From owner-chemistry@ccl.net Thu Jun 22 02:22:00 2006 From: "Nehru Viji Shankar nehruviji]*[yahoo.co.in" To: CCL Subject: CCL: Request for a program code Message-Id: <-31980-060622000603-23534-U+SVJjY7jCqa4B1UKx5tBw_+_server.ccl.net> X-Original-From: "Nehru Viji Shankar" Date: Thu, 22 Jun 2006 00:06:02 -0400 Sent to CCL by: "Nehru Viji Shankar" [nehruviji .. yahoo.co.in] Dear all First i was impressed by the work of CCL.I knew about this only yesterday. I'm a research student working in computaational chemistry. I'm supposed to get the 3D structure of a molecule just by inputing the connection table of it. I heared about Corina & Concord but i cannot use it.so do i have any other program that would do it.kindly inform me about it and also if possible can you kindly give me the source code of any such program. Thanks in advance.. Sincerely Nehru Viji. From owner-chemistry@ccl.net Thu Jun 22 03:32:00 2006 From: "ccl ccl^mail.sioc.ac.cn" To: CCL Subject: CCL: Request for a program code Message-Id: <-31981-060622032627-3692-Y9sSeX/zCIETYgGBO1XmDA(!)server.ccl.net> X-Original-From: ccl Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Thu, 22 Jun 2006 15:25:46 +0800 MIME-Version: 1.0 Sent to CCL by: ccl [ccl^_^mail.sioc.ac.cn] CHEM3D from CambridgeSoft.com can do such conversion. Starting from a multi-SD format file as input, you can get at most 200 3D structures a day. Nehru Viji Shankar nehruviji]*[yahoo.co.in 写道: > Sent to CCL by: "Nehru Viji Shankar" [nehruviji .. yahoo.co.in] > Dear all > > First i was impressed by the work of CCL.I knew about this only yesterday. > > I'm a research student working in computaational chemistry. I'm supposed to get the 3D structure of a molecule just by inputing the connection table of it. I heared about Corina & Concord but i cannot use it.so do i have any other program that would do it.kindly inform me about it and also if possible can you kindly give me the source code of any such program. > Thanks in advance.. > Sincerely > Nehru Viji.> > > > > From owner-chemistry@ccl.net Thu Jun 22 05:28:00 2006 From: "Zaki Safi zaki.safi[#]gmail.com" To: CCL Subject: CCL: chemcraft registration key Message-Id: <-31982-060622051716-10151-BbgGIWqRr2KLrAsDdmnSfQ##server.ccl.net> X-Original-From: "Zaki Safi" Content-Type: multipart/alternative; boundary="----=_Part_4666_1028582.1150964136481" Date: Thu, 22 Jun 2006 10:15:36 +0200 MIME-Version: 1.0 Sent to CCL by: "Zaki Safi" [zaki.safi|,|gmail.com] ------=_Part_4666_1028582.1150964136481 Content-Type: text/plain; charset=UTF-8; format=flowed Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear, If possible can any one kindly give me the registration key of chemcraft program. Thanks in advance.. Sincerely Zaki . -- =========================================== Dr. Zaki Safi Assistant Prof. of Quantum Chemistry Chemistry Department, Faculty of Science Al-Azhar University - Gaza Gaza, Palestine ------=_Part_4666_1028582.1150964136481 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: 7bit Content-Disposition: inline
Dear,

If possible can any one kindly give me the registration key of chemcraft program.
Thanks in advance..
Sincerely
Zaki
.


