From chemistry-request@server.ccl.net Wed Jan 12 20:32:17 2000 Received: from gate-sl1.mdli.com (ns2.mdli.com [208.200.221.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id UAA05867 for ; Wed, 12 Jan 2000 20:32:16 -0500 Received: (from smap@localhost) by gate-sl1.mdli.com (8.8.8/8.8.8) id RAA27177 for ; Wed, 12 Jan 2000 17:29:58 -0800 (PST) Received: from puffin.mdli.com(191.254.19.10) by gate-sl1.mdli.com via smap (V2.1) id xma027175; Wed, 12 Jan 00 17:29:57 -0800 Received: from shepherd.mdli.com by puffin.mdli.com (8.8.5/BCH1.0) id RAA11976; Wed, 12 Jan 2000 17:29:56 -0800 (PST) Received: from mdli.com (ostrich.mdli.com [191.254.14.135]) by shepherd.mdli.com with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.2650.21) id ZFR7BFRN; Wed, 12 Jan 2000 17:29:56 -0800 Sender: lchen@mdli.com Message-ID: <387D2A94.632A0F49@mdli.com> Date: Wed, 12 Jan 2000 17:29:56 -0800 From: Lingran Chen Organization: MDL Information Systems, Inc. X-Mailer: Mozilla 4.07C-SGI [en] (X11; I; IRIX 6.5 IP22) MIME-Version: 1.0 To: chemistry@ccl.net Subject: Summary of "Which four companies are derivatives from Prof. Pople's group?" References: <387A781C.E934D915@mdli.com> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit My previous email on this summary was not distributed automatically by CCL "due to: Problems with message body". I'm try to resend it again with minor change: including Allen Richon's message. -Lingran --------------------------------------------------------------- I have received many replies for my question about Which four companies are derivatives from Prof. Pople's group. and been requested to summarize them. My original question is: > Dear CCLers: > > In the interview article > "Simulating Chemistry: Q&A with John Pople" > at http://www.rdmag.com/features/0699rd/06pople.htm > > Prof. Pople mentioned that > > "As a matter of fact, > four such companies are derivatives from my research group." > > Do you know the names of those four companies? > Gaussian, Inc. > Schrodinger, Inc. (seems not?) > Wavefunction, Inc. ?? > SemiChem, Inc. (seems not?) > > Thanks in advance. > > -Lingran There are almost nothing to summarize because the following web page http://www.hyper.com/pople.html offers the excellent answer to my question. However, it may be interesting to know the "relative" popularities of those four companies from the answers I received. Gaussian Hyercube Q-Chem Wavefunction Lingran 1 0.5 Allen 1 Neil 1 1 1 1 WeiQuan 1 1 0.5 (?) Vitaly 1 1 1 1 Susan 1 Stefan 1 Robert 1 Joseph 1 Joe M 1 1 Jing 1 1 1 1 Jaime 1 1 1 1 Georg 1 David 1 Andrew 1 It's a little surprising to note that most people know the relationship between Prof. Pople and Q-Chem, which was described as "A new and upcoming company" by the above mentioned web site. Why didn't so many people mention Gaussian? This may be because I have already made clear it is one of "Pople's" companies. Besides, Susan told me that 'I believe that there is also a company named "Lorentzian" that is technically separate from Gaussian.' Gerard pointed out that Schroedinger Inc. sells the famous Jaguar software... Andy mentioned that Semichem is with Michael J.S. Dewar. --------------------------------------------------------- Lingran Chen Allen Richon (Network Science) "Ostlund, Neil S." WeiQuan Tian Vitaly Rassolov "Susan R. Atlas" Stefan Fau "Robert J. Doerksen" Joseph Durant Joe M Leonard Jing Kong Jaime Martell Gerard Vergoten schrecke@t12.lanl.gov (Georg Schreckenbach) David Young Andy Holder Andrew Horsfield ------------------------------------------------------- Many thanks to all of you! -Lingran ********************************************************** Lingran Chen, Ph.D. Senior Scientific Programmer MDL Information Systems, Inc. Phone: (510) 895-1313, Ext. 1305 FAX: (510) 614-3616 Email: LCHEN@MDLI.COM ********************************************************** From chemistry-request@server.ccl.net Thu Jan 13 04:15:31 2000 Received: from ciamserv.ciam.unibo.it (root@ciamserv.ciam.unibo.it [137.204.214.10]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA01519 for ; Thu, 13 Jan 2000 04:15:31 -0500 Received: from ciamserv.ciam.unibo.it (treebeard.ciam.unibo.it [137.204.214.23]) by ciamserv.ciam.unibo.it (8.9.3/8.9.3) with ESMTP id KAA14237 for ; Thu, 13 Jan 2000 10:14:08 +0100 Sender: marianna@ciamserv.ciam.unibo.it Message-ID: <387D926F.F21BAC8D@ciamserv.ciam.unibo.it> Date: Thu, 13 Jan 2000 09:53:03 +0100 From: Marianna Fanti Reply-To: marianna@ciamserv.ciam.unibo.it Organization: Universita' di Bologna X-Mailer: Mozilla 4.7 [en] (X11; I; Linux 2.0.36 i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Re: CCL:Help-- XMOL program References: <200001121405.JAA24754@watsci.uwaterloo.ca> <387CF3CC.3B83AD30@fu-berlin.de> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Bernd Melchers wrote: > > Guang-Ping Li wrote: > > > > Dear Sir: > > > > Have you any idea where we can get the XMOL program which > > can be used to display and print molecular structures and > > vibrational normal modes? > > xmol is not supported for years now. In ancient times, i requested the > authors for > ELF-Binaries for IRIX, but they didn't want to compile it anymore. > > Ciao > Bernd Melchers > A program very similar to XMol is Xmakemol. It's able to display vibrational normal modes. You can find it at http://vegemite.chem.nott.ac.uk/~xmakemol/ Ciao, Marianna -- --------------------------------------------------------------------- Marianna Fanti, Ph.D | Dip. di Chimica "G. Ciamician" e-mail: marianna@ciam.unibo.it | Universita' di Bologna, Italy Fax+39-0512099456 Tel +39-0512099498 | via Selmi 2, I-40126 Bologna --------------------------------------------------------------------- Don't fear failure so much that you refuse to try new things --------------------------------------------------------------------- From chemistry-request@server.ccl.net Thu Jan 13 08:27:43 2000 Received: from janus.rz.uni-konstanz.de (janus.rz.uni-konstanz.de [134.34.3.11]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA03356 for ; Thu, 13 Jan 2000 08:27:43 -0500 Received: from stevieray (actually stevieray.biologie.uni-konstanz.de) by janus.rz.uni-konstanz.de with Intranet with SMTP; Thu, 13 Jan 2000 13:20:34 +0100 Message-Id: <3.0.3.32.20000113131753.0097d610@popserver.uni-konstanz.de> X-Sender: pop04225@popserver.uni-konstanz.de X-Mailer: QUALCOMM Windows Eudora Pro Version 3.0.3 (32) Date: Thu, 13 Jan 2000 13:17:53 +0100 To: chemistry@ccl.net From: Frank Neese Subject: Field gradient integrals Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Hi all, I have recently had a little trouble with the implementation of field gradient integrals over GTOs, i.e. where a and b are GTOs centered at points A and B respectively and v(i,j) is a component of the field gradient operator located at center C (= d/dxC d/dyC 1/rC for the x,y component etc). I have used the McMurchie-Davidson algorithm as described in the original article or by Helgaker and Taylor in their extensive review. I noticed that if all centers coincide the results are correct. However, if a and b are located somewhere else and the product a(r)b(r) has a significant amplitude at point C, where the operator is located, the results are incorrect. For example, two unnormalized 1s GTOs (exponent=1.0) located at +1 bohr and the v(z,z) operator at the origin. In general in these cases the algorithm returns <> 0 but it must =0 for the correct integrals. Judging from tests with numerical integration of the same integrals the algorithm appears to produce correct integrals in the case that the amplitude of a*b at point C is very small. I know from other integrals that the F[m] generation, E-coefficients, R-coefficients etc. are all definitively correct and this makes me believe that I have a conceptional problem with the singularity of the operator at the origin and not just with the numerics. I hope that this is a standard problem for anyone who has succesfully implemented these integrals (and related ones like