From dimitris@3dp.com Mon Sep 16 12:12:05 1996 Received: from boris.3dp.com for dimitris@3dp.com by www.ccl.net (8.7.5/950822.1) id LAA08871; Mon, 16 Sep 1996 11:26:02 -0400 (EDT) Received: from europa.3dp.com by boris.3dp.com via SMTP (931110.SGI/930416.SGI) for chemistry@www.ccl.net id AA07884; Mon, 16 Sep 96 11:32:26 -0400 Received: by europa.3dp.com (950413.SGI.8.6.12) id LAA01414; Mon, 16 Sep 1996 11:30:21 -0400 From: "Dimitris Agrafiotis" Message-Id: <9609161130.ZM1412@europa.3dp.com> Date: Mon, 16 Sep 1996 11:30:20 -0400 X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: chemistry@www.ccl.net Subject: aminoacid similarity matrices Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii I am trying to find all the available aminoacid scoring matrices that are used for analyzing protein sequences (eg for phylogenetic analysis, sequence alignment, homology modeling etc). So far, I got my hands on the Dayhoff matrix (many versions of it) which measures the evolu- tionary distance between the aminoacids. I know people have constructed similarity matrices based on physicochemical properties, tertiary structure alignments etc, but I can't locate them on the web. Your help would be greatly appreciated. Thanks, -- Dimitris K. Agrafiotis, PhD | e-mail: dimitris@3dp.com Senior Fellow | tel: (610) 458-6045 3-Dimensional Pharmaceuticals, Inc. | fax: (610) 458-8249 665 Stockton Drive, Suite 104 Exton, PA 19341 From hinsen@ibs.ibs.fr Mon Sep 16 13:12:14 1996 Received: from ibs.ibs.fr for hinsen@ibs.ibs.fr by www.ccl.net (8.7.5/950822.1) id MAA09269; Mon, 16 Sep 1996 12:43:31 -0400 (EDT) Received: from lmshp2.ibs.fr (lmshp4.ibs.fr [192.134.36.222]) by ibs.ibs.fr (8.6.12/8.6.12) with SMTP id SAA26641; Mon, 16 Sep 1996 18:45:16 +0200 Message-Id: <199609161645.SAA26641@ibs.ibs.fr> Received: by lmshp2.ibs.fr (1.37.109.4/16.2) id AA23497; Mon, 16 Sep 96 18:43:17 +0100 Date: Mon, 16 Sep 96 18:43:17 +0100 From: Konrad Hinsen To: CHEMISTRY@www.ccl.net Subject: Protein structure from partial information Dear netters, a discussion with a group of experimentalists has lead me to the following question: are there any established methods to find the atomic configuration of a protein starting from its sequence plus partial information about the global shape, location of certain functional units etc.? This ought to be much easier than the general protein folding problem, although also less clearly defined. Regards, Konrad Hinsen. -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@ibs.ibs.fr Laboratoire de Dynamique Moleculaire | Tel.: +33-76.88.99.28 Institut de Biologie Structurale | Fax: +33-76.88.54.94 41, av. des Martyrs | Deutsch/Esperanto/English/ 38027 Grenoble Cedex 1, France | Nederlands/Francais ------------------------------------------------------------------------------- From fgonzale@lauca.usah.cl Mon Sep 16 14:12:06 1996 Received: from ralun.usach.cl for fgonzale@lauca.usah.cl by www.ccl.net (8.7.5/950822.1) id LAA08847; Mon, 16 Sep 1996 11:21:01 -0400 (EDT) Received: from lauca.usach.cl (lauca.usach.cl [158.170.64.28]) by ralun.usach.cl (8.6.11/8.6.9) with ESMTP id LAA06597; Mon, 16 Sep 1996 11:19:49 -0500 Received: from quantum (danilo@quantum.usach.cl [158.170.64.229]) by lauca.usach.cl (8.6.12/8.6.12) with SMTP id LAA00718; Mon, 16 Sep 1996 11:21:12 -0400 Sender: danilo@lauca.usach.cl Message-ID: <323D7086.593EF3DF@lauca.usah.cl> Date: Mon, 16 Sep 1996 11:21:42 -0400 From: Danilo Gonzalez Nilo Organization: Universidad de Santiago de Chile X-Mailer: Mozilla 2.0 (X11; I; Linux 1.2.8 i486) MIME-Version: 1.0 To: chemistry@www.ccl.net CC: fgonzale@lauca.usach.cl, Eldbjorg.Heimstad@chem.uit.no, felice@bioorganic.ucsb.edu Subject: Summary: H and S with Molecular Dynamics Content-Type: multipart/mixed; boundary="------------40144E64457A0A960604054" This is a multi-part message in MIME format. --------------40144E64457A0A960604054 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers: Several days ago I asked the following questions: ***************************************************************** Dear Friends: I'm looking for any information about Entropy, Enthalpie and free Energie of solvation in caculations with Molecular Dynamics in a solvent box (PBC). ***************************************************************** I