme called "PrologP 5.0" which enables you to estimate log P values for organic molecules from input structural information. For more information, contact: Dr. Zoltan Bencz, Marketing Director CompuDrug Chemistry, Ltd. Fuerst Sandor utca 5 H-1136 Budapest, Hungary Internet: bz@cdk-cgx.hu or mktg@cdk-cgx.hu FAX-nr: (0036 1) 132-2574 Dr. Bencz is most helpful and fluent in English. Needless to say, PrologP 5.0 is also in English. The programme is relatively simple and straightfor- ward, doesn't require VAX or other expensive, high-power computers/work sta- tions, and you can learn how to use it rather quickly without the assistance of a couple of Ph.D. computational chemists standing behind you. What more can you ask for? Best regards, (Dr.) S. Shapiro Institute fuer orale Mikrobiologie und allgemeine Immunologie Zentrum fuer Zahn-, Mund-, und Kieferheilkunde der Universitaet Zuerich Plattenstrasse 11 Postfach CH-8028 Zuerich, Switzerland Internet: toukie@zui.unizh.ch FAX-nr: (0041 1) 261'56'83 ============================================================= Try CHEMICALC-2 from QCPE. Available in PC and VAX (?) versions Stephen B. Bowlus, Ph.D. Computer-Aided Molecular Design Research Division e-mail: bowlus@sandoz.com Sandoz Agro, Inc. Phone: + 1 415 354 3904 975 California Ave. Fax: + 1 415 857 1125 Palo Alto, CA 94304 ============================================================= >From riusal@redvax1.dgsca.unam.mx Thu Aug 25 22:51:09 1994 I have used Hyperchem and chemplus to do LogP calculation of organic compounds and the agreement is quite good. Chemplus is a program that runs under Hyperchem Autodesk use to market Hyperchem but now is market directly from Hypercube from Canada. With my best regars Carlos ============================================================= > Does anybody know of some program or utility to calculate logP > values for organic compounds. Please E-mail directly to me. > I sell a program called MOLGEN which calculates log(p), also, distribution on surface or in a plane of the molecule. The latter calculation is displayable/plottable as a color gradient depiction. It can also calculate conformationally/temperature dependency with respect to log(p). Henry's constant is being added shortly. The program is also a full-featured 3-D modelling program and database with MM2, etc. There is a demo on ccl.net in /pub/chemistry/software/MS-DOS/MOLGEN-demo. Please let me know if I can be of further assistance. PS: I have also used LOGKOW from Syracuse Research, an excellent program, but lacks the feature set in Molgen. Eric _____________________________________________________________________ J. Eric Slone Scientific Consulting Services Serving Government & Industry Since 1982 Internet: eslone@mason1.gmu.edu Compuserve: 73757,2776 "True science teaches, above all, to Fax: (703) 751-6639 doubt, and to be ignorant." Voice: (703) 461-7078 Miguel do Unamuno ______________________________________________________________________ ============================================================= >From shaomeng@helix.nih.gov Thu Aug 25 16:37:32 1994 Dear Pau, We have developed a logP calculation model and the paper concering it has been published in Journal of Chemical Information and Computer Sciences, 1994, Vol. 34, pages 752. I will be gald to send you a reprint if you need. If you are also interested in the program, you can get in touch with Dr. Mario Dimayuga at Case Western Reserve Univ (216)368-3699. I am sure he will be happy to anwser your questions. Hope this will help. With my best regards, -- Ju-Yun Li --- Department of Chemistry Case Western Reserve University Cleveland, Ohio 44106 =========================================================== Computational Chemistry Scientists: I have seen a number of queries on this forum about hydrophobicity. A new program to evaluate HYDROPHOBICITY at the atomistic level recently became available, called HINT. Thanks to Tudor-Ionel Oprea for support comments of HINT. This program is based on empirical data and hydrophobic fragment work of Hansch, Leo, Abraham, and Kellogg. The program can: calculate log P (of small molecules and proteins), score ligand/macromolecule and macromolecule/macromolecule interactions, calculate 3D HYDROPATHY (hydrophobic + hydrophilic) fields, create hydropathic complementarity maps, produce unique 3D hydropathic interaction maps, and is interfaced with InsightII, Sybyl and ChemX. If you are interested in additional information or a free trial of this software, please see the file HINT.note on the CCL archivess (infomeister) or contact me at the address below. You can find a comprehensive list of HINT functionality, the references to publications which describe HINT use, and ordering information in CCL archives. To get it via mail, send a message: select chemistry get info/software-packages/HINT.note to MAILSERV@ccl.net. This file is also available via gopher/anon.ftp/WWW from the /pub/chemistry/info/software-packages/HINT.note