the one electron part of the spin-orbit operator) and I would greatly appreciate if some experienced persons could give me a hint about how to deal with it so I don't have to reinvent the wheel. Your help is much appreciated, best regards, Frank ----------------------------------------- ! Dr. Frank Neese ! ! Fakultaet fuer Biologie ! ! Universitaet Konstanz ! ! D-78457 Konstanz ! ! Germany ! ! e-mail: Frank.Neese@uni-konstanz.de ! ! Tel : 07531/883205 ! ! FAX : 07531/882966 ! ----------------------------------------- From chemistry-request@server.ccl.net Thu Jan 13 05:36:54 2000 Received: from gatekeeper.mahindrabt.com ([202.54.20.162]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA01916 for ; Thu, 13 Jan 2000 05:36:48 -0500 Received: (from uucp@localhost) by gatekeeper.mahindrabt.com (8.9.3/8.8.6) with UUCP id OAA27560 for chemistry@ccl.net; Thu, 13 Jan 2000 14:01:39 +0530 Received: from mahindrabt.com (pc-172-24-7-150.pune.mahindrabt.com [172.24.7.150] (may be forged)) by intranet.pune.mahindrabt.com (8.9.3/8.9.3) with ESMTP id OAA02672 for ; Thu, 13 Jan 2000 14:05:45 +0530 Message-ID: <387D8F04.24419450@mahindrabt.com> Date: Thu, 13 Jan 2000 14:08:28 +0530 From: "Dr. Sudhir A. Kulkarni" Organization: Mahindra British Telecom Limited To: chemistry@ccl.net Subject: Ammonia clusters Hello, Can some one provide me pointers to references on neutral ammonia clusters (NH3)n, cationic clusters (NH3)n+ and anionic clusters (NH3)n- using ab initio or any other theoretical/experimental methods? Thanks in advance. Sudhir Kulkarni (R&D, MBT, Pune) From chemistry-request@server.ccl.net Thu Jan 13 08:07:19 2000 Received: from kasei.materials.ox.ac.uk (kasei.materials.ox.ac.uk [163.1.64.46]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA03286 for ; Thu, 13 Jan 2000 08:07:16 -0500 Received: from localhost (hfield@localhost) by kasei.materials.ox.ac.uk (8.9.3/8.9.3) with ESMTP id MAA16015 for ; Thu, 13 Jan 2000 12:04:33 GMT X-Authentication-Warning: kasei.materials.ox.ac.uk: hfield owned process doing -bs Date: Thu, 13 Jan 2000 12:04:33 +0000 (GMT) From: Andrew Horsfield X-Sender: hfield@kasei.materials.ox.ac.uk Reply-To: Andrew Horsfield To: Computational Chemistry List Subject: Integral meshes for LCAO codes Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I am developing a numerical atomic orbital density functional code for solids (Plato). I am using pseudo-potentials, so have often been able to get away with using the FFT mesh as my integral mesh for integrals involving the exchange and correlation potential. However, it is now clear that as the basis set approaches completeness this approach fails spectacularly (very deep ghost bands form). Increasing the mesh density does not help (I run out of memory before I get sensible answers). It is obvious what has to be done: an atom centered mesh (as appears in DMol, for example) has to be used instead. However, before implementing this (which is a *major* revision to the code), I would welcome any advice >from those who have used such meshes. In particular: o Are there any special considerations that have to be taken into account since I am working with solids? o What are the best partition functions to use? o What are the best quadrature schemes for the radial and for the angular integrals? o How efficiently can such meshes be used for solving Poisson's equation in *solids*? Cheers, Andrew +----------------------------------------------------+ Andrew Horsfield e-mail: horsfield@fecit.co.uk FECIT, 2 Longwalk Road, Stockley Park, Uxbridge, Middlesex UB11 1AB, United Kingdom. phone: +44-(0)181-606-4653 FAX: +44-(0)181-606-4422 +----------------------------------------------------+ From chemistry-request@server.ccl.net Thu Jan 13 08:35:37 2000 Received: from yogi.pc1.uni-duesseldorf.de (root@yogi.pc1.uni-duesseldorf.de [134.99.152.44]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA03431 for ; Thu, 13 Jan 2000 08:35:36 -0500 Received: from yogi.pc1.uni-duesseldorf.de (IDENT:jochen@localhost.localdomain [127.0.0.1]) by yogi.pc1.uni-duesseldorf.de (8.9.3/8.9.3) with SMTP id NAA02426; Thu, 13 Jan 2000 13:37:03 +0100 From: Jochen Kuepper Organization: Heinrich-Heine-Universität To: "Rzepa, Henry" , CHEMISTRY@ccl.net Subject: Re: CCL:Strongest bond in chemistry? Date: Thu, 13 Jan 2000 13:36:30 +0100 X-Mailer: KMail [version 1.0.28] Content-Type: text/plain References: In-Reply-To: MIME-Version: 1.0 Message-Id: <00011313370100.02423@yogi.pc1.uni-duesseldorf.de> Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id IAA03432 On Mit, 12 Jan 2000 Rzepa, Henry wrote: >My candidate is H-NN(+), where the NN triple bond is strengthened by >protonation. So what's the bond energy ? -- Jochen Heinrich-Heine-Universität, Institut für Physikalische Chemie I Universitätsstr. 1, Geb. 26.43.02.29, 40225 Düsseldorf, Germany phone 02118113681 fax 02118115195 -- www-public.rz.uni-duesseldorf.de/~jochen Jochen@Uni-Duesseldorf.de -- Jochen.Kuepper@FernUni-Hagen.de -- Kuepper@ACM.org From chemistry-request@server.ccl.net Thu Jan 13 08:52:45 2000 Received: from inst.augie.edu (inst.augie.edu [192.103.41.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA03490 for ; Thu, 13 Jan 2000 08:52:45 -0500 Received: from viste (orion.augie.edu [204.233.92.66]) by inst.augie.edu (AIX4.3/8.9.3/8.8.8) with SMTP id GAA47294; Thu, 13 Jan 2000 06:45:41 -0600 Message-Id: <4.1.20000113063624.00a24770@inst.augie.edu> X-Sender: viste@inst.augie.edu X-Mailer: QUALCOMM Windows Eudora Pro Version 4.1 Date: Thu, 13 Jan 2000 06:48:41 -0600 To: CHEMISTRY@ccl.net From: Arlen Viste Subject: AutoDock compilation Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear CCLers, Has anyone compiled and installed AutoDock 3 on an IBM RS/6000 under Aix 4.*, or on a PC under Windows NT? Thanks in advance. Arlen Viste, Ph.D. Dept of Chemistry Phone (605) 336-481 Augustana College (SD) http://inst.augie.edu/~viste/ From chemistry-request@server.ccl.net Thu Jan 13 13:46:41 2000 Received: from gaucho.chem.ucsb.edu (gaucho.chem.ucsb.edu [128.111.114.134]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA05115 for ; Thu, 13 Jan 2000 13:46:41 -0500 Received: (from thomas@localhost) by gaucho.chem.ucsb.edu (8.9.2/8.9.1) id JAA04361 for chemistry@ccl.net; Thu, 13 Jan 2000 09:34:13 -0800 From: Thomas Wyttenbach Message-Id: <200001131734.JAA04361@gaucho.chem.ucsb.edu> Subject: Ammonia clusters To: chemistry@ccl.net Date: Thu, 13 Jan 100 09:34:11 +22299913 (PST) X-Mailer: ELM [version 2.4 PL21] Content-Type: text Some work, both experimental and semi-empirical, on protonated ammonia clusters (NH3)n(NH4)+ has been carried out in Jack Beauchamp's lab at CalTech. See: http://www.jlb.caltech.edu Regards, Thomas ===T.Wyttenbach===UCSB===SantaBarbaraCA===wyttenbach@chem.ucsb.edu=== From chemistry-request@server.ccl.net Thu Jan 13 14:43:45 2000 Received: from mail.chemie.fu-berlin.de (root@mail.chemie.fu-berlin.de [160.45.24.23]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA05664 for ; Thu, 13 Jan 2000 14:43:45 -0500 Received: from ki1.chemie.fu-berlin.de ([160.45.24.21]) (2169 bytes) by mail.chemie.fu-berlin.de via sendmail with P:esmtp/R:bind_hosts/T:inet_zone_bind_smtp (sender: ) id for ; Thu, 13 Jan 2000 19:39:31 +0100 (CET) (Smail-3.2.0.109) Received: by ki1.chemie.fu-berlin.de (Smail3.2.0.109) from chemie.fu-berlin.de (160.45.24.163) with esmtp id ; Thu, 13 Jan 2000 19:39:31 +0100 (CET) Sender: rabe@ccl.net Message-ID: <387E1BE3.2B8140E2@chemie.fu-berlin.de> Date: Thu, 13 Jan 2000 19:39:31 +0100 From: Bjoern Rabenstein Organization: Freie Universitaet Berlin, Germany X-Mailer: Mozilla 4.61 [en] (X11; U; Linux 2.2.12-mosix i686) X-Accept-Language: de, en MIME-Version: 1.0 To: Computational Chemistry Mailing List Subject: Simple program for editing protein structure Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi CCLers! I'm just wondering if out there is any small and simple program to interactively manipulate protein (or any large molecular) structures. It would already be sufficient to modify