From r.knegtel@organon.oss.akzonobel.nl Thu Jun 25 04:06:47 1998 Received: from gate2.akzonobel.nl (gate2.oss.akzonobel.nl [192.87.3.6]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id EAA13334 Thu, 25 Jun 1998 04:06:46 -0400 (EDT) Received: (from fwmaster@localhost) by gate2.akzonobel.nl (8.8.4/8.6.12) id KAA15875 for ; Thu, 25 Jun 1998 10:06:45 +0200 (MET DST) Received: by gate2.oss.akzonobel.nl via smap (V1.3) id sma015838; Thu, 25 Jun 98 10:06:43 +0200 Received: by apou01.akzonobel.nl id KAA22497; Thu, 25 Jun 1998 10:13:48 +0200 (MET DST) Received: from organon.oss.akzonobel.nl (orchid.oss.akzonobel.nl) by vesta.oss.akzonobel.nl (PMDF V5.1-7 #22904) with SMTP id <01IYNEFA76RK9DJGFW@vesta.oss.akzonobel.nl> for chemistry@www.ccl.net; Thu, 25 Jun 1998 10:08:54 +0100 Received: (from knegtel@localhost) by organon.oss.akzonobel.nl (950413.SGI.8.6.12/8.6.12) id IAA05525 for chemistry@www.ccl.net; Thu, 25 Jun 1998 08:06:23 +0000 (GMT) Date: Thu, 25 Jun 1998 10:06:23 +0200 (WDT) From: Knegtel Ronald Subject: Secondary structure in unique folds To: chemistry@www.ccl.net Message-id: <199806250806.IAA05525@organon.oss.akzonobel.nl> MIME-version: 1.0 X-Mailer: ELM [version 2.4 PL24 ME8b] Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7bit Dear all, can anyone point me to a paper or website that analyzes the presence and percentages of secondary structure elements in a set of unique protein folds from the PDB (as used for instance in threading). I am aware of databases like SCOP and FSSP but these do not seem to address this particular question. Alternatively, I would be interested in downloading a database of unique folds (is that possible at all, many structure comparison sites only list PDB codes of individual representative folds but do not allow downloading a whole database) and do the analysis myself. Any hints are appreciated, will summarize for food. Cheers, Ronald ------------------------------------------------------------------------------- Dr. Ronald M. A. Knegtel Research Scientist Dept. of Molecular Design and Informatics Phone : +31-412-661469 N.V. Organon, RK2340 Fax : +31-412-662539 P.O. Box 20 5340 BH Oss http://www.organon.nl/ The Netherlands E-Mail : r.knegtel@organon.oss.akzonobel.nl ------------------------------------------------------------------------------- From amolive@dedalus.lcc.ufmg.br Thu Jun 25 16:42:50 1998 Received: from dedalus.lcc.ufmg.br (dedalus.lcc.ufmg.br [150.164.65.10]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id QAA20713 Thu, 25 Jun 1998 16:42:47 -0400 (EDT) Received: from localhost by dedalus.lcc.ufmg.br (AIX 3.2/UCB 5.64/4.03) id AA41978; Thu, 25 Jun 1998 17:36:29 -0300 Organization: Universidade Federal de Minas Gerais - LCC - Brasil Date: Thu, 25 Jun 1998 17:36:29 -0300 (BSC) From: andre mauricio de oliveira To: CHEMISTRY@www.ccl.net Cc: andre mauricio de oliveira Subject: Counter-ions on AMBER calculations Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Can anyone tell me about simulation of counter-ions upon oligonucleotide backbones, employing any model such as Condensation Theory to avoid the use of explicit sodium, potassium or magnesium atoms in AMBER force field calculations? I'm interessed in setting any correction on the distance-dependent dieletric constant present in the coulombic term of AMBER forcefield wich includes charged atoms in the enviroment. Best regards, Andre Mauricio de Oliveira VOICE +55-031-374-1325 +55-031-499-5765 FAX +55-031-499-5700 Laboratorio de QSAR e Modelagem Molecular Nucleo de Estudos em Quimica Medicinal (NEQUIM) NEQUIM's