on www.ccl.net: gopher www.ccl.net 73 (info/software-packages/Hint.note) -- ************** David N. Haney, Ph.D. **************** * Haney Associates Phone - 619-566-1127 * * 12010 Medoc Ln. * * San Diego, CA 92131 Fax - 619-586-1481 * ************** Email - haney@netcom.com *************** ============================================================ A public domain program for calculating logP of small molecules is CHEMICALC-2, available from QCPE for VAX or PC (QCPE 608 or QCMP 129, respectively). Stephen B. Bowlus, Ph.D. Computer-Aided Molecular Design Research Division e-mail: bowlus@sandoz.com Sandoz Agro, Inc. Phone: + 1 415 354 3904 975 California Ave. Fax: + 1 415 857 1125 Palo Alto, CA 94304 ============================================================== Thanks again, Pau Pablo Ballester Cubist Pharmaceuticals, Inc. 24 Emily St. Cambridge MA 02139 E-mail: pau@cubist.com David E. Clark | Proteus Molecular Design Ltd., | Tel: 01625-500555 Lyme Green Business Park, | Fax: 01625-500666 Macclesfield, Cheshire, | Email: D.E.Clark@proteus.co.uk SK11 0JL, UK | Pierre, Spartan is able to calculate LogP's - there is one model in V3.1 and two additional models in V4.0 (which is due to ship in April). Have you seen or used Spartan - I recall that Ciba in the US is running the code... Several models (Bodor, Ghose/Crippen, Villar) have been described in the literature in the last couple of years (J Am Chem Soc and J Comp Chem). Joe -- ------------------------------------------------------------------------ Joe Leonard Wavefunction Inc. 18401 Von Karman, Suite 370 Irvine, CA 92715 I am a professional... 714-955-2120 do not attempt this at home. 714-955-2118 fax jle@wavefun.com Hi, Pierre. > are there some kind of programs available to calculate logP, delta logP, > solvation values preferably on PC or Mac available to an affordable price. The QSAR Properties module of our ChemPlus package will calculate logP, hydration energy, and a variety of other properties. We do not have a version for the Mac; our software runs under Windows on a PC. This ChemPlus module works only with our own .HIN format; to get much use out of the program you would need to use HyperChem. I can send you information about both of these programs if you wish. The academic price for HyperChem is $US995, and for ChemPlus, US$495. Regards, Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com Hypercube Inc, 7-419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" to hyperchem-request@hyper.com I would appreciate it very much if you would forward to me any replies you recieve on this. The CaCHe system includes a program called BlogP by N. Bodor which will calculate logP, with some restrictions after a MOPAC calculation has been performed. Personal Cache is software which will run on a MAC (though I'm not sure it includes MOPAC). Otherwise you will need a server/card for your system. It is very user friendly. ******************************************************************************* Randy Winchester Institute for Drug Development 14960 Omicron Drive San Antonio TX 78210 (210) 677-3800 ph (210) 677-8814 fax rwinches@arnie.iddw.saci.org ******************************************************************************* > are there some kind of programs available to calculate logP, delta logP, >solvation values preferably on PC or Mac available to an affordable price. I would like to see the summary of the responses you receive to this query. Thank you. Wally ======================================================================== Walter E. Reiher III, Ph.D. WallyR@netcom.com Consultant in Computational Chemistry P.O. Box 61056 voice 408-720-0240 Sunnyvale, CA 94088 fax 408-720-0378 Hello, BioByte offers a Mac version of Al Leo's cLogP (Chem. Rev. 1993, 93, 1281). I believe the academic price is approximately $400. You can reach BioByte at P.O. Box 517, Claremont, CA 91711. Email: clogp@medchem.claremont.edu or WWW http://medchem.claremont. edu. Nancy Brichford Monsanto New Ag Products St. Louis, MO nlbric@mtcamm.monsanto.com Im sure others will inform you, but Al Leo's group at Pomona (BioByte), is offering the clogp program for mac, and soon to offer a pc version. (email al@iris.claremont.edu). You might also see Meylan & Howard, Atom/Fragment contribution method for estimating octanol-water partition coeffs", J Pharm Sci, 1995, 84, 83-92 - program LOGKOW. >From: "Dr.Pierre Acklin" >Date: Fri, 31 Mar 1995 14:45:34 +0000 >Subject: CCL:calculated logP > >Dear Netters, > > are there some kind of programs available to calculate logP, delta logP, >solvation values preferably on PC or Mac available to an affordable price. > >Pierre Dear Dr. Acklin: We (BioByte Corp., based in Claremont, CA) have a ClogP calculator available for the Macintosh, called MacLogP. It uses the same fragment based methodology as our Medchem ClogP for the VAX, developed by Drs. Albert Leo and Corwin Hansch. It accepts SMILES input in single and batch