dihedrals and at the same time watch what's happening. I know that this is possible with huge (and expensive...) program packages like InsightII or Quanta, but I think that's not really the main feature of these programs, and I'm not willing to buy a lot of great features I don't want. It would be just nice to quickly load a small programm (best for Unix, so that I don't need to run to the secretary's office or reboot the PC... :-) to change these one or two dihedral angles in my PDB file such that there will be no clashes. After all searching so far I've only found tons of sophisticated viewing programs, but no interactive manipulation programs except as subfeatures of large molecular modelling packages or as molecule builders of quantum chemical programs (which are not suitable for really large molecules). Thanks for any hints! -- Bjoern Rabenstein * PhD student * Freie Universitaet Berlin * Fachbereich Biologie/Chemie/Pharmazie * Inst. f. Chemie * Takustr. 6 * D-14195 Berlin [email] rabe@chemie.fu-berlin.de [phone] +49-30-838-3484 [WWW] http://userpage.chemie.fu-berlin.de/~rabe/ [fax] +49-30-838-3464 From chemistry-request@server.ccl.net Thu Jan 13 15:44:53 2000 Received: from igor.wag.caltech.edu (igor.wag.caltech.edu [131.215.33.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA06011 for ; Thu, 13 Jan 2000 15:44:52 -0500 Received: from wag.caltech.edu (octane2 [131.215.33.125]) by igor.wag.caltech.edu (8.9.3/8.9.3) with ESMTP id LAA229633; Thu, 13 Jan 2000 11:40:32 -0800 (PST) Sender: rpm@wag.caltech.edu Message-ID: <387E2A30.50ADBBE4@wag.caltech.edu> Date: Thu, 13 Jan 2000 11:40:32 -0800 From: "Richard P. Muller" X-Mailer: Mozilla 4.6 [en] (X11; U; IRIX64 6.4 IP30) X-Accept-Language: en MIME-Version: 1.0 To: Bjoern Rabenstein CC: Computational Chemistry Mailing List Subject: Re: CCL:Simple program for editing protein structure References: <387E1BE3.2B8140E2@chemie.fu-berlin.de> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Bjoern Rabenstein wrote: > > Hi CCLers! > > I'm just wondering if out there is any small and simple program to > interactively manipulate protein (or any large molecular) structures. It > would already be sufficient to modify dihedrals and at the same time watch > what's happening. > Konrad Hinsen's program suite Molecular Modeling Tool Kit (MMTK) is a very useful tool for doing this type of work. It requires some knowledge of the Python programming language (which isn't all that difficult). http://starship.python.net/crew/hinsen/MMTK/ There are a number of viewers that are associated with it There is also a good mailing list supporting the project, and Konrad himself is quite helpful should a problem arise. The other advantage to MMTK over a package is that since you have the source code, if it doesn't do everything you like, you can modify it to do what you want. Rick -- Richard P. Muller, Ph.D. rpm@wag.caltech.edu http://www.wag.caltech.edu/home/rpm From chemistry-request@server.ccl.net Thu Jan 13 10:26:13 2000 Received: from mnvax.irfmn.mnegri.it (mnvax.irfmn.mnegri.it [195.61.203.11]) by server.ccl.net (8.8.7/8.8.7) with SMTP id KAA04103 for ; Thu, 13 Jan 2000 10:26:02 -0500 Received: from [195.61.203.156] by mnvax.irfmn.mnegri.it with ESMTP for CHEMISTRY@ccl.net; Thu, 13 Jan 2000 15:21:36 +0100 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Date: Thu, 13 Jan 2000 15:21:33 +0100 To: CHEMISTRY@ccl.net From: Emilio Benfenati Subject: grants available Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id KAA04104 Dear colleagues, I'd like to inform you about the availability of fellowships for graduated students (Pre and Postdoctors) inside the European Community. More details are presented below. NOTICE Pre- and Postdoctoral positions offered Applications are invited from young researchers with an interest in joining a four-year (2000-2003) EU network project aimed at the development of models to predict toxicity, starting Spring 2000. The network consists of laboratories (see the list below) working