--
===========================================
Dr. Zaki Safi
Assistant Prof. of Quantum Chemistry
Chemistry Department, Faculty of Science
Al-Azhar University - Gaza
Gaza, Palestine
------=_Part_4666_1028582.1150964136481-- From owner-chemistry@ccl.net Thu Jun 22 07:11:00 2006 From: "Mikael Johansson mikael.johansson,,helsinki.fi" To: CCL Subject: CCL: chemcraft registration key Message-Id: <-31983-060622070709-6559-MXttaBrSQBN0/JG4ts4VBg^server.ccl.net> X-Original-From: Mikael Johansson Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Thu, 22 Jun 2006 13:11:14 +0300 (EEST) MIME-Version: 1.0 Sent to CCL by: Mikael Johansson [mikael.johansson _ helsinki.fi] Hello Zaki! On Thu, 22 Jun 2006, Zaki Safi zaki.safi[#]gmail.com wrote: > If possible can any one kindly give me the registration key of chemcraft > program. It's available via this link: https://www.plimus.com/jsp/buynow.jsp?contractId=1646946 > Thanks in advance.. No problem. Have a nice midsummer, Mikael J. http://www.iki.fi/~mpjohans/ From owner-chemistry@ccl.net Thu Jun 22 10:39:00 2006 From: "farkas_+_chem.elte.hu" To: CCL Subject: CCL: Request for a program code Message-Id: <-31984-060622085940-14593-bUD/UDsjEOnS3wlj/oC4ew-*-server.ccl.net> X-Original-From: farkas###chem.elte.hu Content-Transfer-Encoding: 7bit Content-Type: multipart/alternative; boundary="=_6301iwo2fwxs" Date: Thu, 22 Jun 2006 14:01:43 +0200 MIME-Version: 1.0 Sent to CCL by: farkas : chem.elte.hu This message is in MIME format. --=_6301iwo2fwxs Content-Type: text/plain; charset=ISO-8859-2; DelSp="Yes"; format="flowed" Content-Description: A =?iso-8859-2?b?bGV2w6ls?= sima text =?iso-8859-2?b?dsOhbHRvemF0YQ==?= Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Hi, I can advice Chemaxon's Marvin package, which provides GUI, command line batch process and Java API access for building 3D structures. Some more details can be found at: http://www.chemaxon.com/forum/viewpost6490.html#6490 The latest version is available in the alpha release of Marvin 4.1: http://www.chemaxon.com/shared/alpha/marvin/index.html It is free for academic users. Best wishes, =D6d=F6n Farkas ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. --=_6301iwo2fwxs Content-Type: text/html; charset=ISO-8859-2 Content-Description: A =?utf-8?b?bGV2w6ls?= HTML =?utf-8?b?dsOhbHRvemF0YQ==?= Content-Disposition: inline Content-Transfer-Encoding: quoted-printable


Hi,

I can advice Chemaxon's Marvin package, which provides GUI, command line bat= ch process and Java API access for building 3D structures. Some more details ca= n be found at:
http://www.che= maxon.com/forum/viewpost6490.html#6490

The lat= est version is available in the alpha release of Marvin 4.1:

http://www.chemaxon.com/shared/alpha/marvin/index.html

It i= s free for academic users.

