From chemistry-request@server.ccl.net Wed May 29 03:22:21 2002 Received: from jingxian.xmu.edu.cn ([210.34.0.19]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4T7MJC18290 for ; Wed, 29 May 2002 03:22:20 -0400 Received: from zjcao ([210.34.15.230]) (authenticated bits=0) by jingxian.xmu.edu.cn (8.12.2/8.12.2) with ESMTP id g4T7RwaT016719 for ; Wed, 29 May 2002 15:27:58 +0800 (CST) Message-ID: <001d01c206e1$7f5d3ba0$e60f22d2@zjcao> From: "zjcao" To: Subject: ONIOM-PCM Date: Wed, 29 May 2002 15:21:49 +0800 MIME-Version: 1.0 Content-Type: text/plain; charset="gb2312" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2600.0000 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from base64 to 8bit by server.ccl.net id g4T7MLC18293 Dear Gaussian Users, I have two problems about PCM and ONIOM-PCM. Q1: I found it is difficult to optimize slightly big models for the PCM calculations, for example the NH4+(H2O)4 model. Would you like to give me some advices? Q2: One paper of Prof. Morokuma (J. Chem. Phys., 2001, v115, 62) said that they have so far integrated only the two-layer MO:MO ONIOM combination with the IEF-PCM method. Wether could I do other ONIOM-PCM calculations using g98 directly, for example, other ONIOM methods and other PCM model? Thanks in advance. ZJ Cao E-mail: zjcao@jingxian.xmu.edu.cn From chemistry-request@server.ccl.net Wed May 29 05:36:36 2002 Received: from mail2.organik.uni-erlangen.de ([131.188.127.212]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4T9aZC20774 for ; Wed, 29 May 2002 05:36:35 -0400 Received: from horan.chemie.uni-erlangen.de (horan [131.188.127.135]) by mail2.organik.uni-erlangen.de (8.8.8/8.1.4-FAU) with ESMTP id LAA13253; Wed, 29 May 2002 11:36:34 +0200 (MET DST) Received: by horan.chemie.uni-erlangen.de (Postfix on SuSE Linux 7.0 (i386), from userid 1046) id 6AE353F835; Wed, 29 May 2002 11:36:34 +0200 (CEST) Received: from localhost (localhost [127.0.0.1]) by horan.chemie.uni-erlangen.de (Postfix on SuSE Linux 7.0 (i386)) with ESMTP id 5270533DBF; Wed, 29 May 2002 11:36:34 +0200 (CEST) Date: Wed, 29 May 2002 11:36:34 +0200 (CEST) From: Lothar Terfloth To: Cc: Subject: Re: CCL:Complete citations In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Chandrika, I guess you have asked for the citation of the "rule of fives" by C. Lipinski. The citation of this article is: Lipinski, C. A., Lombardo, F., Dominy, B. W. and Feeney, P. J. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv. Drug Deliv. Rev. 1997, 23, 3-25. With kind regards, Lothar Terfloth ------------------------------------------------------------------------------ Dr. Lothar Terfloth phone: +49-9131-85-26569 fax: +49-9131-85-26566 Computer-Chemie-Centrum Institut fuer Organische Chemie Universitaet Erlangen-Nuernberg Naegelsbachstr. 25 D-91052 Erlangen email: Lothar.Terfloth@chemie.uni-erlangen.de ------------------------------------------------------------------------------ On Tue, 28 May 2002 Moudgal.Chandrika@epamail.epa.gov wrote: > Hello, > I am looking for complete citations to work published by the Russian > chemist Borodin (1858) who was one of the few to first discover the > relationship between toxicological properties and chemical make up. I > would also like a complete citation for the "five rules of thumb" by > Chris Lapinski. > > My search at the library in house, the public library and the university > library has proven futile. > Any help from members will be much appreciated. > Thanks all in advance for your time and help. > > Sincerely, > Chandrika > > > Chandrika J. Moudgal > National Center for Environmental Assessment, US EPA > 26 W. Martin