From owner-chemistry@ccl.net Sat Aug 12 01:26:01 2006 From: "tejender thakur tejenderthakur]~[india.com" To: CCL Subject: CCL: Textbook on Semiempirical QM Message-Id: <-32378-060812004520-6549-WqZzB7pbKs/mARKt/9zl/A() server.ccl.net> X-Original-From: "tejender thakur" Date: Sat, 12 Aug 2006 00:45:19 -0400 Sent to CCL by: "tejender thakur" [tejenderthakur],[india.com] Dear Thomas, you can find nice details in Book "Quantam Chemistry by I.N. Levine" thanks teje From owner-chemistry@ccl.net Sat Aug 12 06:16:01 2006 From: "Anselm.Horn[]chemie.uni-erlangen.de" To: CCL Subject: CCL: Textbook on Semiempirical QM Message-Id: <-32379-060812061433-16718-kv3W9qeHB1aDOlGaKk9M+w~!~server.ccl.net> X-Original-From: Anselm.Horn*chemie.uni-erlangen.de Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Sat, 12 Aug 2006 12:14:26 +0200 (CEST) MIME-Version: 1.0 Sent to CCL by: Anselm.Horn-.-chemie.uni-erlangen.de Hi Thomas, there is the famous "Approximate Molecular Orbital Theory" of Pople & Beveridge (McGraw Hill, 1970) and Tim Clark's "Handbook of Computational Chemistry" (Wiley, 1985). Then there good review articles about the semiempirical MO methods in the "Encyclopedia of Computational Chemistry" (Wiley, 1995). And finally, in most comprehensive text books about computational chemistry there are chapters describing semiemirical MO theory and its methodological manifestations (e.g. Leach's "Molecular Modellin", Pearson-Prentice Hall, 2001; Cramer's "Essentials of Computational Chemistry", Wiley, 2004). And finally, the online available Mopac2002 manual also may a helpful source (http://www.cachesoftware.com/mopac/Mopac2002manual/ or http://www.fqs.pl/download/MOPAC/mopac_manual_www/index.html). Regards, Anselm Computer-Chemie-Centrum Friedrich-Alexander-Universitaet Erlangen-Nuernberg Germany From owner-chemistry@ccl.net Sat Aug 12 09:02:00 2006 From: "Reynier Suardiaz reynier.suardiaz{=}gmail.com" To: CCL Subject: CCL: funtionals for weak interactions Message-Id: <-32380-060811170715-27079-c1EMeVWgEgs1Z+ilULkaUA]=[server.ccl.net> X-Original-From: "Reynier Suardiaz" Date: Fri, 11 Aug 2006 17:07:14 -0400 Sent to CCL by: "Reynier Suardiaz" [reynier.suardiaz,,gmail.com] Dear CCL members recently a question about funtionals for pi interactions was done. I'm interested in functional that can be used to correctly deal with weak interaction in general, not only pi. Any suggestions, comments and references are welcome. thanks in advance reynier From owner-chemistry@ccl.net Sat Aug 12 09:42:01 2006 From: "Steve Bowlus chezbowlus_+_goldrush.com" To: CCL Subject: CCL: volume calculation Message-Id: <-32381-060811220749-3440-cPHtuNqf+Opiw+0j+Sy6nw#%#server.ccl.net> X-Original-From: Steve Bowlus Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 11 Aug 2006 19:07:22 -0700 MIME-Version: 1.0 Sent to CCL by: Steve Bowlus [chezbowlus#goldrush.com] Volume.f is a Fortran program (GPL) to solve the intersecting spheres problem, "Analytical treatment of the volume and surface area of molecules formed by an arbitrary collection of unequal pheres intersected by planes" L.R. Dodd and D.N. Theodorou MOLECULAR PHYSICS, Volume 72, Number 6, 1313-1345, April 1991 Can be used stand-alone or as a subroutine. It has been several years since I used it, so I don't recall whether it calculates "easily," but certainly very usefully. You can have it if you want it. Cheers, Steve Atilio Anzellotti aanzellotti]^[vcu.edu wrote: > Sent to CCL by: "Atilio Anzellotti" [aanzellotti-.-vcu.edu] > Dear Sir(s), > > I would like to know of any program that can easily calculate the volume of a molecule. > > Many Thanks. > > Atilio. From owner-chemistry@ccl.net Sat Aug 12 10:17:00 2006 From: "=?gb2312?q?=D7=BF=B7=E5=20=BF=C2?= jorphancore*yahoo.com.cn" To: CCL Subject: CCL:G: =?gb2312?q?=BB=D8=B8=B4=A3=BA=20CCL:G:=20Example=20Files/Adding=20New=20F?= =?gb2312?q?F=20parameters=20to=20Gaussian=20Input=20Files?= Message-Id: <-32382-060812052507-12854-zbZFQwxtfyy5pcouzVB/aA(_)server.ccl.net> X-Original-From: =?gb2312?q?=D7=BF=B7=E5=20=BF=C2?= Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-477874786-1155371096=:41808" Date: Sat, 12 Aug 2006 16:24:56 +0800 (CST) MIME-Version: 1.0 Sent to CCL by: =?gb2312?q?=D7=BF=B7=E5=20=BF=C2?= [jorphancore]![yahoo.com.cn] --0-477874786-1155371096=:41808 Content-Type: text/plain; charset=gb2312 Content-Transfer-Encoding: 8bit Dear Hayes, When performing ONIOM calculations, i needs to add FF parameters to the atoms. This is a classic reference about the UFF parameters. Maybe it is helpful to you. J. Am. Chem. SOC. 1992, 114, 10024-10039 "J Hayes hayesjm2002 _ yahoo.com" дµÀ£º Sent to CCL by: "J Hayes" [hayesjm2002,yahoo.com] Dear CCLers, Performing Oniom calculations where i need to define a new UFF forcefield atom type and adjust parameters accordingly. I am aware of the chapter on MM in the Gaussian 03 manual, however, it lacks concrete examples of how to put this into operation. So, could someone please tell me if these files are available somewhere, or could please send me example input files they have? Files where a new atom type is defined greatly appreciated. Many thanks, jhayes hayesjm2002=-=yahoo.comhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtZhuofeng KE (Jonathan Kerr) Theoretical and Computational Laboratory of Chemistry SUN YAT-SEN University, Guangzhou,510275 R.P. China Email: jorphancore{:}yahoo.com.cn --------------------------------- ÇÀ×¢ÑÅ»¢Ãâ·ÑÓÊÏä-3.5GÈÝÁ¿£¬20M¸½¼þ£¡ --0-477874786-1155371096=:41808 Content-Type: text/html; charset=gb2312 Content-Transfer-Encoding: 8bit
Dear Hayes,
 
