From owner-chemistry@ccl.net Mon Mar 31 00:11:01 2008 From: "Raji Raji raji%a%anal.chem.tohoku.ac.jp" To: CCL Subject: CCL:G: emission spectrum Message-Id: <-36595-080331001019-30904-QWK3VOPT87CDVAjjVg7Yjg!=!server.ccl.net> X-Original-From: "Raji Raji" Date: Mon, 31 Mar 2008 00:10:16 -0400 Sent to CCL by: "Raji Raji" [raji(!)anal.chem.tohoku.ac.jp] Dear Thanos, Though you got few replies you didnt get the exact keywords and how to do it. Hence I would like to write few lines. You have to do two step calculations to get the emission spectrum. If you are interested in CIS calculations, then the route section is: 1) Optimization of the first excited state #CIS(Root=1, Direct)/6-311+G(d) Opt SCRF=(CPCM, Solvent=Water) 2) Excited state calculation #CIS(NStates=15, Singlets, Direct)/6-311+G(d) SCRF=(CPCM, Solvent=Water) As for the second part of your question, the programme "SWIZARD" can give the absorption spectrum and I tried only for TDDFT calculations. I have no idea about CIS and emission spectrum. I will be happy if someone could write whether this programme can give emission spectrum calculated by CIS or not. With Kind Regards, Raji. Thanos Constantine Tsipis attsipis~~uoi.gr wrote: >Sent to CCL by: "Thanos Constantine Tsipis" [attsipis^_^uoi.gr] >Hello, >Could you please tell me how could I simulate the emission spectrum of a system with Gaussian03? Exactly what commands should I include in the route section in order to do this with TDDFT and CIS? In addition, could I have the emission spectrum using GaussSum? In the G03 manual it is not clear how one can study the S1 instead of S0 state with TDDFT or CIS. What commands should be included in the route section (td(Root=1)?) >Many thanks in advance. > >Sincerely Yours, >Thanos > >PS : I would appreciate if you send me a few gjf inputs related to these subject. From owner-chemistry@ccl.net Mon Mar 31 04:07:01 2008 From: "Alex Wang yawang-*-chem.ubc.ca" To: CCL Subject: CCL: ISTCP-VI, 19-24 July 2008 at UBC (2nd Announcement) Message-Id: <-36596-080331040539-10039-RW0Y2I1bb1XY8dnYJsgzNA^server.ccl.net> X-Original-From: "Alex Wang" Date: Mon, 31 Mar 2008 04:05:35 -0400 Sent to CCL by: "Alex Wang" [yawang/./chem.ubc.ca] --------------------------------------------------------------------- PLEASE ACCEPT OUR APOLOGIES IF YOU RECEIVE THIS E-MAIL MORE THAN ONCE --------------------------------------------------------------------- ******************* SECOND ANNOUNCEMENT ******************* Sixth International Congress of the INTERNATIONAL SOCIETY FOR THEORETICAL CHEMICAL PHYSICS July 19-24, 2008 University of British Columbia, Vancouver, Canada The ISTCP-VI website (http://www.chem.ubc.ca/istcp6) has been open for registration, abstract submission, and hotel booking. In the coming weeks, please visit the ISTCP-VI website for latest updates. ------------ Dear Colleague, The Sixth Congress of the International Society for Theoretical Chemical Physics (ISTCP-VI) (http://www.chem.ubc.ca/istcp6) will be held on July 19-24, 2008 in the beautiful campus of the University of British Columbia (UBC) at Vancouver, BC, Canada. The history of ISTCP and its Congresses is available at the following link: http://www.chem.ubc.ca/istcp6/ISTCPstory.htm. Held every three years, ISTCP Congresses continue the tradition of showcasing the achievements and advances in all areas of theoretical chemical physics, with special emphasis on the interaction between experimental and theoretical physical chemistry, chemical physics, and materials and life sciences. The scope of ISTCP-VI will cover a broad range of topics that include Biophysical/Medical Simulations, Statistical Mechanics, Quantum Chemistry, Density-Functional Theory, Coupled Clusters, Quantum Monte Carlo, Quantum/Classical Dynamics, Nanosystems, Coherent Control, Ultra-cold Chemistry, AttoScience, and Novel Materials. As usual, the proceedings of the Congress will be published in the International Journal of Quantum Chemistry (IJQC) and Progress in Theoretical Chemistry and Physics (PTCP). Research papers will appear in IJQC (Wiley) while review papers will appear in PTCP (a book series