mode, and output can be given in three levels of verbosity: terse, detailed, and verbose. A 2D depiction is also given to verify structure. In addition to the ability to calculate ClogP, it also contains high confidence measured values for 9000 well-known structures, which can also be searched for by name. We can send you a copy with a 30 day evaluation license either on a diskette or via e-mail. For the e-mail version, you would need to be able to decode BinHex4.0 (.hqx) files. If, after evaluating the program, you should wish to purchase it, we can send you a permanent license for $998. Please e-mail me and let me know if you would like us to send you the evaluation copy, and which method of delivery you would prefer. Looking forward to hearing from you, Michael L. Medlin BioByte License Manager -- michael l. medlin | biobyte al@iris.claremont.edu | phone 909.624.5992 http://iris.claremont.edu/~al/ | fax 909.624.1398 Subject: Time:10:44 AM OFFICE MEMO LOG P Date:3/31/95 MacClogP is a Macintosh version of the well known CLOGP program. MacClogP is available from Biobyte Corp at the following address: Biobyte Corp. 201 West 4th St. Suite 204 Claremont, CA 91711 USA Phone: 909-624-5992 FAX: 909-624-1398 Email: biobyte@medchem.claremont.edu Gene Pierre: There is a code, HINT, which adds onto the Sybyl, InsightII or ChemX molecular modeling interface. This code not only calculates logP but creates 3-D hydropathy fields to assist in understanding docking. HINT is available for SGI only and the commercial price for one machine is $5,000. Should you be interested in trialing this software for free, I will send you a demo license. -- ************** David N. Haney, Ph.D. **************** * Haney Associates Phone - 619-566-1127 * * 12010 Medoc Ln. * * San Diego, CA 92131 Fax - 619-586-1481 * ************** Email - haney@netcom.com *************** Dear Pierre, I am not very familiar with those kinds of calculations, but I think the programs you are looking for are a part of the CAChe Worksystem. CAChe Europe can be reached at: Alan Day European Sales Manager tel (0628) 486000 fax (o628) 474799 in England. Hope this is of any help. Best regards, Mirko Kranenburg University of Amsterdam Dept. of Inorganic Chemistry and Homogeneous Catalysis Nieuwe Achtergracht 166 1018 WV Amsterdam The Netherlands tel. +31-20-5256417 fax. +31-20-5256456 e-mail: mirko@sara.nl Hi Pierre, These are the responses I got for similar question I asked to the net several months ago. You are welcome to use them. I have edited some of them in the sake of space. Cheers, Ramon __________________________________________________________________________ It depends on what you want to do with the logP value. The CompuDrug and Daylight Chemical Information (MedChem) software vare both fairly expensive. A good inexpensive (US$200) option is the Hint! program of Abraham and Kellogg (Virginia Commonwealth University). Glen Kellogg can be reached by email (gkellogg@gems.vcu.edu). It can also plot lipophilicity contours around molecules and can create lipophilic fields for use in CoMFA. Cheers, Dave Dr. David A. Winkler Voice: 61-3-542-2244 Principal Research Scientist Fax: 61-3-543-8160 CSIRO Division of Chemicals and Polymers Private Bag 10 Clayton, Australia. __________________________________________________________________________ I have been interested in the log(P) calculators but also have had difficulty getting information. Also, I'm not sure how accurate they are. When I need to calculate a log(P), I usually do it "by hand" from the data provided by Rekker in his "Hydrophobic Fragmental Constant" work. I am well versed in the method and find it generally gives good answers. We have published a couple of papers with this approach. I'll give you the references in case they might be useful to you: "Development of Hydrophobicity Parameters to Analyze Proteins Which Bear Post- or Cotranslational Modifications", Black, S.D., and Mould, D.R. (1991) Anal. Biochem. 193, 72-82. "Development of Hydrophobicity Parameters for Prenylated Proteins", Black, S.D. (1992) Biochem. Biophys. Res. Commun. 186, 1437-1442. Cheers, =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= = Shaun D. Black, PhD | Internet: shaun%jason.decnet@relay.the.net = = Dept. of Biochemistry | University of Texas Health Center, at Tyler = =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= __________________________________________________________________________ One package for calculating LogP is Polaris from Molecular Simulations Inc. This program employs the protein dipole-Langevin dipole method of Arieh Warshel. This method has been successful in calculating free energies of solvation, free energies of binding, delta pKa, and LogP values. Nick Reynolds Molecular Simulations Inc. 16 New England Executive Park Burlington, MA 01803-5297 USA 1-617-229-9800 __________________________________________________________________________ You can reach compudrug sales person