got some replies which are summarized here. They were very helpful. Thanks to those who replied. =============== Begin of Summary: =========== **************************************************************** Look for articles by William Jorgenson (whole series) and Peter Kollman Peter Tieleman **************************************************************** Check out old work of Straatsma & Berendsen author = "T. P. Straatsma and H. J. C. Berendsen", title = "Free energy of ionic hydration: Analysis of a thermodynamic integration technique to evaluate free energy differences by molecular dynamics simulation", journal = JCP, year = "1988", volume = "89", pages = "5876--5886", David van der Spoel --------------------------------------------------------- EMAIL: spoel@chem.rug.nl WWW: http://rugmd0.chem.rug.nl/~spoel PHONE: 31-50-3634327 FAX: 31-50-3634800 MAIL: Nijenborgh 4, 9747 AG Groningen, The Netherlands. -------------------------------------------------------- ******************************************************************* attachment: AHSPRO_1.DOC John Parikh AHSystems Group 5401 Lakeford Lane, Suite L-1 Bowie, MD 20720 Phone 301.352.0896 Fax 301.352.0199 Website http://www2.ari.net/ahsystemsJ ******************************************************************* Dear Fernando, The basic reference is the book of Allen & Tildesley, Computer Simulations of Liquids, Clarendon Press, 1987. Another good reference is @ARTICLE{ Jorgensen89, AUTHOR = " Jorgensen, W. ", YEAR = 1989 , TITLE = { Free energy calculations: a breakthrough for modelling organic chemistry in solution}, JOURNAL = { Acc.\ Chem.\ Res.} , VOLUME = 22 , PAGES = { 184-189 } } Best wishes, Tom Simonson ****************************************************************** THANKS A LOT!!!!!!!!!! -- Fernando Danilo Gonzalez N. Universidad de Santiago de Chile Facultad de Quimica y Biologia Casilla 40, Correo 33, Santiago, CHILE. mailto:fgonzale@lauca.usach.cl Fax : (562) 681 2108 mailto:danilo@quantum.usach.cl http://quantum.usach.cl/~danilo --------------40144E64457A0A960604054 Content-Type: application/octet-stream Content-Transfer-Encoding: base64 Content-Disposition: attachment; filename="AHSPRO_1.DOC" 0M8R4KGxGuEAAAAAAAAAAAAAAAAAAAAAPgADAP7/CQAGAAAAAAAAAAAAAAABAAAABAAAAAAA AAAAEAAAEgAAAAEAAAD+////AAAAAAUAAAD///////////////////////////////////// //////////////////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////////////////// 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AAAAAAAAAAABAAAFAAAAADARAAADAKoTAAAAAP////8CAAQh//8BAAAh//8CAAAAAACZCwAA MBEAAAAAAQAAAAEAAAAAAHwAAACsEAAArRAAAK4QAACvEAAAsBAAALEQAACyEAAAsxAAALQQ AAC1EAAAthAAALcQAAC4EAAAuRAAALoQAAC7EAAAvBAAAL0QAAC+EAAAvxAAAMAQAADBEAAA whAAAMMQAADEEAAAxRAAAMYQAADHEAAAMBEAAAABMCrwAAABMCrwAAABMCrwAAABMCrwAAAB MCrwAAABMCrwAAABMCrwAAABMCrwAAABMCrwAAABMCrwAAABMCrwAAABMCrwAAABMCrwAAAB MCrwAAABMCrwAAABMCrwAAABMCrwAAABMCrwAAABMCrwAAABMCrwAAABMCrwAAABMCrwAAAB MCrwAAABMCrwAAABMCrwAAABMCrwAAABMCrwAAABMCrwAAABMCoIAQADAADSGgAACgAAAwAA oQ4AANoTAADfEwAACwAMAA4AAAAAADIRAAAHAGUBC0pvaG4gUGFyaWtoEUM6XGhhc2VldFxh cnMuZG9jC0pvaG4gUGFyaWtoGUM6XGhhc2VldFxhaHNwcm9kbGluZS5kb2MLSm9obiBQYXJp a2gcQzpcQUhTeXN0ZW1zXGFoc3Byb2RsaW5lLmRvYwtKb2huIFA= --------------40144E64457A0A960604054-- From oestere@uni-muenster.de Wed Sep 11 09:11:00 1996 Received: from mail.uni-muenster.de for oestere@uni-muenster.de by www.ccl.net (8.7.5/950822.1) id JAA08415; Wed, 11 Sep 1996 09:00:36 -0400 (EDT) From: Received: from urix6.uni-muenster.de (URIX6.UNI-MUENSTER.DE [128.176.0.73]) by mail.uni-muenster.de (8.7.5/8.7.5) with SMTP id PAA38178 for ; Wed, 11 Sep 1996 15:00:23 +0200 Received: by uni-muenster.de (AIX 3.2/UCB 5.64/4.03) id AA19909; Wed, 11 Sep 1996 14:59:33 +0200 Message-Id: <9609111259.AA19909@urix6.uni-muenster.de> Subject: [Q:] energy calculation of large molecule To: chemistry@www.ccl.net (Computer Chemistry List) Date: Wed, 11 Sep 1996 14:59:32 +0200 (MES) X-Mailer: ELM [version 2.4 PL25] Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit Status: RO Content-Length: 527 Dear netters. I have a question concerning the energy calculation of the frontier orbitals of the following molecule: Ru C33 H31 N3 (2+) M= 860.5 g/mol This is substituted Ruthenium-di(bipy) complex