in toxicology, computational chemistry and computer science. Grants are available to work in one of the seven laboratories of the Network. Grant will be from 1650 to 4320 euro/month, depending on qualification, experience and location. Pre-doc positions are compatible with PhD studies. Interested candidates should send an application including CV, summary of research interests and preferred location to: Dr Emilio Benfenati Head, Laboratory of Environmental Chemistry and Toxicology Istituto di Ricerche Farmacologiche "Mario Negri" Via Eritrea 62, 20157 Milano, Italy Tel: +39-02-39014420 Fax: +39-02-39001916 e-mail: benfenati@irfmn.mnegri.it http://www.irfmn.mnegri.it/ambsal/chem-toxi/Default.htm Network Title: Intelligent Modelling Algorithms for the General Evaluation of TOXicities Network Short Title: IMAGETOX The Co-ordinator Istituto di Ricerche Farmacologiche "Mario Negri", Laboratory of Environmental Chemistry and Toxicology, Milan, Italy Contact person: Dr Emilio Benfenati e-mail: benfenati@irfmn.mnegri.it The Members Dr. M. Cronin, Liverpool John Moores University, School of Pharmacy and Chemistry, United Kingdom (m.t.cronin@livjm.ac.uk) Prof. J. Hermens, Utrecht University, Research Institute of Toxicology, Faculty of Veterinary Sciences, The Netherlands (j.hermens@ritox.vet.uu.nl) Prof. G. Gini, Politecnico di Milano, Dipartimento di Elettronica e Informazione, Italy (gini@elet.polimi.it) Dr. M. Vracko, National Institute of Chemistry, Ljubljana, Slovenia (marjan.vracko@ki.si) Prof. G. Schüürmann, UFZ Centre for Environmental Research, Leipzig, Germany (gs@uoe.ufz.de) Prof. M. Karelson, University of Tartu, Department of Chemistry, Estonia (mati@chem.ut.ee). Conditions The researcher must be 35 years old or less at the time of his appointment (allowances are possible for special cases). The researcher must be a holder of a doctoral degree or of a degree in an appropriate subject. The appointment will be for a fixed-term. The applicant must be a national of a Member State of the European Community or of an Associated State or have resided in the European Community for at least five years prior to his appointment. The applicant must not be a national of the state in which the participant's research team appointing him is located and he must not have carried out his normal activities in that state for more than 12 of the 24 months prior to his appointment. Research Program The present project aims to improve the power of models for toxicity prediction. It will take advantage of the recent advances in techniques in computer science (such as multivariate analysis, neural networks, expert systems, machine learning, and simulated annealing). These will be applied to the validation (verifying the robustness of reported models and new predictive ones) and development for real world applications. Different models will be developed for (eco)toxicology and for environmental fate prediction. For (eco)toxicology different species will be considered, as well as different mechanisms of toxic action. In environmental fate, partitioning between compartments in the environment and into biota will be studied, as well as degradation. Emilio Benfenati *********************************************************** Dr Emilio Benfenati Head, Laboratory of Environmental Chemistry and Toxicology Istituto di Ricerche Farmacologiche "Mario Negri" Via Eritrea 62, 20157 Milano, Italy Tel: +39-02-39014420 Fax: +39-02-39001916 e-mail: benfenati@irfmn.mnegri.it http://www.irfmn.mnegri.it/ambsal/chem-toxi/Benfenati.htm http://www.irfmn.mnegri.it/ambsal/chem-toxi/Default.htm http://www.elet.polimi.it/AAAI-PT for AAAI Symp Predictive Toxicology *********************************************************** From chemistry-request@server.ccl.net Thu Jan 13 11:30:20 2000 Received: from rzcomm1.rz.tu-bs.de (rzcomm1.rz.tu-bs.de [134.169.9.107]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA04477 for ; Thu, 13 Jan 2000 11:30:19 -0500 Received: from tu-bs.de (pc1.org-chem.nat.tu-bs.de [134.169.19.154]) by rzcomm1.rz.tu-bs.de (8.9.3 (PHNE_18979)/8.8.6) with ESMTP id QAA08809; Thu, 13 Jan 2000 16:23:06 +0100 (MET) Message-ID: <387DFC91.CA5393FC@tu-bs.de> Date: Thu, 13 Jan 2000 16:25:53 +0000 From: "Dr. =?iso-8859-1?Q?J=F6rg?