Luther King Dr., ML 117 > Cincinnati, OH 45268 > Phone: 513-569-7078 > Fax: 513-569-7475 > e-mail: moudgal.chandrika@epa.gov > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > From chemistry-request@server.ccl.net Wed May 29 03:08:43 2002 Received: from omega.uar.net ([193.124.228.39]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4T78cC18015 for ; Wed, 29 May 2002 03:08:40 -0400 Received: (from root@localhost) by omega.uar.net (8.11.6/8.11.6) id g4T78ZM91899 for chemistry@ccl.net.AVP; Wed, 29 May 2002 10:08:35 +0300 (EEST) Received: from one.icmp.lviv.ua (andrij@[194.44.208.58]) by omega.uar.net (8.11.6/8.11.6) with SMTP id g4T78Ut91864 for ; Wed, 29 May 2002 10:08:33 +0300 (EEST) Date: Wed, 29 May 2002 10:15:02 +0300 (EEST) From: Andrij Baumketner Reply-To: Andrij Baumketner To: chemistry@ccl.net Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, I am interested in numerical studies of glass transition (Tg) in off-lattice protein models and would appreciate any reference to papers addressing this problem. Thanks, Andrij ==================================================== A.Baumketner Dep. of Computational Sciences, Kanazawa University Kakuma, Kanazawa 920-1192, Japan. Tel: 81-76-264-6057 http://cphys.s.kanazawa-u.ac.jp/~lab-hiwa/andrij ==================================================== From chemistry-request@server.ccl.net Wed May 29 05:20:27 2002 Received: from resu1.ulb.ac.be ([164.15.59.200]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4T9KRC20506 for ; Wed, 29 May 2002 05:20:27 -0400 Received: from resu1.ulb.ac.be (resu1.ulb.ac.be [164.15.59.200]) by resu1.ulb.ac.be (8.8.8/3.17.1.ap (resu)) id LAA16034; Wed, 29 May 2002 11:17:53 +0200 (MEST) for chemistry@ccl.net Date: Wed, 29 May 2002 11:17:53 +0200 (MEST) Message-Id: <200205290917.LAA16034@resu1.ulb.ac.be> From: Pierre Mignon To: chemistry@ccl.net Subject: free energy summary X-Mailer: Webmail ULB v2.1 Hello, here are the answers I got from my question upon free energy calculation. Thank's for the informations. **************************************************************************** The following references will provide the information about free energy calculation in bio-molecules. 1) M. Rami Reddy, Mark Erion, and Atul Agarwal' Free Energy Calculations: Use and Limitations in Predicting Ligand Binding Affinities' Reviews in Computational Chemistry, Edited by Lipkowitz and Boyd, Volume 16, Pages 217-303. 2) Free Energy Calculations in Rational Drug Design (a total of 19 chapters in this text book and all are related to free energy calculations), edited by M. Rami Reddy and Mark Erion, Kluwer Academic/Plenum Publishers, New York, 2001. ******************************************************************************* Dear Pierre, here is a little bit longish list of articles from my collection. About the more rigorous methods: @article{70807, author = {P. Kollman}, title = {Free Energy Calculations: Applications to Chemical and Biochemical Phenomena}, journal = {Chem.Rev.}, volume = {93}, pages = {2395-2417}, year = {1993}, keywords = {Review ; AMBER ; free energy ; binding energy ; molecular dynamics ; molecular modelling} } @article{70809, author = {D. L. Beveridge and F. M. DiCapua}, title = {Free energy via molecular simulation: application to chemical and biomolecular systems}, journal = {Annu.Rev.Biophys.Biophys.Chem.}, volume = {18}, pages = {431-492}, year = {1989}, keywords = {free energy ; Review ; molecuar dynamics ; fundamentals} } @article{70820, author = {M. Mezei and D. L. Beveridge}, title = {Free Energy Simulations}, journal = {Ann.NY Acad.Sci.