Harlod Borgsted at (716) 292-6830. I think that this is a New York number. By the way, we have the ProLogP software and would like to comment on a few items. First, It may be limited in that some compounds containing unique fragments will not compute with this software. The method is a fragment addition method where it splits your compound into parts that it has in it's datbase and then adds up the LogP values. Also, Charged compounds and some particular ringsystems cannot be used. And most importantly, isomers are given the same LogP values. Example- move a hudroxyl para, ortho or meta on an aromatic group. The log P will be the same! Or move a hydroxyl around a steroid ring, all will have the same LogP. We compaired to the Daylight Chemical LogP stuff (much more expensive) and found similar limitations. The values were not the same (even close to each other) between the packages). So. for use in QSAR, we do not use either of these. We have found a LogP method that works from the atom level rather than the fragment level and have used it to some extent. It handles all compounds but still has the isomer problem. Contact: Arup K. Ghose at Sterling Winthrop Research group, 81Columbia Turnpike, Rensselaer, NY, 12124 phone: (215) 983-5499 Ref is: J. Med. Chem. 1991, around Jan 17 or so. (sorry I don't have exactly) He developed the software and should give you a copy if you send a tape. Contact him first to set up arrangement. Good luck, Tom PS see the Hansch paper of a few months ago to review usefullness of logP. Debnath, A. K.; Hansch, C.; Kim, K. H.; Martin, Y. C. Mechanistic interpretation of the genotoxicity of nitrofurans (antibacterial agents) using quantitative structure-activity relationships and comparative molecular field analysis. Journal of Medicinal Chemistry. 1993 Apr 16; 36(8): 1007-1016. ################################################## Tom Wiese Department of Biochemistry Wayne State University School of Medicine 540 E. Canfield Detroit, MI 48201 Phone: (313) 577-5605 FAX: (313) 577-2765 email: tom@sgih.roc.wayne.edu ################################################## -- -- ____________________________________________________________________ Dr. Pierre Acklin email: acklin@chbs.ciba.com smail: Ciba-Geigy AG tel: ++41 61 696 23 62 K-136.P.69 tel: ++41 61 696 23 75 CH-4002 Basel fax: ++41 61 696 27 61 _____________________________________________________________________ From PIETRZAK@FRCPN11.IN2P3.FR Wed Apr 5 09:26:54 1995 Received: from frcpn11.in2p3.fr for PIETRZAK@FRCPN11.IN2P3.FR by www.ccl.net (8.6.10/930601.1506) id JAA20187; Wed, 5 Apr 1995 09:12:53 -0400 Message-Id: <199504051312.JAA20187@www.ccl.net> Received: from FRCPN11.IN2P3.FR by frcpn11.in2p3.fr (IBM VM SMTP V2R2) with BSMTP id 4639; Wed, 05 Apr 95 15:12:53 SET Received: from FRCPN11.in2p3.fr (NJE origin PIETRZAK@FRCPN11) by FRCPN11.IN2P3.FR (LMail V1.2a/1.8a) with BSMTP id 3790; Wed, 5 Apr 1995 15:12:53 +0200 Date: Wed, 05 Apr 95 15:04:09 SET From: PIETRZAK@frcpn11.in2p3.fr Subject: potential: heavy atoms To: chemistry@ccl.net Dear Net Users, I am looking for the interaction potential form (analytical) for the following binary systems: Pd-Au, Pt-Cu, Ni-Cu, Cu-Pd, Ag-Pd. It can be a fit to ab initio data or any other source. The potentials are needed for MC/MD calcs. Any information would be greatly appreciated. Tomasz M. Pietrzak. ================================================================== e-mail: pietrzak@frcpn11.in2p3.fr ================================================================== From jbrown@iris7.carb.nist.gov Wed Apr 5 09:56:54 1995 Received: from ENH.NIST.GOV for jbrown@iris7.carb.nist.gov by www.ccl.net (8.6.10/930601.1506) id JAA22121; Wed, 5 Apr 1995 09:43:44 -0400 Received: from iris7.carb.nist.gov by ENH.NIST.GOV (PMDF V4.2-13 #4653) id <01HOZ4CZBBK000C571@ENH.NIST.GOV>; Wed, 5 Apr 1995 09:38:25 EST Received: by iris7.carb.nist.gov (920330.SGI/920502.SGI) for @enh.nist.gov:chemistry@ccl.net id AA01344; Wed, 5 Apr 95 09:40:58 -0400 Date: Wed, 5 Apr 1995 09:40:56 +30000 From: James Brown Subject: Re: CCL:GROMOS PARAMETERS for carbohydrates In-reply-to: <9504022058.AA17190@canada.chem.duke.edu> To: chemistry@ccl.net Message-id: MIME-version: 1.0 Content-type: TEXT/PLAIN; charset=US-ASCII Content-transfer-encoding: 7BIT On Sun, 2 Apr 1995, Brad Isbister wrote: > Kamal Azzaoui is looking for parameters to use in carbohydrate MD. > > > I have done similar studies using AMBER 4.0 and have used the parameters from > SW Homans, Biochemistry, v29, 9110-9118 (1990). They should at least provide a > starting point. You can also look at JW Brady, JACS, v111, 5155-5165 (1988) for > an early paper on Glucose MD in water. Another reference worth examining is Glennon, Zheng, Le Grand, Shutzberg, and Merz, "A Force Field for Monosaccharides and (1->4) Linked Polysaccharides", J. Comp. Chem., Vol. 15, No. 9, pp. 1019-1040, 1994. The ACS Symposium Series 430, "Computer Modeling of Carbohydrate Molecules", edited