published by Springer). With extensive advertising all over the world, we anticipate the total number of participants to ISTCP-VI to reach 350. This will definitely be a wonderful opportunity to know the latest cutting- edge advances in theoretical chemical physics and to network with your colleagues worldwide. Several members of the Honorary Board of Directors of ISTCP (which includes 4 Nobel Laureates and 4 Wolf Prize Awardees) have expressed their intention to attend the Congress. It is our great pleasure to invite you to join us for a five-day scientific fest at UBC during ISTCP-VI. If you would like to attend ISTCP-VI, please first register at in the "Participant" role. Then, submit your abstract at your earliest convenience at . More than one abstract can be submitted. Submitted abstracts can be revised before July 11, 2008, when all abstracts will be printed on paper. If you would like to give a contributed talk, please submit your abstract as early as possible. Then, send a request for an oral presentation to . The Congress Chair will pass your request to pertinent Symposium Organizers for consideration. If you want to pay your registration fee (in Canadian dollars) via wire transfer, please following the instruction below: . If you need an entry visa into Canada, please send the Congress Chair an email request for an invitation letter as soon as possible. With best wishes, The ISTCP-VI Executive Committee Alex Wang (Chair, UBC, Canada) Erkki J. Brandas (Co-chair, President of ISTCP, Sweden) Jean Maruani (Co-chair, France) ------------ About Vancouver Vancouver is the largest city in Western Canada, located at the south- western corner of the province of British Columbia. Situated between the north-shore and coastal mountains and the edge of the Pacific ocean, Vancouver is one of the most beautiful cities in North America, and was recently ranked as "the world's most desirable place to live" in a survey of 127 cities performed by the Intelligence Unit of the magazine The Economist. It is also the hosting city of the 2010 Olympic Winter Games. The vibrant downtown core offers all the amenities of an international destination - from hundreds of restaurants and clubs through countless parks and recreation facilities to world-class sporting and entertainment events (including the Vancouver Symphony Orchestra and the Canucks - the city's major league hockey team). Vancouver's natural surroundings offer limitless opportunities for outdoor pursuits, such as hiking and mountain biking in the Spring and Summer, and skiing at nearby Whistler-Blackcomb resort in Winter. We invite you to explore Vancouver and Beautiful British Columbia at the following web sites: - Tourism Vancouver (http://www.tourismvancouver.com) - Tourism BC (http://www.hellobc.com) ------------ About UBC Highly ranked among the world's best universities, the University of British Columbia holds an international reputation for excellence in advanced research and learning (http://www.ubc.ca/global/index.html). Only 30 minutes from the vibrant heart of downtown Vancouver, the spectacular UBC campus is a 'must-see' for any visitor of the world: snow-capped mountains can be seen meeting the ocean, and breathtaking vistas greet you around every corner. The UBC campus also boasts some of the city's best attractions and recreation facilities, including the Chan Centre for the Performing Arts (mainly music), the Museum of Anthropology, the UBC Botanical Garden, and endless opportunities to explore forested trails in the adjoining 763-hectare Pacific Spirit Regional Park. More attractions of UBC are available at http://www.attractions.ubc.ca. ------------ From owner-chemistry@ccl.net Mon Mar 31 08:44:01 2008 From: "ewe[a]inbox.ru" To: CCL Subject: CCL: L2 capsid protein of Human Papilloma virus IC50 data wanted Message-Id: <-36597-080331082900-14019-swZKIusWQsiwSs6K+Ci8+A-*-server.ccl.net> X-Original-From: ewe%x%inbox.ru Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=koi8-r Date: Mon, 31 Mar 2008 15:41:06 +0400 Mime-Version: 1.0 Sent to CCL by: ewe a inbox.ru Dear CCLers, Could you please advise me where