Best wishes,

=D6d=F6n Farkas



----------------------------------------------------------------
This message was sent using IMP, the Internet Messaging Program.
--=_6301iwo2fwxs-- From owner-chemistry@ccl.net Thu Jun 22 11:14:02 2006 From: "Dr. Seth Olsen s.olsen1 : uq.edu.au" To: CCL Subject: CCL: Background on practical aspects of quantum chemistry? Message-Id: <-31985-060622035124-20403-fOSdAqmBjtpY4vJ5H6dd0A*server.ccl.net> X-Original-From: "Dr. Seth Olsen" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 22 Jun 2006 16:46:35 +1000 MIME-Version: 1.0 Sent to CCL by: "Dr. Seth Olsen" [s.olsen1 a uq.edu.au] Hi CCLers, I'm interested in knowing what kind of resources (books, webpages, review articles, etc.) there are on the more practical aspects of quantum chemistry implementations. I'm looking for something that gives a wide view of the very practical issues and technical (hardware and software) bottlenecks that are commonly encountered. I think many practicing quantum chemists end up getting a feel for these issues over their careers, but they are rarely found in textbooks on the subject. Does anyone know of a resource which fits this description? Cheers, Seth -- ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms Dr Seth Olsen, PhD Postdoctoral Fellow, Biomolecular Modeling Group Centre for Computational Molecular Science Chemistry Building, The University of Queensland Qld 4072, Brisbane, Australia tel (617) 33653732 fax (617) 33654623 email: s.olsen1%x%uq.edu.au Web: www.ccms.uq.edu.au ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms Unless stated otherwise, this e-mail represents only the views of the Sender and not the views of The University of Queensland From owner-chemistry@ccl.net Thu Jun 22 12:02:00 2006 From: "John McKelvey jmmckel,attglobal.net" To: CCL Subject: CCL: Parameterization search techniques Message-Id: <-31986-060622115912-3592-0dm2CA95KKNCZ9XrXWvlkA===server.ccl.net> X-Original-From: John McKelvey Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 22 Jun 2006 11:50:39 -0400 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel~!~attglobal.net] Folks, I am doing some parameterization for a UV-VIS spectroscopic method. Currently I am using an Fletcher-Powell optimizer that uses gradients, and BFGS Hessian updates. I have a fundamental question. Would a simplex method, forgetting algorithym and computational efficiency issues, get me where I might want to be more /_reliably_/? [Currently derivatives are computed using forward and backward bumps, so simplex might not be that inefficient, relatively speaking.] Alternative suggestions are most welcome.. Many thanks.. John McKelvey From owner-chemistry@ccl.net Thu Jun 22 12:58:01 2006 From: "farkas/a\chem.elte.hu" To: CCL Subject: CCL: Request for a program code Message-Id: <-31987-060622100016-19536-G1enabkfcY1aW/o2GzE/SQ\a/server.ccl.net> X-Original-From: farkas{}chem.elte.hu Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-2; DelSp="Yes"; format="flowed" Date: Thu, 22 Jun 2006 15:59:54 +0200 MIME-Version: 1.0 Sent to CCL by: farkas**chem.elte.hu Hi, I can advice Chemaxon's Marvin package, which provides GUI, command line batch process and Java API access for building 3D structures. Some more details can be found at: http://www.chemaxon.com/forum/viewpost6490.html#6490 The latest version is available in the alpha release of Marvin 4.1: http://www.chemaxon.com/shared/alpha/marvin/index.html It is free for academic users. Best wishes, Odon Farkas ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From owner-chemistry@ccl.net Thu Jun 22 16:20:01 2006 From: "makowskm=chemia.uj.edu.pl" To: CCL Subject: CCL: Parameterization search techniques Message-Id: <-31988-060622161837-11580-X2svAH0W6FU6r2ASotQkdw/./server.ccl.net> X-Original-From: makowskm===chemia.uj.edu.pl Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-2 Date: Thu, 22 Jun 2006 22:18:28 +0200 (CEST) MIME-Version: 1.0 Sent to CCL by: makowskm#chemia.uj.edu.pl As far as I understand simplex method it still has a good chance to throw you to any local minimum. You may think of genetic algorithms instead. Regards, Marcin -- Dr Marcin Makowski Jagiellonian University Department of Theoretical Chemistry email:makowskm[-]chemia.uj.edu.pl or Kyushu University email:marcin[-]cube.kyushu-u.ac.jp From owner-chemistry@ccl.net Thu Jun 22 18:33:00 2006 From: "Suman Chakravarti suman.chakravarti.