= Grunenberg" X-Mailer: Mozilla 4.61 [en] (WinNT; I) X-Accept-Language: en,pdf MIME-Version: 1.0 To: Jochen Kuepper CC: "Rzepa, Henry" , CHEMISTRY@ccl.net Subject: Re: CCL:Strongest bond in chemistry? References: <00011313370100.02423@yogi.pc1.uni-duesseldorf.de> Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Jochen Kuepper wrote: > On Mit, 12 Jan 2000 Rzepa, Henry wrote: > > >My candidate is H-NN(+), where the NN triple bond is strengthened by > >protonation. > > So what's the bond energy ? > > -- Jochen The B3LYP/6-311++G** energy second derivative (force constant) of the NN bond in NN-H(+) is 25.4 Nm/Angstrom (compared to 24.6 for N2). So H-NN(+) seems to be a very good candidate.... Jörg -- Jörg Grunenberg, Org. Chemie, Hagenring 30, 38106 Braunschweig email: Joerg.Grunenberg@tu-bs.de phone: +49 531 391 5252 URL: http://www.tu-bs.de/institute/org-chem/grunenberg/grunenberg.html From chemistry-request@server.ccl.net Thu Jan 13 15:56:36 2000 Received: from deimos.cber.nih.gov (deimos.cber.nih.gov [128.231.52.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA06098 for ; Thu, 13 Jan 2000 15:56:36 -0500 Received: from localhost by deimos.cber.nih.gov with SMTP (1.37.109.14/16.2) id AA219092620; Thu, 13 Jan 2000 14:43:40 -0500 Date: Thu, 13 Jan 2000 14:43:40 -0500 (EST) From: Rick Venable To: Bjoern Rabenstein Cc: Computational Chemistry Mailing List Subject: Re: CCL:Simple program for editing protein structure In-Reply-To: <387E1BE3.2B8140E2@chemie.fu-berlin.de> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII One of the more useful simple tools I've found for this is a custom version of Rasmol, from the UC Berkely Chem. Dept.; there are MacOS and Wintel versions of executable programs. The URL is: http://mc2.CChem.Berkeley.EDU/Rasmol/ The major changes vs. the standard Rasmol are: - ability to load more than one molecule - ability to rotate torsions and change conformations On Thu, 13 Jan 2000, Bjoern Rabenstein wrote: > I'm just wondering if out there is any small and simple program to > interactively manipulate protein (or any large molecular) structures. It > would already be sufficient to modify dihedrals and at the same time watch > what's happening. > > I know that this is possible with huge (and expensive...) program packages > like InsightII or Quanta, but I think that's not really the main feature > of these programs, and I'm not willing to buy a lot of great features I > don't want. > > It would be just nice to quickly load a small programm (best for Unix, so > that I don't need to run to the secretary's office or reboot the PC... :-) > to change these one or two dihedral angles in my PDB file such that there > will be no clashes. > > After all searching so far I've only found tons of sophisticated viewing > programs, but no interactive manipulation programs except as subfeatures > of large molecular modelling packages or as molecule builders of quantum > chemical programs (which are not suitable for really large molecules). -- Rick Venable =====\ |=| "Eschew Obfuscation" FDA/CBER Biophysics Lab |____/ |=| Bethesda, MD U.S.A. | \ / |=| ( Not an official statement or Rick_Venable@nih.gov | \ / |=| position of the FDA; for that, http://www.erols.com/rvenable \/ |=| see http://www.fda.gov ) From chemistry-request@server.ccl.net Thu Jan 13 18:25:47 2000 Received: from si.fi.ameslab.gov (si.fi.ameslab.gov [147.155.20.