by French and Brady, is also useful. Regards, ------------------------------------------------------------- | James Brown, Ph.D | I swear by my life and my | | Center for Advanced | love of it that I will | | Research in Biotechnology | never live for the sake of | | 9600 Gudelsky Dr. | another man, nor ask another | | Rockville, MD 20850 | man to live for mine. | | jbrown@iris7.carb.nist.gov | -- John Galt | ------------------------------------------------------------- From choic@gusun.acc.georgetown.edu Wed Apr 5 10:41:56 1995 Received: from gusun.acc.georgetown.edu for choic@gusun.acc.georgetown.edu by www.ccl.net (8.6.10/930601.1506) id KAA25339; Wed, 5 Apr 1995 10:35:28 -0400 Received: by gusun.acc.georgetown.edu; (5.0/1.1.8.2/6Jan9518:19pm) id AA19514; Wed, 5 Apr 1995 10:35:00 +0500 Date: Wed, 5 Apr 1995 10:34:57 -0400 (EDT) From: Cheol Choi To: CHEMISTRY@ccl.net Subject: POLAR of Gaussian? Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII content-length: 329 Hi! Everybody. Now I want to calculate polarizability ans Hyperpolarizabilty using Gaussian program. In fact, those quantities are dependent on direction of electric field. Dose anybody know how Gaussian calculates those quantities? Is there any arcticle about this? Thank you in advance. Cheol Ho Choi Georgetown Univ. From separk@cs.usc.edu Wed Apr 5 11:26:56 1995 Received: from pollux.usc.edu for separk@cs.usc.edu by www.ccl.net (8.6.10/930601.1506) id LAA28090; Wed, 5 Apr 1995 11:22:10 -0400 Received: (separk@localhost) by pollux.usc.edu (8.6.10/8.6.4) id IAA10443 for chemistry@ccl.net; Wed, 5 Apr 1995 08:22:08 -0700 Date: Wed, 5 Apr 95 8:22:08 PDT From: SEONGBIN PARK To: chemistry@ccl.net Subject: Question: measure for surface complementarity Message-ID: Hello, I am looking for references about measure for surface complementarity between two molecules, especially protein/protein (or protein/ligand). Could anyone kindly give me such information ? I would really appreciate it ! Regards, Seongbin Park (separk@pollux.usc.edu) From hinsenk@ERE.UMontreal.CA Wed Apr 5 11:30:13 1995 Received: from condor.CC.UMontreal.CA for hinsenk@ERE.UMontreal.CA by www.ccl.net (8.6.10/930601.1506) id LAA28207; Wed, 5 Apr 1995 11:24:14 -0400 Received: from eole.ERE.UMontreal.CA by condor.CC.UMontreal.CA with SMTP id AA14530 (5.65c/IDA-1.4.4 for chemistry@ccl.net); Wed, 5 Apr 1995 11:23:33 -0400 Received: from cyclone.ERE.UMontreal.CA by eole.ERE.UMontreal.CA (940406.SGI/5.17) id AA26253; Wed, 5 Apr 95 11:23:31 -0400 Received: by cyclone.ERE.UMontreal.CA (940406.SGI/5.17) id AA13777; Wed, 5 Apr 95 11:23:31 -0400 Date: Wed, 5 Apr 95 11:23:31 -0400 From: hinsenk@ERE.UMontreal.CA (Hinsen Konrad) Message-Id: <9504051523.AA13777@cyclone.ERE.UMontreal.CA> To: prabha@laue.biochem.ubc.ca Cc: chemistry@ccl.net In-Reply-To: (message from Prabha Siddarth on Tue, 4 Apr 1995 17:04:18 -0700 (PDT)) Subject: Re: CCL:How to get FTNCHEK On Mon, 20 Mar 1995, Hinsen Konrad wrote: > Since many people have asked me where ftnchek can be found, > I thought it might be helpul to tell everyone: > > You can get ftnchek by ftp from netlib.att.com, directory > /netlib/fortran, file ftnchek.tar.gz. It comes complete > with a manual and test cases. Installation is straightforward > and using it is even easier. There is really *no* excuse for > not using it. > I ftp'd the file but apparently it is a compressed binary file - how can I uncompress it and start to use it? The usual uncompress command in a UNIX machine doesn't work. Since I received several questions of this kind, let's answer them once and for all: File with the extension "gz" are packed with GNU-Zip, the Free Software Foundation's alternative to UNIX compress. If you have GNU-Zip on your machine, you can unpack zipped files with the command gunzip. If you do not have GNU-Zip, I recommend to obtain and install it, since zipped files are becoming more and more common on many ftp servers (they tend to be shorter than compressed files). GNU-Zip is available by ftp from prep.ai.mit.edu, or any of the many other sites that keep GNU software. Installation is straightforward and the resulting programs are small. Finally, don't confuse GNU-Zip with PK-Zip for MS-DOS (which uses the file extension "zip"). Both use the same compression algorithm, but there the similarity ends. GNU-Zip was designed to act like the standard UNIX compress. ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsenk@ere.umontreal.ca Departement de chimie | Tel.: +1-514-343-6111 ext. 3953 Universite de Montreal | Fax: +1-514-343-7586 C.P. 6128, succ. A | Deutsch/Esperanto/English/Nederlands/ Montreal (QC) H3C 3J7 | Francais (phase experimentale) ------------------------------------------------------------------------------- From gavin@vangogh.chem.uab.edu Wed Apr 5 12:57:02 1995 Received: from vangogh.chem.uab.edu for gavin@vangogh.chem.uab.edu by www.ccl.net (8.6.10/930601.1506) id MAA03543; Wed, 5 Apr 1995 12:48:52 -0400 From: Received: by vangogh.chem.uab.edu (AIX 3.2/UCB 5.64/4.03) id AA09878; Wed, 5 Apr 1995 11:43:08 -0500 Date: Wed, 5 Apr 1995 11:43:08 -0500 Message-Id: <9504051643.AA09878@vangogh.chem.uab.edu> To: CHEMISTRY@ccl.net Subject: Instability Dear Netters, I studied Ab Initio calculations of NaOONO. There are some unusual results observed: (a). Unusual high O=N stretching in MP2/6-311+G* calculation. EXP. O=N: 1437 cm-1 in frozen argon. HF/6-311+G* O=N: 1718 cm-1 MP2/6-311+G* O=N: 2408 cm-1 -- unusual high! (b). Unusual IR intensity in O=N stretching. MP2/6-311+G* O=N: 55012 km/mol (IR intensity is 500 km/mol for instense band) (c). O=N stretching is very sensitive to different basis set. MP2/6-311+G* O=N: 2408 cm-1 [55012] km/mol -IR intensity MP2/6-311+G O=N: 1797 cm-1 [7432] MP2/6-311 G* O=N: 2416 cm-1 [55314] MP2/6-311 G O=N: 1829 cm-1 [7676] I think these unusual results are caused by the instability of HF wavefunctions. So, I calculate instability analysis in G92/DFT. I got this messages: " Unable to determine singlet-triplet character of expansion vector. Closed Shell can not continue. Error termination in Lnk1e. " The G92/DFT was able to determine what instability this wavefunction has, RHF -> UHF, but not the orbitals involved. We found that there is a triplet state that is lower in energy than the singlet at HF levels of theory, but singlet is lower for MP2 and DFT levels of theory. Triplet states were searched for, but all of those obtained from the INDO guess were high in energy. The lowest triplet was not found by the INDO guess. There are four references about instability: (1). J. Cizek and J. Paldus, J. Chem. Phys. 47 (1967) 3976. (2). J. Paldus and J. Cizek, Chem. Phys. Letters 3 (1967) 1. (3). J. Paldus and J. Cizek, J. Chem. Phys. 52 (1970) 2919. (4). J. Paldus and J. Cizek, J. Chem. Phys. 54 (1971) 2293. ANY INFO and advise will appreciate! Gavin Tsai From raman@bioc01.uthscsa.edu Wed Apr 5 13:27:00 1995 Received: from thorin.uthscsa.edu for raman@bioc01.uthscsa.edu by www.ccl.net (8.6.10/930601.1506) id NAA05168; Wed, 5 Apr 1995 13:14:15 -0400 Received: from bioc01.uthscsa.edu by thorin.uthscsa.edu with SMTP; Wed, 5 Apr 1995 12:06:52 -0500 (CDT) Received: by bioc01.uthscsa.edu (4.1/SMI-4.1) id AA22470; Wed, 5 Apr 95 12:03:06 CDT From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Message-Id: <9504051703.AA22470@bioc01.uthscsa.edu> Subject: Re: CCL:Question: measure for surface complementarity To: separk@cs.usc.edu (SEONGBIN PARK) Date: Wed, 5 Apr 1995 12:03:02 -0500 (CDT) Cc: chemistry@ccl.net In-Reply-To: from "SEONGBIN PARK" at Apr 5, 95 08:22:08 am X-Mailer: ELM [version 2.4 PL3] Content-Type: text Content-Length: 3339 Seongbin: > I am looking for references about measure for surface complementarity > between two molecules, especially protein/protein (or protein/ligand). > Could anyone kindly give me such information ? > I would really appreciate it ! Here are some important references that should get you started: Badel A; Mornon JP; Hazout S. Searching for geometric molecular shape complementarity using bidimensional surface profiles. Journal of Molecular Graphics, 1992 Dec, 10(4):205-11. Bacon DJ; Moult J. Docking by least-squares fitting of molecular surface patterns. Journal of Molecular Biology, 1992 Jun 5, 225(3):849-58. Walls PH; Sternberg MJ. New algorithm to model protein-protein recognition based on surface complementarity. Applications to antibody-antigen docking. Journal of Molecular Biology, 1992 Nov 5, 228(1):277-97. Helmer-Citterich M; Tramontano A. PUZZLE: a new method for automated protein docking based on surface shape complementarity. Journal of Molecular Biology, 1994 Jan 21, 235(3):1021-31. Leikin S; Parsegian VA. Temperature-induced complementarity as a mechanism for biomolecular assembly. Proteins, 1994 May, 19(1):73-6. Norel R; Lin SL; Wolfson HJ; Nussinov R. Shape complementarity at protein-protein interfaces. Biopolymers, 1994 Jul, 34(7):933-40. Buckle AM; Schreiber G; Fersht AR. Protein-protein recognition: crystal structural analysis of a barnase-barstar complex at 2.0-A resolution. Biochemistry, 1994 Aug 2, 33(30):8878-89. Braden BC; Souchon H; Eisele JL; Bentley GA; Bhat TN; Navaza J; Poljak RJ. Three-dimensional structures of the free and the antigen-complexed Fab from monoclonal anti-lysozyme antibody D44.1. Journal of Molecular Biology, 1994 Nov 4, 243(4):767-81. Cheers -raman -- _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ _/ _/ C.S.RAMAN _/ _/ Department of Biochemistry _/ _/ University of Texas Health Science Center _/ _/ 7703 Floyd Curl Drive _/ _/ San Antonio, TX 78284-7760 _/ _/ USA _/ _/ _/ _/ Tel: (210) 567-6623 _/ _/ Fax: (210) 567-6595 _/ _/ E-mail: raman@bioc01.uthscsa.edu _/ _/ _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ _/ _/ How can it be that mathematics, a product of human thought _/ _/ independent of experience, is so admirably adapted to the _/ _/ objects of reality? "-Albert Einstein" _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ From monge@anny.psgvb.com Wed Apr 5 13:42:07 1995 Received: from anny.psgvb.com for monge@anny.psgvb.com by www.ccl.net (8.6.10/930601.1506) id NAA06799; Wed, 5 Apr 1995 13:38:26 -0400 Received: by anny.psgvb.com (931110.SGI/920502.SGI.AUTO) for chemistry@ccl.net id AA23708; Wed, 5 Apr 95 10:38:21 -0700 Date: Wed, 5 Apr 95 10:38:21 -0700 From: monge@anny.psgvb.com (Alessandro Monge) Message-Id: <9504051738.AA23708@anny.psgvb.com> To: chemistry@ccl.net Subject: Schrodinger, Inc. product and WWW page announcement CCL subscribers: Schrodinger announces the release of PS-GVB Version 2.1. PS-GVB is an ab initio quantum chemistry code which uses pseudospectral methods to solve the equations of electronic structure theory. PS-GVB Version 2.1 features Density Functional Theory (DFT), in addition to Hartree-Fock (HF), Generalized Valence Bond (GVB), Moller-Plesset perturbation theory (MP2), Local MP2, and Restricted CI. DFT solution-phase calculations are available via PS-GVB/SOLV, PS-GVB's unique self-consistent reaction field code using a realistic molecular cavity and a finite element Poisson-Boltzmann solver. Detailed product information about PS-GVB is now available on the WWW. Visit Schrodinger's site at: http://www.psgvb.com/ For more information on PS-GVB contact me by phone at (800) 20-PSGVB or e-mail to monge@psgvb.com. Alessandro ------------------------------------------------------------------------ Alessandro Monge Schrodinger, Inc. monge@psgvb.com (800) 20-PSGVB ------------------------------------------------------------------------ Alessandro Monge Schrodinger, Inc. monge@psgvb.com (800) 20-PSGVB From friedman@tammy.harvard.edu Wed Apr 5 13:56:58 1995 Received: from tammy.harvard.edu for friedman@tammy.harvard.edu by www.ccl.net (8.6.10/930601.1506) id NAA07386; Wed, 5 Apr 1995 13:45:41 -0400 Received: by tammy.harvard.edu (5.64/10.0) id AA07676; Wed, 5 Apr 95 13:47:36 -0400 Date: Wed, 5 Apr 95 13:47:36 -0400 From: friedman@tammy.harvard.edu (Dawn Friedman) Message-Id: <9504051747.AA07676@tammy.harvard.edu> To: chemistry@ccl.net Subject: psi88: ions? SEMI format? Cc: friedman@tammy.harvard.edu I'm struggling with the format for input of Slater exponents in PSI88, which is necessary with the SEMI keyword for semi-empirical wavefunctions. I have the exponents, but... 1) Where in the file is "after the wavefunction"? At the end, after the MO coeffs? I make individual .psi1 files for each orbital. 2) "One atom per line" even for heavy atoms with s, p, or even d exponents? What's the format? 3) Does PSI88 need anparameters from (eg) the PM3 set? 4) The .doc says that "charge is not used" until charge density plots are (re)implemented. Is that why the last hydrogen in my protonated system has "Atomic Number *****"? And is that what's causing a segmentation fault in .psi2, so that the contours being generated and reported by psi1 and psicon can't be turned into a .ps file? I get a tiny .ps file which doesn't even print. 5) Or is it the number of atoms? There used to be a limit in a previous PSI program, but none is mentioned in the documentation -- and I have 52 atoms in this system (which is why I'm using SEMI). Help! --Dawn Friedman friedman@tammy.harvard.edu From melinda@platinum.UWaterloo.ca Wed Apr 5 15:27:01 1995 Received: from watserv1.uwaterloo.ca for melinda@platinum.UWaterloo.ca by www.ccl.net (8.6.10/930601.1506) id PAA13756; Wed, 5 Apr 1995 15:22:40 -0400 Received: from platinum.uwaterloo.ca by watserv1.uwaterloo.ca with SMTP id ; Wed, 5 Apr 95 15:22:32 -0400 Received: by platinum.UWaterloo.ca (950215.SGI.8.6.10/930416.SGI) id PAA21967; Wed, 5 Apr 1995 15:22:27 -0400 Date: Wed, 5 Apr 1995 15:22:25 -0400 (EDT) From: Melinda Gugelchuk Subject: Q:HF vs LDA Eigenvalues To: CHEMISTRY@ccl.net Message-Id: Hello Netters, Is there anybody out there who can explain to me the theoretical differences between HF and LDA eigenvalues. I am trying to compare the electronic structure of an organometallic complex calculated with HF to that calculated with LDA methods. Will I really be comparing the same quantities? Thanks in advance, Melinda Gugelchuk Department of Chemistry University of Waterloo melinda@pt.uwaterloo.ca From GAUSSIAN@cmchem.chem.cmu.edu Wed Apr 5 15:31:36 1995 Received: from cmchem.chem.cmu.edu for GAUSSIAN@cmchem.chem.cmu.edu by www.ccl.net (8.6.10/930601.1506) id PAA13096; Wed, 5 Apr 1995 15:13:45 -0400 From: Date: Wed, 5 Apr 1995 15:08:13 -0400 (EDT) To: chemistry@ccl.net Message-Id: <950405150813.20e007c5@cmchem.chem.cmu.edu> Subject: Announcement: Gaussian 94 now available ------------------------------------------------------------------------- GAUSSIAN, INC. Carnegie Office Park Building 6 Pittsburgh, PA 15106 USA Phone - 412-279-6700 Fax - 412-279-2118 email - info@gaussian.com Gaussian, Inc. is pleased to announce the release of Gaussian 94, the latest development in the Gaussian series of programs. Gaussian 94 is available immediately for