From chemistry-request@server.ccl.net Wed Mar 21 01:42:47 2001 Received: from wn1.sci.kun.nl ([131.174.8.1]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2L6gcD31240 for ; Wed, 21 Mar 2001 01:42:42 -0500 Received: from studs3.sci.kun.nl by wn1.sci.kun.nl via studs3.sci.kun.nl [131.174.124.4] with ESMTP for id f2L6gXT28798 (8.11.1/3.14); Wed, 21 Mar 2001 07:42:33 +0100 (MET) From: "E.L. Willighagen" Received: by studs3.sci.kun.nl via egonw@localhost for CHEMISTRY@ccl.net id f2L6gW121105 (8.11.1/3.4); Wed, 21 Mar 2001 07:42:32 +0100 (MET) Date: Wed, 21 Mar 2001 07:42:32 +0100 (MET) Message-Id: <200103210642.f2L6gW121105@studs3.sci.kun.nl> To: CHEMISTRY@ccl.net Subject: OpenSource Catagorization (was: DCD and software reuse) > > My guess is that the impact of significant amounts of > > *reusable* source-code building blocks would be profound and world > > changing. > I agree completely, but I wonder how many others do. There are lists with GPL software (chemistry). And looking at the number, there are enough programms to start with... This link (look for green GPL marks :) http://SAL.KachinaTech.COM/Z/2/index.shtml There is also an initiative called OpenScience which is a catagorization of OpenSource (GPL/BSD/etc license): http://www.openscience.org/ But it is not just focused on chemistry... So the actual problem looks coordination ideed. > Some sort of coordination sounds like a very good idea. > But it would be nice to have a catalogue of projects, OpenScience? Egon From chemistry-request@server.ccl.net Wed Mar 21 01:50:46 2001 Received: from iitkgp.iitkgp.ernet.in ([202.141.127.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2L6oeD31293 for ; Wed, 21 Mar 2001 01:50:41 -0500 Received: from cts.iitkgp.ernet.in (cts.iitkgp.ernet.in [144.16.192.220]) by iitkgp.iitkgp.ernet.in (8.9.3/8.9.3) with ESMTP id MAA15280 for ; Wed, 21 Mar 2001 12:18:40 -0500 (GMT) Received: from localhost (rajarshi@localhost) by cts.iitkgp.ernet.in (8.9.3/8.9.3) with ESMTP id MAA08517 for ; Wed, 21 Mar 2001 12:05:02 +0530 X-Authentication-Warning: cts.iitkgp.ernet.in: rajarshi owned process doing -bs Date: Wed, 21 Mar 2001 12:05:02 +0530 (IST) From: Rajarshi Guha X-X-Sender: To: CompuChem List Subject: Metal Force Fields - Summary Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, a week ago I had posted a question regarding force fields for metals. The question was: >Hi, >could anybody point me to reviews/links of force fields for metallic >systems - I'm more interested in the nature of the force fields themselves >rather than the applications to specific systems. I recieved several very informative replies which I have summarised below. ############################################################################### From: Isaac B. Bersuker Date: Tue, 13 Mar 2001 11:24:14 -0800 You are correctly rising the question of the nature of force fields for metal containing systems because, strictly speaking, there are no general force fields in these cases. See my book by Wiley, New York, 1996, maybe you will find something of interest with regard to your question. Isaac Bersuker -- Dr. Isaac B. Bersuker Institute for Theoretical Chemistry Department of Chemistry & Biochemistry The University of Texas at Austin Austin, TX 78712, USA Ph: (512) 471-4671 Fax: (512) 471-8696 Email: bersuker@eeyore.cm.utexas.edu ###################################################################### Date: Tue, 13 Mar 2001 19:25:12 +0100 From: Jeremy Greenwood This sounds like a question for which Per-Ola Norrby would be a good person ask. Email: pon@kemi.dtu.dk (alt. peo@compchem.dfh.dk) His recent review is "Co-ordination Chemistry Reviews 212 (2001) 79-109 HTH Jeremy ---------------------------------------------------------------------- Jeremy Greenwood jeremy.greenwood@i.am Department of Medicinal Chemistry bh +45 35306117 Royal Danish School of Pharmacy fx +45 35306040 Universitetsparken 2, DK-2100 Copenhagen, Denmark ah +45 32598030 ---------------------------------------------------------------------- 'Any excuse will serve a tyrant.' -- Aesop ---------------------------------------------------------------------- ###################################################################### Date: Tue, 13 Mar 2001 20:25:09 +0100 From: Per-Ola Norrby The second edition of "Molecular Modeling of Inorganic Compounds" by P. Comba and T.W. Hambley just came out (I got it today). Also, try these as leads: "Deriving Force Field Parameters for Coordination Complexes" Per-Ola Norrby and Peter Brandt, Coord. Chem. Rev. 2001, 212, 79-109 "Recipe for an organometallic force field" Per-Ola Norrby, in Computational Organometallic Chemistry, Ed: T. Cundari; Marcel Dekker: New York, 2001, 7-37 Best, Per-Ola Norrby -- ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Per-Ola Norrby, Assoc. Professor, http://compchem.dfh.dk/PeO/ Technical University of Denmark, Dept. of Chem., Org. Chem. Building 201, Kemitorvet, DK-2800 Kgs. Lyngby, Denmark tel +45-45252123, fax +45-45933968 Email: pon@kemi.dtu.dk (alt. peo@compchem.dfh.dk) ###################################################################### Date: Tue, 13 Mar 2001 23:15:39 -0500 From: David White Raj, There is an excellent book coming out edited by Tom Cundari called "Computational Organometallic Chemistry", which will give you many references (Marcel-Dekker). Also, there is a book by Peter Comba, which has some parameters. I have parameters for Cr and Rh. Tony Rappe has also written a book called Molecular Mechanics Across Chemistry (I think), published by University Science Books. Hope this helps, Dave ********************************************************************** David P. White, PhD Phone: (910) 962-7499 Assistant Professor Fax: (910) 962-3013 Wilmington Institute for the Structural Design of Organometallic Materials (WISDOM) Department of Chemistry University of North Carolina at Wilmington 601 South College Road Wilmington, NC 28403 http://aa.uncwil.edu/wisdom ###################################################################### Date: Wed, 14 Mar 2001 12:47:27 -0500 From: Shyam Vyas Hi Rajarshi, The classic metal forcefield is the Sutton-Chen potential. A.P. Sutton and J. Chen Phil. Mag. Lett., 61, 139 (1990) The GULP simulation code has a library of these parameters, the following link may be of use to you. http://www.ch.ic.ac.uk/gale/Research/gulp.html#Overview Also you should look at the work of David Bacon at University of Liverpool. http://www.liv.ac.uk/mateng/research/research_98/metals.htm Cheers, Shyam ###################################################################### Date: Thu, 15 Mar 2001 03:24:08 -0800 From: Darren Fayne Hi Rajarshi, Here is a few reviews that I'm sure will be of interest to you. (a) Brubaker, G.R. and Johnson, D.W., Coord. Chem. Rev., 1984, 53, 1-36; (b) Hancock, R.D., Progr. Inorg. Chem. 1989, 37, 187; (c) Landis, C.R., Root, D.M. and Cleveland, T., Molecular mechanics force fields for modeling inorganic and organometallic compounds, "Reviews in Computational Chemistry", Lipowitz, K.B. and Boyd, D.B., (Eds.) Vol. 6, 1995, p. 73-148; (d) Hay, B.P., Coord. Chem. Rev., 126, 1993, 177-236; (e) Comba, P., Coord. Chem. Rev., 1999, 185-186, 81-98. Enjoy the reading..... Darren --- Darren Fayne School of Chemical Sciences, Dublin City University, Dublin, Eire. ###################################################################### ------------------------------------------------------------------------ Rajarshi Guha | "If you don't get a good night Dept. of Chemistry | kiss, you get Kafka dreams." IIT Kharagpur. | | Hobbes email: rajarshi@presidency.com | rajarshi@cts.iitkgp.ernet.in | web : www.psynet.net/jijog | ------------------------------------------------------------------------- From chemistry-request@server.ccl.net Wed Mar 21 07:53:06 2001 Received: from alien.biochem.wfubmc.edu ([152.11.118.46]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2LCpwD01011 for ; Wed, 21 Mar 2001 07:52:07 -0500 Received: from localhost (zhangxd@localhost) by alien.biochem.wfubmc.edu (SGI-8.9.3/8.9.3) with ESMTP id HAA68272; Wed, 21 Mar 2001 07:50:44 -0500 (EST) Date: Wed, 21 Mar 2001 07:50:44 -0500 From: Zhangxd To: Didier MATHIEU cc: chemistry@ccl.net Subject: question about AutoDock In-Reply-To: <200103201741.SAA05417@styx.bruyeres.cea.fr> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII hi, everyone I just use AutoDock one week ago, I wonder to know how to obtain the pdb file of the liang and the protein after docking (I use the command autodock3 -p *.dpf -l *.glg )? Thank in advance! xiaodong From chemistry-request@server.ccl.net Wed Mar 21 10:15:59 2001 Received: from physics.msuiit.edu.ph ([202.78.82.11]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2LFEYD02790 for ; Wed, 21 Mar 2001 10:15:44 -0500 Received: by physics.msuiit.edu.ph (Postfix, from userid 701) id