From tajkhors@mbp-sgi7.inet.dkfz-heidelberg.de Sun Aug 2 11:32:53 1998 Received: from mbp-sgi7.inet.dkfz-heidelberg.de (mbp-sgi7.inet.dkfz-heidelberg.de [193.174.59.125]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id LAA12489 Sun, 2 Aug 1998 11:32:52 -0400 (EDT) Received: by mbp-sgi7.inet.dkfz-heidelberg.de (951211.SGI.8.6.12.PATCH1502/940406.SGI.AUTO) for chemistry@www.ccl.net id AAA26064; Mon, 3 Aug 1998 00:34:37 GMT From: "Emadeddin Tajkhorshid" Message-Id: <9808021734.ZM26062@mbp-sgi7.inet.dkfz-heidelberg.de> Date: Sun, 2 Aug 1998 17:34:30 -0700 Reply-To: E.Tajkhorshid@DKFZ-Heidelberg.de X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@www.ccl.net (Computational Chemistry List) Subject: small peptide models (summary) Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear all I got two answers to my question and many requests for the summary. Many thanx to Wayne Steinmetz and Randall B. Murphy for their replies. ***************************************************************************** Original Q: > I am looking for some examples of small polypeptide structures which can be > used for testing the efficiency of a program doing some semiempirical > calculations. With this regard, the experimentally resolved structures which > are not very large are the main intrest. Any other model which may be > interesting or any reference with this regard is highly appreciated. **************************************************************************** From: Wayne Steinmetz Date: Mon Jul 27, 5:43pm -0700 To: E.Tajkhorshid@DKFZ-Heidelberg.de Cc: Subject: Re: CCL:small peptide models Check the recent work of Barbara Imperiali at Cal Tech. Her group prepared a small tetra or hexapeptide which had a well defined beta turn in solution. The conformation was confirmed by NMR. I can't give you the reference as the file was lost by a student. Another noteworthy paper appeared in the 10 July 1998 issue of Science. Vol 281, pp. 253-256. Kortemme et al. designed and prepared a peptide with 20 amino acids. The peptide has a well defined three-stranded beta=sheet. Steve Mayo designed and prepared a peptide with 28 amino acids that has the zinc-finger motif without zinc. Science, vol. 278, pp. 82-87 (3 October 1997). For a review of small helical peptides, see Bryson et al., volume 270, pp. 935-941, 10 Nov. 1995. You did not indicate how small is small. Conotoxins are fairly small peptides whose well defined conformation and whose stability is due to the presence of 2 disulfide bridges. This family of toxins has received a great deal of attention as small peptides often do not have a well defined structure. **************************************************************************** From: Randall B. Murphy Ph.D. Date: Wed Jul 29, 10:18am -0400 To: E.Tajkhorshid@DKFZ-Heidelberg.de Cc: Subject: Re: CCL:small peptide models Enkephalin may be the best. We have done it, so have lots of other people, and there are many experimental, NMR, and X-ray structures to commpare. It would be nice if it was a little more rigid, but to us this is a good choice. There are several Scheraga papers using calculations to compare to various NMR structures. We have one in PNAS in I think 1985, so this goes back a ways. best regards Randall B. Murphy Associate Professor of Chemistry New York University randy.murphy@nyu.edu ******************************************************************************** -- Emad ********************************************************************* E. Tajkhorshid German Cancer Research Center; DKFZ Tel: +49 6221 42 2340 Dept. Molecular Biophysics (H0200) FAX: +49 6221 42 2333 P.O.Box 101949 69009 Heidelberg, Germany Email: E.Tajkhorshid@DKFZ-Heidelberg.de ********************************************************************* * "Never express yourself more clearly than you think." -Niels Bohr * ********************************************************************* From gusev@javanet.com Sun Aug 2 15:00:44 1998 Received: from mail1.javanet.com (mail1.javanet.com [205.219.162.10]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id PAA12779 Sun, 2 Aug 1998 15:00:44 -0400 (EDT) Received: from monaco (ct-hartford-us217.javanet.com [209.150.32.80]) by mail1.javanet.com (8.8.8/8.7) with SMTP id PAA13321 for ; Sun, 2 Aug 1998 15:00:44 -0400 (EDT) Message-Id: <3.0.5.32.19980802145829.008fde30@mail.javanet.com> X-Sender: gusev@mail.javanet.com X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.5 (32) Date: Sun, 02 Aug 1998 14:58:29 -0400 To: chemistry@www.ccl.net From: Vladimir Gusev Subject: SUMMARY: Web examples of modeling lipid bilayers Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Hello CCL, Below is the summary of excelent references I received in reply to my question. I thank everybody who replied. Vladimir > I would appreciate any pointers to the modeling (MD or MC) of > systems with lipid bilayers presented on the web. --------------------------- We have some hydrated DPPC bilayer coordinates and references to publications for MD simulations of the fluid phase at the URL http://nmr1.cber.nih.gov/ under "Downloads" -- Rick Venable =====\ |=| "Eschew Obfuscation" FDA/CBER Biophysics Lab |____/ |=| Bethesda, MD U.S.A. | \ / |=| ( Not an official statement or rvenable@deimos.cber.nih.gov | \ / |=| position of the FDA; for that, http://nmr1.cber.nih.gov/ \/ |=| see http://www.fda.gov ) http://www.erols.com/rvenable ---------------------------- There is some information on my homepage but I haven't updated it in a long time. http://rugmd0.chem.rug.nl/~tieleman/tieleman.html, projects Peter -- email: tieleman@chem.rug.nl adress: Dept. of Biophysical Chemistry telephone: 31-50-3634338 Nijenborgh 4 fax: 31-50-3634800 9747 AG Groningen Netherlands ---------------------------- From: Eugene Leitl Try the MEMBRANE link at http://www.lrz.de/~heller/ I've used his EGO software, and it works just fine. Regards, Eugene ---------------------------- Dear Vladimir, have a look to: http://www.lrz-muenchen.de/~heller/membrane/membrane.html and http://www.umass.edu/microbio/rasmol/bilayers.htm hope it helps bye Bruno Dr Bruno Manunza Molecular Modeling Lab DISAABA (Dept. of Agricultural Environm. Sci) University of Sassari V.le Italia 39 07100 Sassari, ITALY phone: 39 79 229215 fax: 39 79 229276 e-mail: bruno@antas.agraria.uniss.it web: http://antas.agraria.uniss.it ---------------------------- From: ross@cgl.ucsf.EDU See also 'lipids' under http://www.amber.ucsf.edu/amber/0Net/index.html Bill Ross From ep7@dent.okayama-u.ac.jp Sun Aug 2 20:02:38 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 UAA13122 Sun, 2 Aug 1998 20:02:36 -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 JAA15808 for ; Mon, 3 Aug 1998 09:03:49 +0900 (JST) Message-Id: <199808030003.JAA15808@deews1.dent.okayama-u.ac.jp> Date: Mon, 3 Aug 1998 09:21:21 +0900 To: CHEMISTRY@www.ccl.net Subject: ESP MIME-Version: 1.0 Content-Type: text/plain; charset=iso-2022-jp X-Mailer: Eudora-J(1.3.8.5-J13) Dear Sir: What is the aim of ESP ? (1) The determination of atomic charge for molecules itself ? (2) the determination of charge for the electrostatic interaction beteen molecules ? (3) others. Thank you. From ep7@dent.okayama-u.ac.jp Sun Aug 2 20:08:34 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 UAA13156 Sun, 2 Aug 1998 20:08:32 -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 JAA15834 for ; Mon, 3 Aug 1998 09:09:50 +0900 (JST) Message-Id: <199808030009.JAA15834@deews1.dent.okayama-u.ac.jp> Date: Mon, 3 Aug 1998 09:27:22 +0900 To: CHEMISTRY@www.ccl.net Subject: CCL: Summary: Hydrogen bond MIME-Version: 1.0 Content-Type: text/plain; charset=iso-2022-jp X-Mailer: Eudora-J(1.3.8.5-J13) Dear Masao Masamura There is a good collection compiled by S. Scheiner in a book published by Oxford University Press, 1997. The title is "Hydrogen Bonding, A Theoretical Perspective". -- Emad ********************************************************************* E. Tajkhorshid German Cancer Research Center; DKFZ Tel: +49 6221 42 2340 Dept. Molecular Biophysics (H0200) FAX: +49 6221 42 2333 P.O.Box 101949 69009 Heidelberg, Germany Email: E.Tajkhorshid@DKFZ-Heidelberg.de ********************************************************************* * "Never express yourself more clearly than you think." -Niels Bohr * ********************************************************************* From: "rv" Date: Tue, 28 Jul 1998 16:34:22 -0700 X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: ep7@dent.okayama-u.ac.jp Subject: Re: CCL:Hydrogen bond Content-Type: text/plain; charset=us-ascii X-UIDL: 6424159f83dd6dc7f669064691095784 Hydrogen Bonding in Biological Structures by Jeffrey and Saenger, Springer Verlag, 1994 is a good reference and a good starting point for hydrogen bond metrology and comparison of experimental and theoretical methods for H-bond determination. Regina Valluzzi Tufts Biotechnology Center -- rv From: PUDZIANA@watson.bms.com Date: Wed, 29 Jul 1998 10:52:12 -0500 (EST) Subject: Re: CCL:Hydrogen bond To: ep7 Content-transfer-encoding: 7BIT X-UIDL: 236f67f4dfb0761f01b6b100673b8000 Masao - Because I'm very familiar with my own work(!!) let me mention the following articles: A. T. Pudzianowski, "Current computational approaches to the strong hydrogen bond," Recent Research Developments in Physical Chemistry 1 (1997), 81-97; A. T. Pudzianowski, "A Systematic Appraisal of Density Functional From: PUDZIANA@watson.bms.com Date: Wed, 29 Jul 1998 10:52:12 -0500 (EST) Subject: Re: CCL:Hydrogen bond To: ep7 Content-transfer-encoding: 7BIT X-UIDL: 236f67f4dfb0761f01b6b100673b8000 Masao - Because I'm very familiar with my own work(!!) let me mention the following articles: A. T. Pudzianowski, "Current computational approaches to the strong hydrogen bond," Recent Research Developments in Physical Chemistry 1 (1997), 81-97; A. T. Pudzianowski, "A Systematic Appraisal of Density Functional Methodologies for Hydrogen Bonding in Binary Ionic Complexes," J. Phys. Chem. 100, (1996), 4781-4789; A. T. Pudzianowski, "MP2/6-311++G(d,p) study of ten ionic hydrogen-bonded binary systems: Structures, normal modes, thermodynamics, and counterpoise energies," J. Chem. Phys. 102 (1995), 8029-8039; A. T. Pudzianowski, "Comment on 'The protonated water dimer: Extensive theoretical studies of H5O2+,' [J. Chem. Phys. 101, 4878 (1994)]," J. Chem. Phys. 102 (1995), 7761. These papers also have extensive references to theoretical, computa- tional, and experimental work published prior to 1996, so they should still be useful. Cheers, Andrew Pudzianowski Masao Masamura Preventive Dentistry Okayama University Dental School Shikata-cho, 2-5-1 Okayama 700 Japan FAX: 81-86-235-6714 e-mail: ep7@dent.okayama-u.ac.jp From ep7@dent.okayama-u.ac.jp Sun Aug 2 20:12:06 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 UAA13199 Sun, 2 Aug 1998 20:12:01 -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 JAA15854 for ; Mon, 3 Aug 1998 09:13:17 +0900 (JST) Message-Id: <199808030013.JAA15854@deews1.dent.okayama-u.ac.jp> Date: Mon, 3 Aug 1998 09:30:50 +0900 To: CHEMISTRY@www.ccl.net Subject: CCL:Summary:B3LYP MIME-Version: 1.0 Content-Type: text/plain; charset=iso-2022-jp X-Mailer: Eudora-J(1.3.8.5-J13) From: gaussian.com!fox@lorentzian.com (Doug Fox) Subject: Re: CCL:B3LYP To: uunet!dent.okayama-u.ac.jp!ep7%lorentzian.com@uunet.uu.net Date: Sat, 1 Aug 1998 14:27:22 -0400 (EDT) X-Mailer: ELM [version 2.4 PL24] Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit X-UIDL: ef0b257699492adda8799c98dbbaafde help > > Dear Sir: > > I would like to ask about B3LYP. > > 1. B3LYP can compute electron correlation ? The LYP portion of this functional addresses electron correlation. > 2. B3LYP can compute hydrogen bond ? This is not the method of choice for these non-bonded type interactions but there is no fundamental limitation. All of the functionals are developed around either paired electrons, i.e. noble gas atoms, or models of the uniform electron gas. Neither of these limits is a good model for hydrogen bonds. > 3. B3LYP can use for negative cluster ? Here there is some controversy based on theoretical arguments that DFT should do poorly for electron affinities and thus anions. However, the empirical evidence suggests that B3LYP and BHandH do tolerably well. > > Masao Masamura > Preventive Dentistry > Okayama University Dental School > Shikata-cho, 2-5-1 > Okayama 700 > Japan > FAX: 81-86-235-6714 > e-mail: ep7@dent.okayama-u.ac.jp Douglas J. Fox Director of Technical Support help@gaussian.com