}, volume = {482}, pages = {1-23}, year = {1986}, keywords = {free energy ; Review ; molecular dynamics ; ligand docking} } @incollection{80101, author = {A. E. Mark and W. F. van Gunsteren}, editor = {P. M. Dean and G. Jolles and C. G. Newton}, title = {Free Energy Calculations in Drug Design: A Practical Guide}, booktitle = {New Perspectives in Drug Design}, chapter = {10}, pages = {185-200}, publisher = {Academic Press}, year = {1995}, keywords = {drug design ; binding energy ; molecular dynamics ; gromos} } @article{80122, author = {J. A. McCammon}, title = {Free energy from simulation}, journal = {Curr.Op.Struct.Biol.}, volume = {1}, pages = {196-200}, year = {1991}, keywords = {free energy ; ligand docking ; free energy calculation} } About the MM-PBSA which is less rigorous but faster: @article{80023, author = {J. Wang and P. Morin and W. Wang and P. Kollman}, title = {Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of efavirenz by docking and MM-PBSA}, journal = {J.Am.Chem.Soc.}, volume = {123}, pages = {5221-5230}, year = {2001}, keywords = {free energy ; ligand docking ; molecular dynamics ; AMBER ; MM-PBSA} } @article{70831, author = {W. Wang and O. Donini and C. M. Reyes and P. A. Kollman}, title = {Biomolecular simulations: recent developments in force fields, simulations of enzyme catalysis, protein--ligand, protein--protein, and protein-nucleic acid noncovalent interactions}, journal = {Ann.Rev.Biophys.Biomol.Struct.}, volume = {30}, pages = {211-243}, year = {2001}, keywords = {force field ; Review ; drug design ; ligand docking ; protein protein interactions ; protein nucleic acid interaction ; protein rna interactions ; protein dna interactions} } A very general review focused on calculation of binding energies (very good introduction): @article{80029, author = {M. L. Lamb and W. L. Jorgensen}, title = {Computational approaches to molecular recognition}, journal = {Curr.Op.Chem.Biol.}, volume = {1}, pages = {449-457}, year = {1997}, keywords = {recognition} } Hope this helps, Oliver. ****************************************************************************** This is shamefully self-promoting, but the excellent recent book "Computational Biochemistry & Biophysics" (eds. Becker, Mackerell, Roux, Watanabe; Marcel Dekker) has a free energy overview chapter by yours truly... Tom Simonson ****************************************************************************** Dear Pierre : At http://www.biophysics.org/img/Bloomfield.V-Thermo.pdf you will find an excellent review on Thermodynamics and Statistical Thermodynamics. There is a lot of information on free energy in biological system. As a favor please sumarize this discussion or send me the results, because I am also working on it. Best ****************************************************************************** Mignon Pierre PhD student Free University of Brussel (VUB) Dienst Algemene Chemie (ALGC) Pleinlaan, 2 1050 Brussels Belgium Tel + 32 2 629 35 16 Fax + 32 2 629 33 17 e-mail pmignon@vub.ac.be From chemistry-request@server.ccl.net Wed May 29 07:20:18 2002 Received: from estrella.pasteur-lille.fr ([194.254.237.