When performing ONIOM calculations, i needs to add FF parameters to the atoms. This is a classic reference about the UFF parameters. Maybe it is helpful to you.
 
J. Am. Chem. SOC. 1992, 114, 10024-10039
 
 

"J Hayes hayesjm2002 _ yahoo.com" <owner-chemistry{:}ccl.net> дµÀ£º
Sent to CCL by: "J Hayes" [hayesjm2002,yahoo.com]
Dear CCLers,

Performing Oniom calculations where i need to define a new
UFF forcefield atom type and adjust parameters accordingly.
I am aware of the chapter on MM in the Gaussian 03 manual,
however, it lacks concrete examples of how to put this
into operation.

So, could someone please tell me if these files are available
somewhere, or could please send me example input files they
have?
Files where a new atom type is defined greatly appreciated.

Many thanks,
jhayes
hayesjm2002=-=yahoo.com


http://www.ccl.net/cgi-bin/ccl/send_ccl_message
http://www.ccl.net/cgi-bin/ccl/send_ccl_message
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http://www.ccl.net/spammers.txt






Zhuofeng KE  (Jonathan Kerr)  
Theoretical and Computational Laboratory of Chemistry   
SUN YAT-SEN University,
Guangzhou,510275
R.P. China
Email: jorphancore{:}yahoo.com.cn

ÇÀ×¢ÑÅ»¢Ãâ·ÑÓÊÏä-3.5GÈÝÁ¿£¬20M¸½¼þ£¡ --0-477874786-1155371096=:41808-- From owner-chemistry@ccl.net Sat Aug 12 17:20:00 2006 From: "Roland Dunbrack Roland.Dunbrack _ fccc.edu" To: CCL Subject: CCL: ArboDraw: a program for visualization of phylogenetic trees Message-Id: <-32383-060812171332-19775-i3t/Y4uE2wpkL3sFcf5f+g.:.server.ccl.net> X-Original-From: Roland Dunbrack Content-Type: multipart/alternative; boundary=Apple-Mail-5-1013451639 Date: Sat, 12 Aug 2006 16:25:10 -0400 Mime-Version: 1.0 (Apple Message framework v624) Sent to CCL by: Roland Dunbrack [Roland.Dunbrack*|*fccc.edu] --Apple-Mail-5-1013451639 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed We have developed a program for creating and saving images of phylogenetic trees, called ArboDraw. The program can input a tree in standard Newick format (used by Clustal W and other programs) or a FASTA-formatted file used as input to the MUSCLE alignment program (R. Edgar, 2004), included and automatically installed with ArboDraw. The image of the tree can be changed in many ways -- fonts, horizontal and vertical scales, and different branches can be rendered in different colors. Annotations from the FASTA file can be viewed on mouseover of the sequence labels, and these labels and annotations can be edited by right-click. The program is currently available for Windows, and is free to both commercial and academic users. The installation begins with a single click of the download package. It is available from: http://dunbrack.fccc.edu/ArboDraw I hope you find it useful. Roland Dunbrack **************************************** * Roland L. Dunbrack, Jr. * Member * Institute for Cancer Research * Fox Chase Cancer Center * 333 Cottman Avenue * Philadelphia PA 19111 * (215) 728-2434 * (215) 728-2412 (fax) * Roland.Dunbrack /a\ fccc.edu * http://dunbrack.fccc.edu (research) * http://dunbrack.org (genealogy) **************************************** --Apple-Mail-5-1013451639 Content-Transfer-Encoding: 7bit Content-Type: text/enriched; charset=US-ASCII We have developed a program for creating and saving images of phylogenetic trees, called ArboDraw. The program can input a tree in standard Newick format (used by Clustal W and other programs) or a FASTA-formatted file used as input to the MUSCLE alignment program (R. Edgar, 2004), included and automatically installed with ArboDraw. The image of the tree can be changed in many ways -- fonts, horizontal and vertical scales, and different branches can be rendered in different colors. Annotations from the FASTA file can be viewed on mouseover of the sequence labels, and these labels and annotations can be edited by right-click. The program is currently available for Windows, and is free to both commercial and academic users. The installation begins with a single click of the download package. It is available from: http://dunbrack.fccc.edu/ArboDraw I hope you find it useful. Roland Dunbrack **************************************** * Roland L. Dunbrack, Jr. * Member * Institute for Cancer Research * Fox Chase Cancer Center * 333 Cottman Avenue * Philadelphia PA 19111 * (215) 728-2434 * (215) 728-2412 (fax) * Roland.Dunbrack /a\ fccc.edu * http://dunbrack.fccc.edu (research) * http://dunbrack.org (genealogy) **************************************** --Apple-Mail-5-1013451639--