Homepage: http://www.qui.ufmg.br/~nequim Departamento de Quimica ICEx Federal University of Minas Gerais Av Antonio Carlos 6627 Pampulha ZIP CODE 31270-901 Belo Horizonte MG Brazil From ep7@dent.okayama-u.ac.jp Thu Jun 25 21:00:54 1998 Received: from deews1.dent.okayama-u.ac.jp (deews1.dent.okayama-u.ac.jp [150.46.202.36]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id VAA23453 Thu, 25 Jun 1998 21:00:51 -0400 (EDT) From: ep7@dent.okayama-u.ac.jp Received: from [150.46.140.80] (yobou2.dent.okayama-u.ac.jp [150.46.140.80]) by deews1.dent.okayama-u.ac.jp (8.8.8/3.6W) with SMTP id KAA20340 for ; Fri, 26 Jun 1998 10:01:46 +0900 (JST) Message-Id: <199806260101.KAA20340@deews1.dent.okayama-u.ac.jp> Date: Fri, 26 Jun 1998 10:18:05 +0900 To: CHEMISTRY@www.ccl.net Subject: Summary: (H2O)2 MIME-Version: 1.0 Content-Type: text/plain; charset=iso-2022-jp X-Mailer: Eudora-J(1.3.8.5-J13) Thank you for kind advice. I would like to ask about paper for interaction energy of water dimer corrected BSSE. Date: Wed, 24 Jun 1998 12:02:14 +0200 (MET DST) From: Dorothee Berthomieu To: ep7@dent.okayama-u.ac.jp Subject: Re: CCL:(H2O)2 Content-Type: TEXT/PLAIN; charset=US-ASCII X-UIDL: 5774c4a9f894d97f57d2f9a3eb3d396f I can recommand you the article "Ab initio studies of hydrogen bonds : the water dimer paradigm" from Steve Scheiner in Annu. Rev. Phys. Chem. 1994 , vol 45: pp23-56 Dorothee Berthomieu ENSCM LMCCCO Montpellier (FRANCE) Date: Wed, 24 Jun 1998 11:21:33 -0500 (CDT) From: Tapas Kar To: ep7@dent.okayama-u.ac.jp cc: CHEMISTRY@www.ccl.net Subject: Re: CCL:(H2O)2 Content-Type: TEXT/PLAIN; charset=US-ASCII X-UIDL: 06e8dce6cd71033b747a17d57a25d1f3 Here is a good reference for you. "Hydrogen Bonding, A theoretical perspective" by Steve Scheiner, Oxford Univ. Press. ISBN 0-19-509011-x The most comprehensive study of the H2O dimer that I know is: "A systematic ab initio study of the water dimer in hierarchies of basis sets and correlation models" Halkier A, Koch H, Jorgensen P, Christiansen O, Nielsen IMB, Helgaker T THEORETICAL CHEMISTRY ACCOUNTS 97: (1-4) 150-157 OCT 1997 (the journalis the former Theoretica Chimica Acta. This was in the Jan Alml\"of memorial issue, whilch has plenty of other great stuff in it) JM --------------------------------------------------------------------------- dr. Jan M.L. Martin Senior Lecturer, Computational Chemistry Department of Organic Chemistry/Kimmelman Building, Room 262 Weizmann Institute of Science/Rechovot 76100/ISRAEL FAX +972(8)9344142 Phone +972(8)9342533 E-mail comartin@wicc.weizmann.ac.il *** research group WWW home page http://theochem.weizmann.ac.il/ *** ---- kol ha-olam kulo gesher tzar me'od, v'ha-ikar lo l'hitpached k'lal --- In reply to a question by Masao Masamura, for refs to the water dimer and BSSE, E.Lewars supplied some dimer references. I would like to add the following to his list: M.Schuetz et al., J.Chem.Phys. 107 (1997) 4597. This study treats the dimer at the MP2 level with _very_ large basis sets and explicitly discusses the influence of BSSE and other errors. E.Lewars also pointed to a reference on the water hexamer (Chem Phys Letters 1991, 176, 41-45). This work is by now slightly outdated, in particular it arrives at a proposed global minimum that is qualitatively different from later work using higher-level calculations (MP2 instead of HF-SCF), e.g. - C.J.Tsai and K.D.Jordan, Chem.Phys.Lett. 213 (1993) 181. - D.C.Clary et al., Nature 381 (1996) 501; J.Phys.Chem. 100 (1996) 18014. Note that recent experimental work seems to be in agreement with the cage structure found in these theoretical studies: - Saykally et al., J.Phys.Chem. A 101 (1997) 8995. I should also mention that M.Schuetz, Prof. H.