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA06886 for ; Thu, 13 Jan 2000 18:25:47 -0500 Received: (from pradipta@localhost) by si.fi.ameslab.gov (AIX4.2/UCB 8.7/8.7) id QAA36686 for chemistry@ccl.net; Thu, 13 Jan 2000 16:22:56 -0600 (CST) From: Pradipta Bandyopadhyay Message-Id: <200001132222.QAA36686@si.fi.ameslab.gov> Subject: Free energy calculations! To: chemistry@ccl.net (CCL) Date: Thu, 13 Jan 2000 16:22:56 -0600 (CST) X-Mailer: ELM [version 2.4 PL25] Content-Type: text hi everyone, What is the best way to calculate free energy from Monte Carlo simulation? I know there are several recipies for this but not sure which one is the best ( and easiest to calculate). Also, can anyone tell me a good reference to the calculation of potential of mean force ( which is also a free energy quantity)? Though the formula is simple I guess there are some numerical tricks to make it work. Thanks. Pradipta -- ***************************************** * Dr. Pradipta Bandyopadhyay * * Department of Chemistry * * Iowa State Unievrsity * * Ames, IA 50011 * * e-mail: pradipta@si.fi.ameslab.gov * * URL: http://www.msg.ameslab.gov/ * * Group/pradipta/index.html * ***************************************** ------------------------------------------------------------------------------ You may my glories and my state dispose, But not my griefs; still am I king of those. -- William Shakespeare, "Richard II" ------------------------------------------------------------------------------ From chemistry-request@server.ccl.net Thu Jan 13 23:47:40 2000 Received: from qtp.ufl.edu (zwart.qtp.ufl.edu [128.227.89.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id XAA08148 for ; Thu, 13 Jan 2000 23:47:39 -0500 Received: from icream3 (icream3 [128.227.192.183]) by qtp.ufl.edu (8.9.1a/8.9.1) with SMTP id WAA14241 for ; Thu, 13 Jan 2000 22:43:19 -0500 (EST) Message-Id: <200001140343.WAA14241@qtp.ufl.edu> Date: Thu, 13 Jan 2000 22:43:19 -0500 (EST) From: Stefan Fau Reply-To: Stefan Fau Subject: Summary - software for periodic systems To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: TEXT/plain; charset=us-ascii Content-MD5: 4M7Oz9G7Pcm/uB2Yif1T0A== X-Mailer: dtmail 1.3.0 CDE Version 1.3 SunOS 5.7 i86pc i386 Hi, finally, I present the summary. I'd like to thank Chris Charwel, Andrew Horsfield, Philip Lindan, Anatoli Korkin, Georg Schreckenbach, Alexander Hofmann and Eduardo Menendez Proupin. The following programs were mentioned: * CASTEP as a part of MSI's Cerius 2 package. Uses GGA-DFT based molecular dynamics on a combination of plane waves and pseudopotentials. Optimizes atomic positions and cell parameters. http://www.msi.com/materials/cerius2/castep.html * WIEN97, by P. Blaha, K. Schwarz and J. Luitz of the Technical University of Vienna: uses LSDA+GGA DFT in a full potential linearized augmented plane wave (FP-LAPW) basis. Can do optimizations. Costs 350 $ (academic). http://info.tuwien.ac.at/theochem/wien97/ * VASP, by Prof. Hafner's workgroup at the Technical University of Vienna: Uses finite temperature ab initio molecular dynamics on projector augmented plane waves (PAW) or a combination of plane waves and ultrasoft pseudopotentials. Does analytyical (?) gradient geometry optimizations of atomic positions and cell parameters. http://tph.tuwien.ac.at/~vasp/ * DMOL3, in MSI's Cerius 2, too. Uses GGA-DFT on atom centered basis sets. A molecular DFT program that can also work with periodic boundary conditions. Is restricted to one k-point, can not optimize cell parameters. http://www.msi.com/materials/cerius2/dmol3.html * CPMD, developed/improved at the Max Planck Institut for Research on Solids in Stuttgart, Germany by Prof. Parinello's group. http://parrserv2.mpi-stuttgart.mpg.de/ * FHIMD98, developed at the Fritz-Haber-Institut of the Max-Planck- Gesellschaft in Berlin, Germany by Prof. Scheffler's group. It is a DFT based MD code, using local or GGA functionals on a combination of plane waves and pseudopotentials. It optimizes atomic positions. Cost: 300$, demo version and FHIMD96 are free http://www.fhi-berlin.mpg.de/th/fhimd * C. Pisani, J. Mol. Struc. (THEOCHEM) 1999, 463, 125 A review article on band structure calculations. Have a nice year, Stefan ______________________________________________________________________ Dr. Stefan Fau fau@qtp.ufl.edu Quantum Theory Project University of Florida Gainesville FL 32611-8435