can I find data of binding small molecules to L2 capsid protein of Human Papilloma virus. I am looking for molecular structures of inhibitors and IC50 values. Thank you in advance, Alex From owner-chemistry@ccl.net Mon Mar 31 09:19:00 2008 From: "Alex Wang yawang:_:zodiac.chem.ubc.ca" To: CCL Subject: CCL: ISTCP-VI, 19-24 July 2008 at UBC (2nd Announcement) Message-Id: <-36598-080331050621-12844-im7pgTgz6ZhUC3qV53q6aA]=[server.ccl.net> X-Original-From: Alex Wang Content-Transfer-Encoding: 8BIT Content-Type: TEXT/PLAIN; charset=ISO-8859-1 Date: Mon, 31 Mar 2008 00:39:20 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Alex Wang [yawang..zodiac.chem.ubc.ca] --------------------------------------------------------------------- PLEASE ACCEPT OUR APOLOGIES IF YOU RECEIVE THIS E-MAIL MORE THAN ONCE --------------------------------------------------------------------- ******************* SECOND ANNOUNCEMENT ******************* Sixth International Congress of the INTERNATIONAL SOCIETY FOR THEORETICAL CHEMICAL PHYSICS July 19-24, 2008 University of British Columbia, Vancouver, Canada The ISTCP-VI website (http://www.chem.ubc.ca/istcp6) has been open for registration, abstract submission, and hotel booking. In the coming weeks, please visit the ISTCP-VI website for latest updates. ------------ Dear Colleague, The Sixth Congress of the International Society for Theoretical Chemical Physics (ISTCP-VI) (http://www.chem.ubc.ca/istcp6) will be held on July 19-24, 2008 in the beautiful campus of the University of British Columbia (UBC) at Vancouver, BC, Canada. The history of ISTCP and its Congresses is available at the following link: http://www.chem.ubc.ca/istcp6/ISTCPstory.htm. Held every three years, ISTCP Congresses continue the tradition of showcasing the achievements and advances in all areas of theoretical chemical physics, with special emphasis on the interaction between experimental and theoretical physical chemistry, chemical physics, and materials and life sciences. The scope of ISTCP-VI will cover a broad range of topics that include Biophysical/Medical Simulations, Statistical Mechanics, Quantum Chemistry, Density-Functional Theory, Coupled Clusters, Quantum Monte Carlo, Quantum/Classical Dynamics, Nanosystems, Coherent Control, Ultra-cold Chemistry, AttoScience, and Novel Materials. As usual, the proceedings of the Congress will be published in the International Journal of Quantum Chemistry (IJQC) and Progress in Theoretical Chemistry and Physics (PTCP). Research papers will appear in IJQC (Wiley) while review papers will appear in PTCP (a book series published by Springer). With extensive advertising all over the world, we anticipate the total number of participants to ISTCP-VI to reach 350. This will definitely be a wonderful opportunity to know the latest cutting- edge advances in theoretical chemical physics and to network with your colleagues worldwide. Several members of the Honorary Board of Directors of ISTCP (which includes 4 Nobel Laureates and 4 Wolf Prize Awardees) have expressed their intention to attend the Congress. It is our great pleasure to invite you to join us for a five-day scientific fest at UBC during ISTCP-VI. If you would like to attend ISTCP-VI, please first register at in the "Participant" role. Then, submit your abstract at your earliest convenience at . More than one abstract can be submitted. Submitted abstracts can be revised before July 11, 2008, when all abstracts will be printed on paper. If you would like to give a contributed talk, please submit your abstract as early as possible. Then, send a request for an oral presentation to . The Congress Chair will pass your request to pertinent Symposium Organizers for consideration. If you want to pay your registration fee (in Canadian dollars) via wire transfer, please following the instruction below: . If you need an entry visa into Canada, please send the Congress Chair an email request for an invitation letter as soon as possible. With best wishes, The ISTCP-VI Executive Committee Alex Wang (Chair, UBC, Canada) Erkki J. Brändas (Co-chair, President of ISTCP, Sweden) Jean Maruani (Co-chair, France) ------------ About Vancouver Vancouver is the largest city in Western Canada, located at the south- western corner of the province of British Columbia. Situated between the north-shore and coastal mountains and the edge of the Pacific ocean, Vancouver is one of the most beautiful cities in North America, and was recently ranked as "the world's most desirable place to live" in a survey of 127 cities performed by the Intelligence Unit of the magazine The Economist. It is also the hosting city of the 2010 Olympic Winter Games. The vibrant downtown core offers all the amenities of an international destination - from hundreds of restaurants and clubs through countless parks and recreation facilities to world-class sporting and entertainment events (including the Vancouver Symphony Orchestra and the Canucks - the city's major league hockey team). Vancouver's natural surroundings offer limitless opportunities for outdoor pursuits, such as hiking and mountain biking in the Spring and Summer, and skiing at nearby Whistler-Blackcomb resort in Winter. We invite you to explore Vancouver and Beautiful British Columbia at the following web sites: - Tourism Vancouver (http://www.tourismvancouver.com) - Tourism BC (http://www.hellobc.com) ------------ About UBC Highly ranked among the world's best universities, the University of British Columbia holds an international reputation for excellence in advanced research and learning (http://www.ubc.ca/global/index.html). Only 30 minutes from the vibrant heart of downtown Vancouver, the spectacular UBC campus is a 'must-see' for any visitor of the world: snow-capped mountains can be seen meeting the ocean, and breathtaking vistas greet you around every corner. The UBC campus also boasts some of the city's best attractions and recreation facilities, including the Chan Centre for the Performing Arts (mainly music), the Museum of Anthropology, the UBC Botanical Garden, and endless opportunities to explore forested trails in the adjoining 763-hectare Pacific Spirit Regional Park. More attractions of UBC are available at http://www.attractions.ubc.ca. ------------ -- ---------------------------------------------------------------------- Yan Alexander Wang Office Rm#: Chemistry D334 Associate Professor Office Tel: (604) 822-6773 Department of Chemistry Cell Phone: (604) 816-6773 University of British Columbia Lab(s) Rm#: Chemistry D319 2036 Main Mall, Chemistry Building Lab(s) Tel: (604) 822-6549 Vancouver, BC V6T 1Z1, Canada Office Fax: (604) 822-2847 http://www.chem.ubc.ca/faculty/wang E-mail: yawang],[chem.ubc.ca "Always have compassion for others and use wisdom to deal with our own problems." -- Ven. Dr. Chan-Master Sheng-Yen (Chan: Chinese for Zen) ---------------------------------------------------------------------- From owner-chemistry@ccl.net Mon Mar 31 09:53:01 2008 From: "Maurizzio m.argonni,gmail.com" To: CCL Subject: CCL: Titration curves using Generalized Born Model Message-Id: <-36599-080331013439-29146-+tXcGZKh7cLp/NhuYTQEPQ:+:server.ccl.net> X-Original-From: Maurizzio Content-Type: multipart/alternative; boundary="----=_Part_2325_178463.1206937820364" Date: Mon, 31 Mar 2008 00:30:19 -0400 MIME-Version: 1.0 Sent to CCL by: Maurizzio [m.argonni\a/gmail.com] ------=_Part_2325_178463.1206937820364 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear CCL'ers: I would like to know if any of you is aware of free software that allows the computation of theoretical titration curves of ionizable residues in proteins using a Generalized Born approach rather than the more common Poisson-Boltzmann approach implemented in programs like UHBD and Delphi. Any help is greatly appreciated. Maurizzio ------=_Part_2325_178463.1206937820364 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
Dear CCL'ers:
 
I would like to know if any of you is aware of free software that allows the computation of theoretical titration curves of ionizable residues in proteins using a Generalized Born approach rather than the more common Poisson-Boltzmann approach implemented in programs like UHBD and Delphi. Any help is greatly appreciated.