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4TBKHC22907 for ; Wed, 29 May 2002 07:20:17 -0400 Received: from adelaide.pasteur-lille.fr (adelaide.pasteur-lille.fr [193.49.178.2]) by estrella.pasteur-lille.fr (8.12.1/jtpda-5.4) with ESMTP id g4TB4frg014496 for ; Wed, 29 May 2002 13:04:41 +0200 Received: from pasteur-lille.fr (pax-97.pasteur-lille.fr [194.254.248.97]) by adelaide.pasteur-lille.fr (8.11.6/8.11.6/SuSE Linux 0.5) with ESMTP id g4TBJJ323764 for ; Wed, 29 May 2002 13:19:19 +0200 Sender: Julien.Michel@pasteur-lille.fr Message-ID: <3CF4B929.DC4902E3@pasteur-lille.fr> Date: Wed, 29 May 2002 13:19:05 +0200 From: Julien Michel Organization: IBL UMR8525 Institut Pasteur de Lille X-Mailer: Mozilla 4.76C-SGI [en] (X11; I; IRIX64 6.5 IP30) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Autodock ligand intramolecular energy References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-MailScanner: Found to be clean Dear members of the list, While using the program Autodock3, I recently discovered that the computed intramolecular energy of a given ligand will depend on the number of rotatable torsion previously defined in the lig.pdbq file. For example, if I evaluate the energy ( epdb )of the same ligand in the same conformation, but with a different number of rotatable bonds defined, the number of computed non nonded intramolecular interactions are different and the same interaction can lead to different energies. I stress that i'm mentioning the non bonded intramolecular energy and not the intramolecular torsional penalty which depend on the number of rotatable bonds. I find this behaviour surprising and I do not understand the reasons behind it . I understand that this energy is computed by using the various Lennard Jones depending on the type of atoms considered in the pairwise interaction and I don't see why #rotatable or not# would influence this...Can anyone explain me the reason of this behaviour ? Julien MICHEL From chemistry-request@server.ccl.net Wed May 29 10:10:49 2002 Received: from linux03.euroware.it ([213.82.3.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4TEAFC27868 for ; Wed, 29 May 2002 10:10:49 -0400 Received: from winnt01.euroware.it (winnt01 [192.168.32.125]) by linux03.euroware.it (8.9.3/8.9.3) with ESMTP id QAA14447 for ; Wed, 29 May 2002 16:02:17 +0200 Received: by winnt01.euroware.it with Internet Mail Service (5.5.2653.19) id ; Wed, 29 May 2002 16:11:55 +0200 Message-ID: From: Antonio Riganelli To: "'chemistry@ccl.net'" Subject: EUCO-CC4 conference announcement Date: Wed, 29 May 2002 16:11:54 +0200 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" ************* Second announcement EUCO-CC4 ******************** *********** June 15 Deadline for abstracts and early registration ***************** The fourth European Computational Chemistry Conference (EUCO-CC4) will be held in Assisi (Italy) 1-6 September 2002. The EUCO-CC4 will deal with the main aspects of computational chemistry both at research (academic and industrial) and educational level. The focal points of the conference will be: 1. High level ab initio treatments on small molecules and elementary processes 2. Models and simulations for complex systems 3. Approximate methods for large molecules 4. Statistical treatments and chemical education by considering separately "Theory and Methods" and "Technology and Application". There will be two introductory plenary lectures (T. Hey and R. Carbo), 11 invited lectures (A. Bottoni, M.E. Casida, D.C. Clary, G. Cruciani, K. Faegri, A.P.J. Jansen, C. Millot, C. Rayez, G. Rozenberg, J.P.G. Szalay, R.J. Whewell); 26 contributed talks. There will be also two after dinner poster sessions introduced by a before dinner short (1 minute, 1 transparency per poster) presentation. The lectures will be given by outstanding scientists of the field. All the information related to the conference are available on the Web site: http://www.chm.unipg.it/chimgen/mb/cong/EUCO-CC4/index.html From chemistry-request@server.ccl.net Wed May 29 10:11:28 2002 Received: from ns1.tudelft.nl ([130.161.180.