and we like to calculate the HUMO and LUMO energies. In your opinion: What might be the best way to do this on such a big molecule containing a heavy atom? Is it possible anyway? With best regards, R. Oestereich oestere@uni-muenster.de Institute for Analytical Chemistry University of Regensburg Germany From cdac.ernet.in!gadre@parcom.ernet.in Wed Sep 11 11:11:03 1996 Received: from sangam.ncst.ernet.in for cdac.ernet.in!gadre@parcom.ernet.in by www.ccl.net (8.7.5/950822.1) id KAA08869; Wed, 11 Sep 1996 10:14:22 -0400 (EDT) Received: (from root@localhost) by sangam.ncst.ernet.in (8.7.5) id TAA05817 for CHEMISTRY@www.ccl.net; Wed, 11 Sep 1996 19:42:30 +0530 (GMT+05:30) >Received: from parcom.UUCP by iucaa (4.1/SMI-4.1) id AA19324; Wed, 11 Sep 96 15:44:09+050 Received: from parcom by sangam.ncst.ernet.in; Wed, 11 Sep 1996 19:42 GMT Received: from parcom.UUCP by iucaa (4.1/SMI-4.1) id AA19324; Wed, 11 Sep 96 15:44:09+050 Received: by parcom.cdac.ernet.in (4.1/SMI-4.1) id AA21410; Wed Sep 11 15:22:32 1996 (GMT + 0530) Date: Wed Sep 11 15:22:32 1996 (GMT + 0530) From: gadre@cdac.ernet.in Message-Id: <9609110952.AA21410@parcom.cdac.ernet.in> To: CHEMISTRY@www.ccl.net Subject: References on Semiempirical calc for biomolec? Content-Type: text Status: RO Content-Length: 286 Dear Sirs : Some references reporting results fn semiempirical calculations on interaction energies of biomolecules would be appreciated. Can you comment on the reliability of such calculations? Thank You, Shridhar Gadre (e-mail : gadre@parcom.ernet.in ; gadre@unipune.ernet.in) From rino@ibc.wustl.edu Wed Sep 11 17:11:10 1996 Received: from wugate.wustl.edu for rino@ibc.wustl.edu by www.ccl.net (8.7.5/950822.1) id QAA11357; Wed, 11 Sep 1996 16:29:43 -0400 (EDT) Received: from ibc.wustl.edu (ibc.wustl.edu [128.252.122.174]) by wugate.wustl.edu (8.7.5/8.7.3) with SMTP id PAA24570 for ; Wed, 11 Sep 1996 15:30:26 -0500 Received: by ibc.wustl.edu (SMI-8.6/SMI-SVR4) id PAA10605; Wed, 11 Sep 1996 15:30:23 -0500 Date: Wed, 11 Sep 1996 15:30:23 -0500 (CDT) From: Rino Ragno To: Computational Chemistry List Subject: H-bond FF parameters? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Status: RO Content-Length: 1303 Dear netters, Maybe the following is a trivial question and I apologise for this. I would like to know if there is a parameter set to calculate H-bond interaction including halogens (Br, I, Cl and F). Any advice will be appreciated. Thank to all. Rino ++---------------------------------------------------------------------------++ ++---------------------------------------------------------------------------++ || || || Dr. Rino Ragno E-mail: rino@wucmd.wustl.edu || || Institute for Biomedical Computing or: rino@ibc.wustl.edu || || Center for Molecular Design Phone : 314-362-2273 || || Box 8036, Washington University FAX : 314-362-0234 || || 700 South Euclid Avenue || || St. Louis, Missouri 63110 || || U. S. A. || || || ++---------------------------------------------------------------------------++ ++---------------------------------------------------------------------------++ From schrecke@zinc.chem.ucalgary.ca Mon Sep 16 18:12:13 1996 Received: from zinc.chem.ucalgary.ca for schrecke@zinc.chem.ucalgary.ca by www.ccl.net (8.7.5/950822.1) id RAA10939; Mon, 16 Sep 1996 17:43:26 -0400 (EDT) From: Received: by zinc.chem.ucalgary.ca (AIX 3.2/UCB 5.64/4.03) id AA20929; Mon, 16 Sep 1996 15:23:16 -0600 Message-Id: <9609162123.AA20929@zinc.chem.ucalgary.ca> Subject: ECP and PP -- summary To: chemistry@www.ccl.net Date: Mon, 16 Sep 1996 15:23:06 -0600 (MDT) Reply-To: schrecke@zinc.chem.ucalgary.ca (Georg Schreckenbach) Organization: Department of Chemistry, University of Calgary X-Mailer: ELM [version 2.4 PL23] Content-Type: text Hi everybody, a few days ago, I posted an enquiry regrading the difference between effective core potentials and pseudopotentials. Here is my summary. First the question: ------------------------------------------------------------------------------ I have just read the interesting summary by Dale Braden in the CCL on ECP's. One of the questions he raised in his original posting was whether there is a difference between "effective core potentials" and "pseudopotentials". To my limited knowledge, there is none. But maybe