several computer platforms including Cray (UniCOS), DEC Alpha AXP (OSF/1), HP-700 (HP-UX), IBM RS/6000 (AIX), and Silicon Graphics (IRIX). At this time, Convex (UNIX), Fujitsu (UXP/M), and NEC SX-3 (SuperUX) versions of Gaussian 94 are not immediately available, but are in final testing. Gaussian 94 continues the tradition of expanding the limits of computational chemistry. Among new features are magnetic properties, generalized cavity solvation effects, and automated G1, G2 and Complete Basis Set (CBS) high-accuracy energy models. Geometry optimizations are faster than ever; they can now be performed in redundant internal coordinates. Gaussian 94 also offers synchronous transit guided quasi-Newton methods for locating transition structures. Performance improvements include network parallel capability, using the Linda environment from SCIENTIFIC Computing Associates, to complement enhanced shared-memory parallel features. Density functional theory (DFT) methods are now standard in Gaussian 94. We remind users that we maintain a mailing list for those interested in subscribing to our free newsletter, Gaussian NEWS. The newsletter discusses new implementations, updates, and future developments of the Gaussian system of programs. It also informs subscribers about upcoming user meetings and workshops, and contains features such as user profiles and technical notes. To subscribe to Gaussian NEWS, please e-mail your full mailing address to info@gaussian.com. In addition to our regular mailing list, we continue to maintain an electronic mailing list for those interested in news regarding the Gaussian system of programs. We invite any interested parties to subscribe to either or both lists. We also welcome any comments or suggestions you might have. If you would like to obtain a license for Gaussian 94 at your site or if you desire additional information regarding the Gaussian series of programs, please contact us at the address or telephone numbers given above, or send electronic mail to info@gaussian.com. Yours Sincerely, David J. Moses, Ph.D. Vice President, C.O.O. ------------------------------------------------------------------------- This notice is sent without warranty of any kind, expressed or implied. Gaussian is a registered trademark of Gaussian, Inc. All other trademarks are the property of their respective holders. Specifications and availability subject to change without notice. From JDA03546@niftyserve.or.jp Wed Apr 5 19:42:02 1995 Received: from inetnif.niftyserve.or.jp for JDA03546@niftyserve.or.jp by www.ccl.net (8.6.10/930601.1506) id TAA19705; Wed, 5 Apr 1995 19:31:42 -0400 Received: by inetnif.niftyserve.or.jp (8.6.9+2.4W/3.3W8-950117-Mail-Gateway) id IAA04892; Thu, 6 Apr 1995 08:31:23 +0900 Message-Id: <199504052331.IAA04892@inetnif.niftyserve.or.jp> Date: Thu, 06 Apr 1995 08:28:00 +0900 From: =?ISO-2022-JP?B?GyRCQG5FZyEhSXAbKEI=?= Subject: IR intensity To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=iso-2022-jp Dear CCL'ers We are trying to determine the orientation of the adsorbed molecules on the surface by IR using polarized light. It seems to be possible to calculate the intensity from each component of dipole moment derivetives, but are there any programs that can do this automatically or rather easy way? We have gaussian. Thanks in advance. From rmiller@hplato.hpl.hp.com Wed Apr 5 21:57:04 1995 Received: from hplabs.hpl.hp.com for rmiller@hplato.hpl.hp.com by www.ccl.net (8.6.10/930601.1506) id VAA21377; Wed, 5 Apr 1995 21:42:03 -0400 Received: from hplato.hpl.hp.com by hplabs.hpl.hp.com with SMTP (1.37.109.16/15.5+ECS 3.3+HPL1.1SU) id AA067362521; Wed, 5 Apr 1995 18:42:02 -0700 Received: by hplato.hpl.hp.com (1.37.109.8/15.5+ECS 3.3+HPL1.1) id AA21824; Wed, 5 Apr 1995 18:55:09 -0700 From: Robert Miller Message-Id: <9504060155.AA21824@hplato.hpl.hp.com> Subject: heterogeneous nucleation To: chemistry@ccl.net Date: Wed, 5 Apr 95 18:55:09 PDT Mailer: Elm [revision: 70.85] Colleagues; Have any of you attempted to simulate vapor nucleation? Do any of you have thoughts on the topic? I will post a summary of any and all replies. -- Sincerely, Robert Miller, PhD Hewlett-Packard Laboratories e-mail: rmiller@hplato.hpl.hp.com From gavin@vangogh.chem.uab.edu Wed Apr 5 22:57:05 1995 Received: from vangogh.chem.uab.edu for gavin@vangogh.chem.uab.edu by www.ccl.net (8.6.10/930601.1506) id WAA22226; Wed, 5 Apr 1995 22:54:56 -0400 From: Received: by vangogh.chem.uab.edu (AIX 3.2/UCB 5.64/4.03) id AA09906; Wed, 5 Apr 1995 21:49:12 -0500 Date: Wed, 5 Apr 1995 21:49:12 -0500 Message-Id: <9504060249.AA09906@vangogh.chem.uab.edu> To: CHEMISTRY@ccl.net Subject: CCL Email ADDRESS Cc: gavin@vangogh.chem.uab.edu Dear Netter, Someone can give me the E-mail address of CCL if I want to post the questions to everyone. I always have the trouble using the CHEMISTRY@ccl.net address. How can I get the information that show me to use archive search in CCL. Your help will be appreciated! Gavin Tsai