^-^.case.edu" To: CCL Subject: CCL: Request for a program code Message-Id: <-31989-060622153325-7597-SlGYGGzN40/oWCtOOtG77g^-^server.ccl.net> X-Original-From: Suman Chakravarti Content-Disposition: inline Content-Language: en Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Thu, 22 Jun 2006 14:56:13 -0400 MIME-Version: 1.0 Sent to CCL by: Suman Chakravarti [suman.chakravarti!^!case.edu] May be this web page will be useful for converting connectivity to 3D structures. Check it out. http://cactus.nci.nih.gov/services/translate/ Regards Suman ----- Original Message ----- > From: "farkas/achem.elte.hu" Date: Thursday, June 22, 2006 1:10 pm Subject: CCL: Request for a program code To: "Chakravarti, Suman K. " > Sent to CCL by: farkas**chem.elte.hu > Hi, > > I can advice Chemaxon's Marvin package, which provides GUI, command > line batch process and Java API access for building 3D structures. > Some more details can be found at: > http://www.chemaxon.com/forum/viewpost6490.html#6490 > > The latest version is available in the alpha release of Marvin 4.1: > > http://www.chemaxon.com/shared/alpha/marvin/index.html > > It is free for academic users. > > Best wishes, > > Odon Farkas > > > > > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging Program. > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, please > changethe strange characters on the top line to the || sign. You can > also> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+-+ > > > > From owner-chemistry@ccl.net Thu Jun 22 21:07:00 2006 From: "Sidney R. Santana santanasidney*yahoo.com.br" To: CCL Subject: CCL: Parameterization search techniques Message-Id: <-31990-060622203733-23730-lWH5YcGkJhbc1LcamlUB4A|server.ccl.net> X-Original-From: "Sidney R. Santana" Date: Thu, 22 Jun 2006 20:37:28 -0400 Sent to CCL by: "Sidney R. Santana" [santanasidney-,-yahoo.com.br] Dear CCL Users, I understand "Generalized Simulated Anneling"[1] (GSA) methods, like "Variable Step Size Generalized Simulated Annealing"[2] and "Simplified Generalized Simulated Annealing"[3,4], are the best function optimizer method to find not local minimum but the global minimum !!! Much better than simplex, modified simplex, steepest ascent and other methods. [1] I. O. Bohachevsky, M. E. Johnson, M. L. Stein, Technom. 28 (1986) 209 [2] J. H. Kalivas, N. Roberts, J. M. Sutter, Anal. Chem. 61 (1989) 2024 [3] C. Tsallis, D.A. Stariolo, Ann. Rev. Comput. Phys. 2 (1995) 353 [4] C. Tsallis, D.A. Stariolo, Phys. A 233 (1996) 395 You can see some improvements and aplications of GSA in the papers of professor Kleber C. Mundim and M. A. Moret, for example [5-6] [5] M. A. Moret, P. M. Bisch, K. C. Mundim, Biophys. J. 82 (1998) 1123 [6] A. DallIgna Jr, R. S. Silva, L. E. Dardenne, K. C. Mundim, Genet. Mol. Bio. 27 (2004) 616 Professor Kleber C. Mundim is an expert in this subject. http://www.unb.br/iq/kleber/GSA/ Best Regards, Sidney Ramos de Santana Ps-Graduao em Cincia de Materiais (PGMTR) Laboratrio de Qumica Terica e Computational (LQTC) Centro de Cincia Exatas e da Natureza (CCEN) Universidade Federal of Pernambuco (UFPE) e-mail: santanasidney_at_yahoo.com.br --------------------------------------------------------- Sent to CCL by: makowskmchemia.uj.edu.pl As far as I understand simplex method it still has a good chance to throw you to any local minimum. You may think of genetic algorithms instead. Regards, Marcin -- Dr Marcin Makowski Jagiellonian University Department of Theoretical Chemistry email:makowskm a chemia.uj.edu.pl or Kyushu University email:marcin a cube.kyushu-u.ac.jp --------------------------------------------------------- Sent to CCL by: John McKelvey [jmmckel~!~attglobal.net] Folks, I am doing some parameterization for a UV-VIS spectroscopic method. Currently I am using an Fletcher-Powell optimizer that uses gradients, and BFGS Hessian updates. I have a fundamental question. Would a simplex method, forgetting algorithym and computational efficiency issues, get me where I might want to be more /_reliably_/? [Currently derivatives are computed using forward and backward bumps, so simplex might not be that inefficient, relatively speaking.] Alternative suggestions are most welcome.. Many thanks.. John McKelvey