From kozelka@citi2.fr Sat Nov 30 13:50:16 1996 Received: from galaad.citi2.fr for kozelka@citi2.fr by www.ccl.net (8.8.3/950822.1) id NAA20947; Sat, 30 Nov 1996 13:03:05 -0500 (EST) Received: from bisance.citi2.fr by galaad.citi2.fr; (5.65/1.1.8.2/20Jun94-0455PM) id AA00637; Sat, 30 Nov 1996 19:03:28 +0100 Received: by bisance.citi2.fr (5.0/SMI-SVR4) id AA13103; Sat, 30 Nov 1996 19:02:33 --100 From: kozelka@citi2.fr (JirKa Kozelka) Message-Id: <9611301802.AA13103@bisance.citi2.fr> Subject: Z-matrix,summary To: chemistry@www.ccl.net Date: Sat, 30 Nov 1996 19:02:33 +0100 (MET) X-Mailer: ELM [version 2.4 PL23] Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit Dear netters, Some days ago, I submitted the following question: ************ Just a simple question concerning geometry optimization using G94. If you want to keep the local symmetry of a functional group, say, a methyl group, how do you do it? Can one use algebraic expressions in the Z-matrix, such as in the following input for acetaldehyde: H C 1 1.08 O 2 1.33 1 120. C 2 1.54 3 120. 1 180. H 4 ch 2 hcc 1 hcch H 4 ch 2 hcc 1 hcch+120. H 4 ch 2 hcc 1 hcch-120. ch 1.01 hcc 120. hcch 180. ***************** I have obtained several replies from kind people. The solution is quite simple, so I am a little ashamed. Nevertheless, it is good to know that G94 does not accept composite expressions. As an example, I reproduce below the reply from Stefan. ******************** Hi JirKa, in G94 you have to use popt (or addredundant), if you want to constrain some degrees of freedom. It implies opt=z-matrix instead of the normal redefinition of your structure into redundant internal coordinates. You must not use algebraic expressions like "hcch+120" in the z-matrix, but you can achieve the same effect with the following z-matrix: H C 1 1.08 O 2 1.33 1 120. C 2 1.54 3 120. 1 180. H 4 ch 2 hcc 1 hcch H 4 ch 2 hcc 5 120. H 4 ch 2 hcc 5 -120. ch 1.01 hcc 120. hcch 180. Yours, Stefan Stefan Fau, fau@mailer.uni-marburg.de FB Chemie der Philipps-Universitaet Marburg, Hans-Meerwein-Str. D-35032 Marburg *************************** Jirka Kozelka Universite Rene Descartes, Paris kozelka@citi2.fr fax +331-42 86 83 87 From arthur@csb0.IPC.PKU.EDU.CN Sat Nov 30 21:50:21 1996 Received: from csb0.IPC.PKU.EDU.CN for arthur@csb0.IPC.PKU.EDU.CN by www.ccl.net (8.8.3/950822.1) id VAA22350; Sat, 30 Nov 1996 21:44:49 -0500 (EST) Received: by csb0.IPC.PKU.EDU.CN (920330.SGI/940406.SGI.AUTO) for chemistry@www.ccl.net id AA04141; Sun, 1 Dec 96 10:44:24 -0800 Date: Sun, 1 Dec 1996 10:44:22 -0800 (PST) From: Arthur Wang To: CCL mailing list Cc: Structrual Biology List Subject: Summary: Molecular Modeling Software for Undergraduate Education Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters, Last week I posted the question: "What is the appropriate modeling software for undergraduate education of structural chemistry". Now I have received dozens of answers, which are proved to be very valuable. Now here is the summary: ------------------------------------------------------------------------- My original question is: Very fortunately we get the funds that we have long been searching for. What we want now is a set of molecular modeling softwares mainly for undergraduate education. Would you please offer your kind hands to point out what we should get and where we could get them? These softwares are supposed to meet these requirement: o Run on PCs, under DOS or WINDOWS. o Free on-line or commercial available. o The most popular ones. You know there are already so many softwares doing modeling. Here we want some smart ones like ALCHEMY2000. o Proper for undergraduate education. Please focus on structural chemistry. Necessary functions include: * 3D structure generation, visualization and manipulation; * Quantum mechanics and Molecular mechanics calculation; * Crystal structure modeling (inorganic and organic) * macromolecules as well as small molecules. -------------------------------------------------------------------------- Thank all these netters for their kind help: Jawahar Swaminathan Robert K. Szilagyi J. Eric Slone Jeffrey J Gosper Clifford Felder Morten Langgaard Ross Underhill Ajit J. Thakkar N.Ganesh Stephanie T.-Nagle Sri Krishna Alan Shusterman Dragan Vuckovic Joel Polowin Janet E. Nelson Xiao-Chuan Wang Willie Cui Li,Songmei Anil kumar P Marys Kolodziej Bob Joseph Kimberley Cousins Alexandre Hocquet Shawn Butler Ajit J. Thakkar Yufeng Wei --------------------------------------------------------------------------- These following names have been mentioned: HyperChem: http://www.hyper.com/ Spartan: http://www.wavefun.com/ AccuModel: http://www.microsimulations.com/ Chem-X: http://www.awod.com/netsci/Companies/CDL/products.html Chem-3D: http://www.camsci.com/ Alchemy 2000: http://www.tripos.com/ Rasmol and WinPDB, for pdb visualizaion FREE on line, ftp.pdb.bnl.gov or http://www.pdb.bnl.gov/ Molgen, for DOS platforms FREE on line, http://www.patriot.net/users/eslone ftp:\\www.ccl.net\pub\chemistry\software\MS-DOS Re_view, enable molecular visualization, animation and etc. FREE on line, http://www.brunel.ac.uk/depts/chem/ch241s/re_view/re_view.htm hmo10.zip Student Huckel molecular orbital calculator FREE on line, http://www.simtel.net/pub/simtelnet/msdos/chemstry/hmo10.zip ftp://ftp.simtel.net/pub/simtelnet/msdos/chemstry/hmo10.zip ---------------------------------------------------------------------------- We will probably make choice between HyperChem, PC-Spartan, AccModel and Alchemy2000. In fact, these are the ones that have got the most votes. :-) Best wishes, Arthur _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ Arthur Wang Doctoral Candidate _/ _/ Molecular Design Lab _/ _/ Institute of Physical Chemistry, Peking University _/ _/ Beijing 100871, P.R.China _/ _/ _/ _/ E-mail: arthur@ipc.pku.edu.cn _/ _/ Tel: 86-10-2751490 Fax: 86-10-2751725 _/ _/ WWW: http://www.ipc.pku.edu.cn/moldes/arthur/home.html _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/