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4TEBSC27933 for ; Wed, 29 May 2002 10:11:28 -0400 Received: from CONVERSION-DAEMON.mailhost2.tudelft.nl by mailhost2.tudelft.nl (PMDF V6.0-025 #40925) id <0GWV00E01M31NO@mailhost2.tudelft.nl> for chemistry@ccl.net; Wed, 29 May 2002 16:11:27 +0200 (MEST) Received: from listserv.tudelft.nl (listserv.tudelft.nl [130.161.180.33]) by mailhost2.tudelft.nl (PMDF V6.0-025 #40925) with ESMTP id <0GWV00AGVM319I@mailhost2.tudelft.nl> for chemistry@ccl.net; Wed, 29 May 2002 16:11:25 +0200 (MEST) Received: from stm-ltc2.dct.tudelft.nl (stm-ltc2.dct.tudelft.nl [130.161.196.198]) by listserv.tudelft.nl (8.10.2+Sun/8.10.2) with ESMTP id g4TEBG328920 for ; Wed, 29 May 2002 16:11:25 +0200 (MEST) Received: from STM-LTC2/SpoolDir by stm-ltc2.dct.tudelft.nl (Mercury 1.47) ; Wed, 29 May 2002 16:11:24 +0000 (MET-1MEST) Received: from SpoolDir by STM-LTC2 (Mercury 1.47); Wed, 29 May 2002 16:11:10 +0000 (MET-1MEST) Date: Wed, 29 May 2002 16:11:04 +0200 From: Martijn Zwijnenburg Subject: periodic DFT To: chemistry@ccl.net Message-id: <3CF4FD7E.5489.71B4B70E@localhost> MIME-version: 1.0 X-Mailer: Pegasus Mail for Win32 (v3.12c) Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Priority: normal Hi, After having some background in molecular DFT calculations I'm now starting to do some periodic (plane wave) DFT calculations. However, I haven't been able to find a book which treats periodic DFT calcualtions in any detail (plane wave basis sets/ pseudo potentials/ augmented spherical wave basis sets/ ultrasoft potentials/ mixing etc.). So I would like to ask if somebody could advise me a book on this subject. Regards, Martijn ------------------------------------------------------------------------- Martijn Zwijnenburg Lab. of Applied Organic Chemistry and Catalysis Delft University of Technology Julianalaan 136 2628 BL Delft The Netherlands Tel: 0031-(0)152782691 Fax: 0031-(0)152784700 e-mail: M.A.Zwijnenburg@tnw.tudelft.nl web page: http://come.to/tock From chemistry-request@server.ccl.net Wed May 29 10:46:54 2002 Received: from suncom.rz.hu-berlin.de ([141.20.1.31]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4TEksC28830 for ; Wed, 29 May 2002 10:46:54 -0400 Received: from impact1.chemie.hu-berlin.de (impact1.chemie.hu-berlin.de [141.20.72.25]) by suncom.rz.hu-berlin.de (8.9.3/8.9.3) with ESMTP id QAA17407; Wed, 29 May 2002 16:46:50 +0200 (MET DST) Received: (from ah@localhost) by impact1.chemie.hu-berlin.de (SGI-8.9.3/8.9.3) id QAA94863; Wed, 29 May 2002 16:46:49 +0200 (MESZ) Date: Wed, 29 May 2002 16:46:49 +0200 From: "Dr. Alexander Hofmann" To: Martijn Zwijnenburg Cc: chemistry@ccl.net Subject: Re: CCL:periodic DFT Message-ID: <20020529164649.J195801@impact1.chemie.hu-berlin.de> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.2.5i Hello Martijn, check out one special article of the NIC-Series, available online from http://www.fz-juelich.de/nic-series/Volume1/marx.pdf written by Dominik Marx. Or check out the 1992 Paper of Michael Payne in rev. Mod. Phys 64 (1992). I'm sorry, that I can't suggest a real book. For more technical problems related the mentioned programs check out the corresponding discussion lists of the programmers. Yours Alex -- Dr. Alexander Hofmann Humboldt-Universitaet zu Berlin Institut fuer Chemie Arbeitsgruppe Quantenchemie Brook-Taylor-Strasse 2 12489 Berlin ah@chemie.hu-berlin.de Tel.: +49-30-2093-7138 Fax.: +49-30-2093-7136 http://www.chemie.hu-berlin.de/ag_sauer/index.html PGP-Key: wwwkeys.de.pgp.net ID: D9D62D35 From chemistry-request@server.ccl.net Wed May 29 09:14:15 2002 Received: from web12808.mail.yahoo.com ([216.136.174.43]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g4TDEEC26102 