A38B26312A; Wed, 21 Mar 2001 23:15:22 +0800 (PHT) Received: from localhost (localhost [127.0.0.1]) by physics.msuiit.edu.ph (Postfix) with ESMTP id 8D436579AA for ; Wed, 21 Mar 2001 23:15:22 +0800 (PHT) Date: Wed, 21 Mar 2001 23:15:22 +0800 (PHT) From: Arnold Alguno To: CompuChem List Subject: IP's and EA's of a conducting polymers Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII hello guys, How to determine the Ionization Potentail (IP) and Electron Affinity (EA) of the conducting polymers emplyoying DFT calculations? Furthermore, aside > from HOMO/LUMO difference, what are other procedures to determine the Band gap of a polymer? thanks. _________ Very truly yours, ARNOLD C. ALGUNO IITHEP, Department of Physics MSU-IIT, Iligan City Philippines alguno@physics.msuiit.edu.ph Mobile Phone No.:+63-919-427-8205 From chemistry-request@server.ccl.net Wed Mar 21 12:39:06 2001 Received: from water.cc.mcgill.ca ([132.206.27.29]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2LHd1D04713 for ; Wed, 21 Mar 2001 12:39:06 -0500 Received: from ariya430 (ariya430.Chem.McGill.CA [132.206.175.28]) by water.cc.mcgill.ca (8.11.1/8.11.0) with SMTP id f2LHd0t02732 for ; Wed, 21 Mar 2001 12:39:00 -0500 (EST) Message-Id: <200103211739.f2LHd0t02732@water.cc.mcgill.ca> From: "Alexei Khalizov" Organization: Chemistry Dept., McGill University To: chemistry@ccl.net Date: Wed, 21 Mar 2001 12:42:12 -0500 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: Reduced moment of inertia Priority: normal X-mailer: Pegasus Mail for Win32 (v3.01d) Dear all, I need to calculate the reduced moment of inertia for a hindered rotation (Ir) in order to correct molecular partition function. Is there any program to do it? I know that it is very a simple procedure for symmetrical coaxial rotors, especially if rotation is free, and it can be done with a pencil and paper (S.W. Benson, Thermochemical kinetics). It is still not very difficult for unsymmetrical cases, but involves some mathematical transformations involving calculation of the moment of inertia of each fragment about an axis, which is parallel to the bond connecting those fragments and passing through the center of gravity of the fragment. I have tried GEOM program (UNIMOL package, R.G. Gilbert, S.C. Smith, Theory of unimolecular and recombination reactions), but there are two problems. First, it calculates moments of inertia of the fragments about the bond connecting fragments, not about the axis parallel to it and passing through the center of gravity of the fragment. Second, it looks that there is a bug in the program, since it produces zero moment of inertia for a fragment where it should not be zero. For example, in hydrogen peroxide, H2O2, all three moments of inertia of OH group about axis passing through O-O bond must be non-zero, but program produces: PRINCIPAL MOMENTS OF INERTIA AROUND PIVOT 0.955 0.955 0.000 (AMU ANGSTROM**2) I have also tried Gaussian98 with undocumented command freq=hindrot (described in http://www.gaussian.com/thermo.htm), which is implementation of P.Y. Ayala, H.B. Schlegel, J.Chem.Phys., v.108, 2314, 1998. It also produces strange and in some cases corrupted results. Sincerely, Alex ------------------------- Dr. Alexei Khalizov Department of Chemistry McGill University, 801 Sherbrooke St. W., Montreal, Quebec, CANADA, H3A 2K6 Phone: (514) 398-6920 Fax: (514) 398-2382 From chemistry-request@server.ccl.net Wed Mar 21 14:13:36 2001 Received: from johnson.mail.mindspring.net ([207.69.200.177]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2LJDZD06654 for ; Wed, 21 Mar 2001 14:13:35 -0500 Received: from smui03.slb.mindspring.net (smui03.slb.mindspring.net [199.174.114.22]) by johnson.mail.mindspring.net (8.9.3/8.8.5) with ESMTP id OAA30862; Wed, 21 Mar 2001 14:13:21 -0500 (EST) From: bradleym@mindspring.com Received: by smui03.slb.mindspring.net id OAA0000021913; Wed, 21 Mar 2001 14:16:21 -0500 (EST) Date: Wed, 21 Mar 2001 14:16:21 -0500 To: chemistry@ccl.net Cc: kscug@vt.edu Subject: Summary: Prediction of UV absorbance Sender: bradleym@mindspring.com Message-ID: X-Originating-IP: 64.182.4.166 Thanks for the many responses, the following are available for UV prediction. gaussian98 a.7 for TDHF(or RPA), CIS, TDDFT and ZINDO hyperchem for ZINDO and other semiempirical methods mopac2000 for inclusion of MOS-F (semiempirical methods) ... I have since tried ZINDO (Cerius2), and it works quite well.