From chemistry-request@server.ccl.net Thu Aug 30 01:40:16 2001 Received: from mailstore1.netcologne.de (IDENT:mirapoint@[194.8.194.121]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7U5eGM11038 for ; Thu, 30 Aug 2001 01:40:16 -0400 Received: from cosmologic.de (dial-213-168-96-172.netcologne.de [213.168.96.172]) by mailstore1.netcologne.de (Mirapoint) with ESMTP id AAW48791; Thu, 30 Aug 2001 07:40:12 +0200 (CEST) Message-ID: <3B8DD24E.7604BB33@cosmologic.de> Date: Thu, 30 Aug 2001 07:42:38 +0200 From: "Dr. Andreas Klamt" Organization: COSMOlogic GmbH&CoKG X-Mailer: Mozilla 4.7 [de] (Win98; I) X-Accept-Language: en,pdf MIME-Version: 1.0 To: rah rach CC: chemistry@ccl.net Subject: Re: CCL:Phthalates, Data? References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Our COSMOtherm is able to predict physical property data as temperature dependent vapor pressure (and hence normal BP), solubility, activity coefficients, partition coefficients, etc.It is based on DFT/COSMO calculations for the compounds. We have successfully treated some phthalates as well in the past. Have a look to our web-site www.cosmologic.de. Andreas Klamt rah rach schrieb: > > Hi every one , > > I am looking for data( physical properties data , as normal boiling point , vapour pressure ,....) for the phthalates > compounds . If any one can helpe me by indicating any source ( programs, databook, articles,...etc) I would appreciate that > very much . > thanks in advance. > R.Rachid > > ------------------------------------------------------------------------------------------------------------------------------ > Get your FREE download of MSN Explorer at http://explorer.msn.com > > -= 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 -- -------------------------------------------------------------------------------- Dr. Andreas Klamt COSMOlogic GmbH&CoKG Burscheider Str. 515 51381 Leverkusen, Germany Tel.: 49-2171-73168-1 Fax: ...-9 e-mail: andreas.klamt@cosmologic.de web: www.cosmologic.de -------------------------------------------------------------------------------- COSMOlogic Your Competent Partner for Computational Chemistry and Fluid Thermodynamics -------------------------------------------------------------------------------- From chemistry-request@server.ccl.net Thu Aug 30 11:01:13 2001 Received: from physics.lsu.edu ([130.39.182.96]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7UF1CM07826 for ; Thu, 30 Aug 2001 11:01:12 -0400 Received: from localhost (vani@localhost) by physics.lsu.edu (8.9.2/8.9.2) with ESMTP id JAA26159 for ; Thu, 30 Aug 2001 09:59:35 -0500 (CDT) Date: Thu, 30 Aug 2001 09:59:34 -0500 (CDT) From: Vemparala Satyavani To: chemistry@ccl.net Subject: temperature for MD of a protein Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, thanks for all the replies to my previous question. I resolved the issue with abrormal bond energies. I have a question regarding the temperature at which MD needs to run for a protein. I am new to PDB files, so this might be a trivial question. The starting coordinates to simulate a protein are taken from the PDB. 1.How does one decide at what temperature the MD run needs to be done? 2.In other words, experimentally, when a PDB structure is determined, is temperature a relevant factor? 3. would the structure be different if done at a different temperature? 4. is the temperature information encoded in the PDB file? Thanks vani From chemistry-request@server.ccl.net Thu Aug 30 08:29:27 2001 Received: from shiva.jussieu.fr ([134.157.0.129]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7UCTQM05129 for ; Thu, 30 Aug 2001 08:29:27 -0400 Received: from liliput.lct.jussieu.fr (liliput.lct.jussieu.fr [134.157.90.1]) by shiva.jussieu.fr (8.11.3/jtpda-5.3.3) with ESMTP id f7UCTPO06865 for ; Thu, 30 Aug 2001 14:29:26 +0200 (CEST) Received: from (pollet@localhost) by liliput.lct.jussieu.fr (8.10.1/jtpda-5.3.3) id f7UCTUV26487 for chemistry@ccl.net; Thu, 30 Aug 2001 14:29:30 +0200 (FRA Ete) From: rodolphe.pollet@lct.jussieu.fr (Rodolphe Pollet) Message-Id: <200108301229.f7UCTUV26487@liliput.lct.jussieu.fr> Subject: CCL:SUMMARY ab initio methods To: chemistry@ccl.net Date: Thu, 30 Aug 2001 14:29:29 +0200 (FRA Ete) X-Mailer: ELM [version 2.4ME+ PL66 (25)] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Dear CCLers, Many thanks for replies to my question : "I am looking for a single reference, such as a review article or a book, about the ab initio methods MRCI, CASPT2, AQCC, ... These ones are indeed not covered in the Szabo&Ostlund." Here is the list of answers that i received. Rodolphe Pollet --- I would recommend Trygve Helgaker, Poul Jorgensen and Jeppe Olsen's book "Molecular Electronic-Structure Theory", ISBN 0471967556. It's a rather massive and detailed treatment of different ab initio methods. (Olli Lehtonen) --- A superb book is "Molecular Electronic-Structure Theory" by T. Helgaker, P. Jorgensen and J. Olsen (John Wiley & Sons Ltd, Chichester, 2000, ISBN 0-471-96755-6). If you are looking for reviews on applications of CASPT2, you may find the following useful: M. Merchan, L. Serrano-Andres, M. P. Fuelscher and B. O. Roos, "Multiconfigurational Perturbation Theory Applied to Excited States of Organic Compounds", in "Recent Advances in Multireference Methods", ed. K. Hirao, World Scientific Publishing Company, Amsterdam, The Netherlands, 1998. B. Roos, "Theoretical studies of electronically excited states of molecular systems using multiconfigurational perturbation theory", Acc. Chem. Res., 32, 137-144, 1999. (Chris Page) --- You may want to look the text by Knowles and Werner available at http://www.fz-juelich.de/nic-series/Volume3/Volume3.html Ab Initio Methods for Electron Correlation in Molecules Peter Knowles, University of Birmingham, United Kingdom Martin Schutz, Hans-Joachim Werner, Universitat Stuttgar (Pedro) --- try http://www.fz-juelich.de/nic-series/ Ab Initio Methods for Electron Correlation in Molecules Peter Knowles, Martin Schutz, and Hans-Joachim Werner published in Modern Methods and Algorithms of Quantum Chemistry, Proceedings, Second Edition, J. Grotendorst (Ed.), John von Neumann Institute for Computing, Julich, NIC Series (Qadir) ___ I know it's not quite what you are looking for (I've never found a book that covered all those methods together), but one great book is Molecular Electronic-Structure Theory by Trygve Helgaker, Poul Jorgenson, and Jeppe Olsen (authors of the DALTON ab initio package). This work fills the gap between Szabo and Ostlund and modern ES Theory. It is strictly ab initio (no DFT) and covers via second quantization, in amazing depth: HF, CI, MCSCF, Coupled-Cluster Theory (especially), and Perturbation theories. It doesn't really cover MRCI in depth, but covering MCSCF and CI essentially gets you that, and I don't think AQCC is in it. It also doesn't cover relativistic models and makes no mention of ECP basis sets, as well. But, it contains a vast amount of information in its 900+ pages of materia, including many comparisons between the models. This book costs an arm and a leg (approx. US$300), but is worth that cost. (Matt Thompson) ___ Try "Computational chemistry", by David Young, Wiley, 2001 "Quantum chemistry" by I. N. Levine, Prentice Hall, Fifth Ed., Prentice hall, 2000--chapters 15-17, very good introductions, with refs. (EL) From chemistry-request@server.ccl.net Thu Aug 30 08:16:17 2001 Received: from janus.hosting4u.net ([209.15.2.37]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f7UCGHM04934 for ; Thu, 30 Aug 2001 08:16:17 -0400 Received: (qmail 2958 invoked from network); 30 Aug 2001 12:16:17 -0000 Received: from zeus.hosting4u.net (HELO proinformatix.com) (209.15.2.56) by mail-gate.hosting4u.net with SMTP; 30 Aug 2001 12:16:17 -0000 Received: from yersina ([202.138.17.161]) by proinformatix.com ; Thu, 30 Aug 2001 07:16:13 -0500 Reply-To: From: "Sergio Manzetti" To: "Chemistry Discussion G" Subject: Domain Decomposition in GROMACS Date: Thu, 30 Aug 2001 22:14:44 -0700 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) X-MIMEOLE: Produced By Microsoft MimeOLE V5.00.2919.6700 Importance: Normal Hello, I wonder if someone has tested domain decomposition in GROMACS, and what kind of parameters he/she eventually used. All tips&trix are welcome Sergio ____________________________________________________________________________ ___________________________ Sergio Manzetti Research Scholar Centre of Molecular Biotechnology/ Supercomputer Facility Queensland University of Technology 2 George St. BRISBANE 4000 QLD AUSTRALIA email: s.manzetti@student.qut.edu.au Tlf: +61 7 3864 1434 www: http://www.life.sci.qut.edu.au/html/research/cmgenetics.html www2: http://www.its.qut.edu.au/hpc/ From chemistry-request@server.ccl.net Thu Aug 30 04:25:52 2001 Received: from mail.ihep.ac.cn ([202.38.128.1]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7U8HRM02895 for ; Thu, 30 Aug 2001 04:17:27 -0400 Received: from Wangjm (aspw04.ihep.ac.cn [202.122.38.26]) by mail.ihep.ac.cn (8.11.2/8.11.0) with SMTP id f7U87We02141 for ; Thu, 30 Aug 2001 16:07:32 +0800 Message-Id: <200108300807.f7U87We02141@mail.ihep.ac.cn> Date: Thu, 30 Aug 2001 16:15:29 +0800 From: Denny To: "chemistry@ccl.net" Subject: ECP calculation of La using Gaussian 98 Organization: Tsinghua University X-mailer: FoxMail 3.0 beta 1 [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Hi all, When I calculate the energy of La atom, if I change the initial orbit guess with the keyword guess=alter, I even find lower enery. Then it means Gaussian 98 can't give the ground state of La automatically? If so then how can I be sure the orbital order what I get correspond to the ground state? In addition I even found using the same input file, Gaussian 98 for windows A3 and Gaussian 98 for linux A7 can give different results. Even the number of primitive basis functions are different. What goes wrong? Denny dilys98@mails.tsinghua.edu.cn From chemistry-request@server.ccl.net Thu Aug 30 10:53:36 2001 Received: from mmb1.vsnl.net.in ([202.54.1.72]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7UErZM07708 for ; Thu, 30 Aug 2001 10:53:36 -0400 Received: from bom2.vsnl.net.in (unknown [203.199.88.73]) by mmb1.vsnl.net.in (Postfix) with ESMTP id 5460338166 for ; Thu, 30 Aug 2001 20:23:18 +0530 (IST) Message-ID: <3B8E5177.B5548469@bom2.vsnl.net.in> Date: Thu, 30 Aug 2001 20:15:11 +0530 From: meenatul X-Mailer: Mozilla 4.7 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 To: CCL Subject: DOCK and chirality Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I am using DOCK 4 for studying docking of certain molecules which are stereoisomers( D and L) and experimentally it was known that only one of the isomer is active.What protocol I should use when handling such molecules? I would like to know whether DOCK can consider the chirality during calculation? I have tried using auto-match as well as manual match (with node maxi =4) with grid based energy scoring method (rigid docking) but I have not found distinguishable results out of it.Can anyone suggest some solution for this particular type of problem? Thank you. Meena From chemistry-request@server.ccl.net Thu Aug 30 06:02:30 2001 Received: from mel.ruc.dk ([130.225.220.27]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7UA2TM25997 for ; Thu, 30 Aug 2001 06:02:29 -0400 Received: from smtprelay.ruc.dk (smtprelay.ruc.dk [130.225.220.22]) by mel.ruc.dk (8.9.3/8.9.1) with ESMTP id MAA00726; Thu, 30 Aug 2001 12:02:28 +0200 (MET DST) Received: from virgil.ruc.dk (virgil.ruc.dk [130.225.220.110]) by smtprelay.ruc.dk (8.9.3+Sun/8.9.3) with ESMTP id LAA19262; Thu, 30 Aug 2001 11:39:47 +0200 (MEST) Received: from VIRGIL/SpoolDir by virgil.ruc.dk (Mercury 1.44); 30 Aug 01 12:02:28 +0100 Received: from SpoolDir by VIRGIL (Mercury 1.44); 30 Aug 01 12:02:23 +0100 From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter To: Frank Jensen , chemistry@ccl.net Date: Thu, 30 Aug 2001 12:02:00 +0100 Subject: CCL:combination of b3lyp and cc-pVQZ X-Confirm-Reading-To: "Jens Spanget-Larsen" X-pmrqc: 1 Priority: normal X-mailer: Pegasus Mail for Windows (v2.23) Message-ID: <1A38EE7A57ED@virgil.ruc.dk> Frank Jensen: > We have recently done some benchmarking of > various basis set for DFT. For the H,C,N,O,F molecules > in the G3 data set, the MAD and Maximum error of some > popular basis sets for total atomization energies > with the BLYP functional are (kJ/mol): > > MAD Max > > 6-31G* 16 64 > cc-pVDZ 41 82 > cc-pVTZ 3.6 14.5 > cc-pVQZ 2.9 10.9 > > These numbers are errors relative to a saturated basis > set, i.e. the Kohn-Sham limit. These data are interesting. Why does cc-pVDZ perform so much worse than cc-pVTZ? Is this an indication that the valence-triple-zeta extension is physically very significant, or does the cc-pVDZ basis set suffer from som particular 'unbalance'? Comparison with the relatively satisfactory 6-31G* results might suggest that something is 'wrong' with cc-pVDZ. Any similar benchmarks for Raman intensities? Jens >--< =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- JENS