for ; Wed, 29 May 2002 09:14:14 -0400 Message-ID: <20020529131414.11635.qmail@web12808.mail.yahoo.com> Received: from [64.94.101.217] by web12808.mail.yahoo.com via HTTP; Wed, 29 May 2002 06:14:14 PDT Date: Wed, 29 May 2002 06:14:14 -0700 (PDT) From: amor san juan Subject: Sybyl alternative To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi CClers: Would someone please inform me any alternative freewares to the commercial Sybyl molecular modeling package. My goal is to add both charges & Hydrogens to ligand and macromolecule. For the past weeks, I tested the capabilities of chemsketch5 & babel 1.6 but it is not successful as compared to data generated from Sybyl. Thanks for the help & patience. Sincerely, Amor __________________________________________________ Do You Yahoo!? Yahoo! - Official partner of 2002 FIFA World Cup http://fifaworldcup.yahoo.com From chemistry-request@server.ccl.net Wed May 29 08:34:14 2002 Received: from relay2.uni-heidelberg.de ([129.206.210.211]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4TCYDC24934 for ; Wed, 29 May 2002 08:34:14 -0400 Received: from akcomba.oci.uni-heidelberg.de (akcomba.oci.uni-heidelberg.de [129.206.40.111]) by relay2.uni-heidelberg.de (8.12.1/8.12.1) with ESMTP id g4TCY7xa017263 for ; Wed, 29 May 2002 14:34:07 +0200 (MET DST) Received: by akcomba.oci.uni-heidelberg.de with Internet Mail Service (5.5.2650.21) id ; Wed, 29 May 2002 14:43:03 +0200 Message-ID: <31404621DE99D3119A16525400E1A5A80B06F5@akcomba.oci.uni-heidelberg.de> From: "Remenyi, Rainer" To: "'chemistry@ccl.net'" Subject: CCL:G98 unrecogized IType in G98 Date: Wed, 29 May 2002 14:42:57 +0200 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g4TCYEC24935 Dear CCLers, I am running a transition state search with G98 with the following input: ------------------------------------------------------------- % chk=TransState #P B3Lyp/6-31G(d) guess=read iop(6/7=3) scf=(maxcycle=200) opt=QST2 Übergangszustand Edukt -1 1 cu n 1 ncu2 c 2 cn3 1 cncu3 . . . . Übergangszustand Produkt -1 1 cu n 1 ncu2 c 2 cn3 1 cncu3 . . . . --------------------------------------------------------------------------- The job is running, but in the output there is the following message: ---------------------------------------------------------------------------- ----------- ---------------------------- ! Initial Parameters ! ! (Angstroms and Degrees) ! ------------------------ ------------------------- ! Name Definition TS Reactant Product Derivative Info. ! ---------------------------------------------------------------------------- - ! R1 R(1,2) 1.7853 1.8387 1.8146 estimate D2E/DX2 ! ! R2 R(1,5) 1.9264 1.8775 2.0039 estimate D2E/DX2 ! . . ! D60 D(20,18,19,25) 4.2125 0.8488 19.9158 Unrecognized IType in ! . . -------------------------------------------------------------------- Does anybody know what unrecognized IType means in this case. Thanks, Rainer Rainer Remenyi Anorganisch-Chemisches Institut Im Neuenheimer Feld 270 69120 Heidelberg Germany phone ++ 49 6221 54 8653 fax ++ 49 6221 54 6617 e-mail: remenyi@akcomba.oci.uni-heidelberg.de From chemistry-request@server.ccl.net Wed May 29 12:07:04 2002 Received: from jacobus.chem.smu.edu ([129.119.201.27]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4TG74C31427 for ; Wed, 29 May 2002 12:07:04 -0400 Received: from localhost (zmz@localhost) by jacobus.chem.smu.edu (8.11.6/8.11.6) with ESMTP id g4TFxLw31738 for ; Wed, 29 May 2002 10:59:21 -0500 Date: Wed, 29 May 2002 10:59:21 -0500 (CDT) From: Pearl Zheng To: Subject: How to set base fragment manually(FlexX) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, I am using Sybyl FlexX. When I try to reproduce experimental result of 4ts1. The auto selection of base fragment didn't give a good result. the article "J. Mol. Biol.