-J.Werner and myself have just developed an improved NEMO potential that reproduces ab-initio MP2 energies of all the important pentamer and hexamer minimum structures perfectly (including the cage). A paper on these results will be submitted in a few weeks. Bernd Hartke -- PD Dr. Bernd Hartke e-mail: hartke@theochem.uni-stuttgart.de Dep. of Theoretical Chemistry e-mail: bernd.hartke@rus.uni-stuttgart.de University of Stuttgart http://www.theochem.uni-stuttgart.de/~hartke Pfaffenwaldring 55 Phone: +49-711-685-4409 70569 Stuttgart FAX: +49-711-685-4442 GERMANY X-Sender: rothw@mail.rz.uni-duesseldorf.de X-Mailer: Windows Eudora Light Version 1.5.2 Content-Type: text/plain; charset="us-ascii" To: ep7@dent.okayama-u.ac.jp From: Wolfgang Roth Subject: Re: CCL:(H2O)2 Date: Wed, 24 Jun 1998 19:07:22 +0000 X-UIDL: b79c75bb4184e7f61e06e79b7745e6f1 This are - to my knowledge - two of the newest papers about this topic: Theor. Chem. Acta 97 (1997) p. 150-157 J. Chem. Phys. 107 (1997) p. 4597 See also J. Phys. Chem. A 102 (1998) 754 Yours Wolfgang Roth ==W=R======================W=o=l=f=g=a=n=g==R=o=t=h== Heinrich-Heine-Universitaet Krabbenburg 29 Physikalische Chemie I "Boverhaus" 40225 Duesseldorf 40723 Hilden Germany = "http://www-public.rz.uni-duesseldorf.de/~rothw/" = From peter@cherwell.com Wed Jun 24 13:25:30 1998 Received: from congo.cherwell.com (congo.cherwell.com [193.82.249.202]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id NAA02841 Wed, 24 Jun 1998 13:25:29 -0400 (EDT) Received: from tamar.cherwell.com ([193.82.249.230]) by congo.cherwell.com (Post.Office MTA v3.1.2 release (PO205-101c) ID# 0-0U10L2S100) with SMTP id AAA406 for ; Wed, 24 Jun 1998 18:25:24 +0100 Message-Id: <3.0.5.32.19980624182521.008c8a80@cherwell.com> X-Sender: peter@cherwell.com X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.5 (32) Date: Wed, 24 Jun 1998 18:25:21 +0100 To: chemistry@www.ccl.net From: Peter Tebbutt Subject: ChemSymphony Beans Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear CCLers ChemSymphony has a new site which will be found at: http://www.chemsymphony.com/ The 'newest' element of the site is under the 'extranet' button where we have a MOPAC demo, a demonstration of co-operation with the ChemDraw plug-in from CambridgeSoft, and a SMILES demo which deploys some aspects of ChemSymphony's data conversion mechanisms. These are applets built with ChemSymphony Beans, which like all JavaBeans require a JDK 1.1 environment for the deployment applets or applications built with Beans. Make sure that you have the latest browser, or download the Java Plug-in freely available from Sun. We tell you how to do this on the 'Help' page. You may have seen ChemSymphony applets before: the key points about ChemSymphony Beans is that there are now many more components (eg a 2D Drawing tool, and a 3D Editing/Builder component), AND that these components can be used to build a great variety of applets and applications for use on intranets. We are demonstrating this technology through the internet, you may need to be patient while the applet arrives at your system. Obviously this 'speed to download' should not be a problem on a private intranet. There will be more new stuff on the site soon, so please enjoy the demonstrations, come back for more and start building high-impact intranets for your colleagues! with best wishes Peter Tebbutt Cherwell Scientific Publishing e-mail peter@cherwell.com