SPANGET-LARSEN Office: +45 4674 2710 Department of Chemistry Fax: +45 4674 3011 Roskilde University (RUC) Cell-Phone: +45 2320 6246 P.O.Box 260 E-Mail: JSL@virgil.ruc.dk DK-4000 Roskilde, Denmark http://virgil.ruc.dk/~jsl =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- From chemistry-request@server.ccl.net Thu Aug 30 02:34:44 2001 Received: from lancelot.imb-jena.de ([192.124.248.76]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7U6YhM12724 for ; Thu, 30 Aug 2001 02:34:43 -0400 Received: (from pineda@localhost) by lancelot.imb-jena.de (SGI-8.9.3/8.8.8) id IAA01696; Thu, 30 Aug 2001 08:32:44 +0200 (CEST) From: pineda@imb-jena.de (Felipe Pineda) Message-Id: <10108300832.ZM118506@lancelot.imb-jena.de> Date: Thu, 30 Aug 2001 08:32:44 +0000 In-Reply-To: Prashant Desai "CCL:Bootstrap" (Aug 29, 11:03am) References: <3B8C7EAF.482F90BF@bol.net.in> X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: Prashant Desai , Posting Question on CCL Subject: Re: CCL:Bootstrap Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii hello Prashant Desai, the following is the result of a pubmed search using the query bootstrap* qsar, but i'm sure there is much more relevant references. anyway i hope it's a starting point. best regards felipe 1: Ecotoxicol Environ Saf 1995 Jun;31(1):37-48 Applicability of CoMFA in ecotoxicology: a critical study on chlorophenols. Briens F, Bureau R, Rault S, Robba M. Centre d'Etudes et de Recherche sur le Medicament de Normandie, UFR des Sciences Pharmaceutiques, France. Comparative molecular field analysis (CoMFA) is used to relate ecotoxicological data with steric and electrostatic fields of chemicals forming an intentionally selected homogeneous set, the chlorophenols, for which reliable data are abundant in literature. Among these data, those concerning 16 different biological systems were selected, leading to predictive CoMFA QSAR in 14 of the cases. This is attested by cross-validation and bootstrapping, which also authorize the prediction of the chlorophenols toxicity values, when they are missing. The quality of obtained CoMFA models and the applicability of the method are discussed. The results are very promising, and they encourage further investigation into CoMFA in ecotoxicology. PMID: 7544263 [PubMed - indexed for MEDLINE] On Aug 29, 11:03am, Prashant Desai wrote: > Subject: CCL:Bootstrap > I am looking out for information about theory and application of > Bootstrap algorithm as applied for vaidation of QSAR equations. > Any relevant refrences and reprints are welcome. > Prashant Desai > Senior Research Fellow > Dept. Pharm. Chem. > Bombay College of Pharmacy > University of Mumbai > Mumbai, IndiA. > > > -= 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 > > > > >-- End of excerpt from Prashant Desai -- ********************************************************************** * Felipe Pineda,PhD * * Institut fuer Molekulare Biotechnologie * * AG Theoretische Biophysik * * Beutenbergstrasse 11, Jena Vox: +49-3641-65-6491 * * Postfach 100 813, D-07708 Jena, Germany Fax: -6495 * * web: www.imb-jena.de/~pineda * ********************************************************************** ********************************************************************** * DISCLAIMER: Unless indicated otherwise, everything in this note is * * my personal opinion, not an official statement of my employer * ********************************************************************** From chemistry-request@server.ccl.net Thu Aug 30 14:42:20 2001 Received: from mail.iitk.ac.in ([203.200.95.130]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7UIfmM11878 for ; Thu, 30 Aug 2001 14:41:48 -0400 Received: from qasid.cc.iitk.ac.in (qasid.cc.iitk.ac.in [172.31.1.16]) by mail.iitk.ac.in (8.9.3+Sun/8.9.3) with ESMTP id AAA29812 for ; Fri, 31 Aug 2001 00:10:46 +0530 (IST) Received: from Debug (IDENT:nobody@[210.212.54.11]) by qasid.cc.iitk.ac.in (8.9.2/8.9.2) with SMTP id XAA25076 for ; Thu, 30 Aug 2001 23:58:26 +0530 (IST) Message-Id: <200108301828.XAA25076@qasid.cc.iitk.ac.in> To: CHEMISTRY@ccl.net From: ranjan@iitk.ac.in Subject: any free software for ETH calculations Date: Thu, 30 Aug 2001 18:17:51 GMT X-Mailer: Endymion MailMan Standard Edition v3.0.35 Dear CClers, Could any one tell me if there are free softwares available for doing Extended huckel calculations. . Chinmoy