one of the experts could comment on this question? -- I couldn't find a definite answer in the mentioned summary. So my question is, what -- if any -- is the difference between PP's and ECP's? Just curious ... ------------------------------------------------------------------------------ I got a number of interesting responses. See also the comment by A. Ehlers in the earlier summary on the subject. Thank you to all who took the time to write to me. Yours, Georg Here are the responses: ------------------------------------------------------------------------------ From: cory@bohr.chem.mun.ca (Cory C. Pye) An effective core potential includes a pseudopotential as part of its definition, as well as including some other terms that improve the asymptotic behaviour of the pseudopotential, like a Z/r term and l(l+1)/r^2 . I am a little rusty on these, but there is a nice book "Pseudopotential Theory of atoms and molecules" which I found extremely helpful. The name of the author escapes me at the moment. -Cory ************* ***************** ! Cory C. Pye *** ** ** ** ! Graduate Student and Unpaid Sys Admin ** * **** ! Theoretical and Computational Chemistry ** * * ! cory@bohr.chem.mun.ca ** * * ! http://www.ucs.mun.ca/~cory/index.html *** * * ** ! ***************** ! Les Hartree-Focks ************* ! (Apologies to Montreal Canadien Fans) ------------------------------------------------------------------------------ From: mbdtssa Hi Georg, I have mostly seen the term Pseudopotential used in connection with plane wave basis set ab initio catlculations, and ECP used for Gaussian basis set ab initio calculations. The reason for having two different names could be that Pseudopotentials must give very smooth pseudowavefunctions, to limit the size of the basis set expansion, and so must be of a slightly differnt form to ECP's. Hope this helps! Simon. ------------------------------------------------------------------------------ From: kaupp@vsibm1.mpi-stuttgart.mpg.de (Martin Kaupp) The theoretical basis for all modern (atomic) pseudopotentials is the generalized Phillips-Kleinman pseudopotential (gPK) ansatz (see Weeks, Hazi, Rice, Adv. Chem. Phys. 1969, 16, 283). It provides the separation of the Schroedinger equation into valence and core part (no approximation involved up to this point, no saving either). Based on this, there are two major schools (I neglect the solid-state physics community for the moment, where the term pseudopotential is sometimes used in a somewhat wider context): a) the Huzinaga-type model-core-potentials (MCP) which include explicit projection operators on core basis functions, i.e. they keep the radial nodes of the pseudo-valence orbitals. The philosophy of this ansatz involves a 'model potential' which effectively replaces the core-valence exchange and Coulomb terms occuring when one adopts the gPK ansatz within Hartree-Fock theory. b) the more common semi-local pseudopotentials or ECPs (however, I have also seen the term ECP used for pseudopotentials of the MCP type, so things are not quite as systematic as one would like) make use of the hermitian nature of the gPK operator. They include projectors on spherical harmonics (the name semi-local refers to the fact that one multiplies local radial terms with these projectors) and feature nodeless pseudo-valence orbitals. Both types of PPs have in common the fit of free parameters in the PP to atomic data (usually ab initio all-electron, could also be experimental), and the frozen-core approximation (i.e. superposition of atomic PP for molecules, solids, etc.). Different 'sub-schools' may be distinguished by the type of data used for fitting and the fitting procedure. There is much more to be said about the whole business, but I hope this helps a bit. Regards, Martin ------------------------------------------------------------------------------ END OF SUMMARY -- ============================================================================== Georg Schreckenbach Tel: (Canada)-403-220 8204 Department of Chemistry FAX: (Canada)-403-289 9488 University of Calgary Email: schrecke@zinc.chem.ucalgary.ca 2500 University Drive N.W., Calgary, Alberta, Canada, T2N 1N4 ==============================================================================