(1996)261, 470-489" used phenol subunit as a base fragment. Please give some information of how to select a base fragment manually while using FlexX. Any answer is appreciated. ---Mingzhu in SMU From chemistry-request@server.ccl.net Wed May 29 12:27:58 2002 Received: from dobit2.rug.ac.be ([157.193.42.8]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4TGRwC32232 for ; Wed, 29 May 2002 12:27:58 -0400 Received: from hartree4.rug.ac.be (hartree4.rug.ac.be [157.193.91.12]) by dobit2.rug.ac.be (8.11.1/8.11.1) with ESMTP id g4TGRvT20235 for ; Wed, 29 May 2002 18:27:57 +0200 (MEST) Received: from inchem34 (inchem34.rug.ac.be [157.193.91.54]) by hartree4.rug.ac.be (AIX4.2/UCB 8.7/8.7) with SMTP id SAA08380 for ; Wed, 29 May 2002 18:28:51 +0100 (NFT) Message-Id: <4.1.20020529181914.00a324f0@hartree4.rug.ac.be> X-Sender: patrick@hartree4.rug.ac.be X-Mailer: QUALCOMM Windows Eudora Pro Version 4.1 Date: Wed, 29 May 2002 18:29:02 +0200 To: chemistry@ccl.net From: Patrick Bultinck Subject: wavefunction stability issues Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear all, Can anybody refer me to a good reference on the different sources of wave function instability ? Especially as on how to judge whether a certain post SCF calculation will help. Also, it is sometimes stated that wave function instability would indicate the necessity of electron correlation. At this day and age, only single reference (Hartree-Fock) dynamical electron correlation techniques can be used for the larger molecules I am looking at. What good is MP2, CC etc. when the reference is not appropriate ? Really, for a good result a technique like mrci would be very interesting, but for some systems (and computer resources), even a large CAS+PT is impossible. So how to handle this ? Any references ? As a side question: would anybody have any idea what percentage of post-scf calculations being done has ever had the stability of its HF reference checked ? Thanks, Patrick Bultinck Ghent University Belgium From chemistry-request@server.ccl.net Wed May 29 17:02:41 2002 Received: from rhodopsin.usask.ca ([128.233.48.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4TL2fC06303 for ; Wed, 29 May 2002 17:02:41 -0400 Received: from pc.chemie.tu-darmstadt.de (localhost.localdomain [127.0.0.1]) by rhodopsin.usask.ca (8.11.6/8.11.6) with ESMTP id g4TKtjp12235 for ; Wed, 29 May 2002 14:55:46 -0600 Sender: thomas@localhost.localdomain Message-ID: <3CF54051.B50C055@pc.chemie.tu-darmstadt.de> Date: Wed, 29 May 2002 14:55:45 -0600 From: Thomas Exner X-Mailer: Mozilla 4.78 [en] (X11; U; Linux 2.4.8-34.1mdk i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Density matrix in G98 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers, I have an unusual g98 question: I use a program developed in our group to approximate the electron density matrix based on a Hartree-Fock calculation with a specific basis set. To compare the accuracy of this approximation, I would like to compare energies calculated with these density matrices and energies calculated directly with g98. My question is now, if it is possible to read a density matrix in g98 and then calculate energies with this density matrix? Any help is highly appreciated. Best wishes, Thomas -- ____________________________________________________________________ Dr. Thomas Exner Department of Physical Chemistry Physical Chemistry I University of Technology Darmstadt (TUD) Petersenstr. 20 Auf der Marienhoehe 5 64287 Darmstadt 64297 Darmstadt Germany Germany phone: +49-6151-16 2398 +49-6151-537165 fax: +49-6151-16 4298 e-mail: exner@pc.chemie.tu-darmstadt.de texner@gmx.net WWW: http://www.pc.chemie.tu-darmstadt.de/staff/exner/ Computational, Theoretical & Mathematical Chemistry Department of Chemistry University of Saskatchewan 110 Science Place 431 Edmund Park Saskatoon, SK, S7N 5C9 Saskatoon, SK, S7H 0Z4 Canada Canada phone: +1-306-966-5357 +1-306-382-5397 fax: +1-306-966-4730 ____________________________________________________________________ From chemistry-request@server.ccl.net Wed May 29 17:17:27 2002 Received: from mercury.chem.northwestern.edu (daemon@[129.105.116.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4TLHRC06654 for ; Wed, 29 May 2002 17:17:27 -0400 Received: from localhost (hutchisn@localhost) by mercury.chem.northwestern.edu (8.11.6+Sun/8.11.6) with ESMTP id g4TLHMJ03743; Wed, 29 May 2002 16:17:22 -0500 (CDT) Date: Wed, 29 May 2002 16:17:22 -0500 (CDT) From: Geoff Hutchison To: amor san juan cc: Subject: Re: CCL:Sybyl alternative In-Reply-To: <20020529131414.11635.qmail@web12808.mail.yahoo.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII > My goal is to add both charges & Hydrogens to ligand > and macromolecule. For the past weeks, I tested the > capabilities of chemsketch5 & babel 1.6 but it is not > successful as compared to data generated from Sybyl. Yes, and as was mentioned the last time you asked this question, ChemSketch is a 2D program. So you're not going to get "correct" coordinates. > Therefore addition of hydrogens and any further manipulations are > nonsense. You should use a real modelling application. (Couldn't have said it better.) There are several free/open source modeling programs, such as PyMol and Ghemical. There's even a website with links to all sorts of open source software: -- -Geoff Hutchison Marks/Ratner Groups (847) 491-3295 Northwestern Chemistry From chemistry-request@server.ccl.net Wed May 29 21:00:33 2002 Received: from web12801.mail.yahoo.com ([216.136.174.36]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g4U10WC22671 for ; Wed, 29 May 2002 21:00:33 -0400 Message-ID: <20020530010031.76218.qmail@web12801.mail.yahoo.com> Received: from [61.9.73.249] by web12801.mail.yahoo.com via HTTP; Wed, 29 May 2002 18:00:31 PDT Date: Wed, 29 May 2002 18:00:31 -0700 (PDT) From: amor san juan Subject: Re: CCL:Sybyl alternative To: Geoff Hutchison Cc: chemistry@ccl.net In-Reply-To: MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Sir: Chemsketch5 can do 3D optimization yet, it differs > from Sybyl file and that is my disturbance. Thanks --- Geoff Hutchison wrote: > > > My goal is to add both charges & Hydrogens to > ligand > > and macromolecule. For the past weeks, I tested > the > > capabilities of chemsketch5 & babel 1.6 but it is > not > > successful as compared to data generated from > Sybyl. > > Yes, and as was mentioned the last time you asked > this question, > ChemSketch is a 2D program. So you're not going to > get "correct" > coordinates. > > > > Therefore addition of hydrogens and any further > manipulations are > > nonsense. You should use a real modelling > application. > > (Couldn't have said it better.) > > There are several free/open source modeling > programs, such as PyMol and > Ghemical. > > > > > There's even a website with links to all sorts of > open source software: > > > > -- > -Geoff Hutchison > > Marks/Ratner Groups (847) 491-3295 > Northwestern Chemistry > > > __________________________________________________ Do You Yahoo!? Yahoo! - Official partner of 2002 FIFA World Cup http://fifaworldcup.yahoo.com