 
Maurizzio 
------=_Part_2325_178463.1206937820364-- From owner-chemistry@ccl.net Mon Mar 31 14:00:02 2008 From: "Daniel M Oberlin dmo!=!cambridgesoft.com" To: CCL Subject: CCL: Practical optimization of FMM / Fast Multipole Method (electrostatics) Message-Id: <-36600-080331111328-17515-vj/eRwjKxq4DW6CL7oabVw]![server.ccl.net> X-Original-From: "Daniel M Oberlin" Date: Mon, 31 Mar 2008 11:13:24 -0400 Sent to CCL by: "Daniel M Oberlin" [dmo]~[cambridgesoft.com] Hello, I am interested in the fast multipole method for electrostatic calculations (FMM) in conjunction with molecular force field calculations. In particular, I am interested in the problem of optimization of the FMM function. My question is, how is optimization of FMM done in practice? Are analytical gradients calculated? And if so, has the gradient function been derived and made publicly available somewhere? Or does one use a non-gradient based approach with this function? Thank you for any information. Sincerely, Dan Daniel M. Oberlin CambridgeSoft Corporation 100 CambridgePark Drive Cambridge, MA 02140 USA 617.259.9959 dmo,cambridgesoft.com From owner-chemistry@ccl.net Mon Mar 31 19:13:00 2008 From: "Andrey.Bliznyuk++anu.edu.au" To: CCL Subject: CCL: Practical optimization of FMM / Fast Multipole Method (electrostatics) Message-Id: <-36601-080331190642-3974-YFhVYmupf9miDiQXlN/oKA(!)server.ccl.net> X-Original-From: Andrey.Bliznyuk(-)anu.edu.au Date: Tue, 01 Apr 2008 09:35:09 +1100 Sent to CCL by: Andrey.Bliznyuk ~~ anu.edu.au Hi, > My question is, how is optimization of FMM done in practice? > Are analytical gradients calculated? And if so, has the gradient > function been derived and made publicly available somewhere? > Or does one use a non-gradient based approach with this function? If I understand correctly, you want to do geometry optimisation using FMM for coulomb interactions. Yes, analytical gradients of FMM are easily obtainable. This is just gradients of the Legendre polynomials which are, naturally, Legendre polynomials. Best wishes, Andrey From owner-chemistry@ccl.net Mon Mar 31 20:35:00 2008 From: "Matt James Ketterer mkettere]![iupui.edu" To: CCL Subject: CCL: Modifying Tinker parameter sets for zinc ion (amber99 or charm27) Message-Id: <-36602-080331203229-17881-peO8DNXTfkuKFE3gubr40g++server.ccl.net> X-Original-From: "Matt James Ketterer" Date: Mon, 31 Mar 2008 20:32:25 -0400 Sent to CCL by: "Matt James Ketterer" [mkettere^^^iupui.edu] Hello all. I am trying to run the various programs in Tinker on zinc metallo betalactamase, and am having trouble reading or manually inserting the zinc ion (or any metal ion) into the active site to run calculations. I have tried editing of xyz files manually to include the metal ion parameter set number but Tinker still would not read it or perform calculations. I don't know if the parameter sets which include the zinc or Mg+ or other ions (amber99 or charmm27)have been implemented in Tinker or if the current version of the program is equipped to handle all of the atoms in the parameter sets. Currently I have tried the amber99 and charmm27 parameter sets, and have manually entered the coordinates to the xyz file with the proper format and atom number but to no avail. I have also tried to use the xyzedit.x program to insert the zinc ion, also without progress. Also, I wasn't sure if the sequence file generated with the protein file needs to include a general metal ion code such as MTL to recognize the metal. Any help would be greatly appreciated. Thanks Matt Ketterer mkettere#%#iupui.edu From owner-chemistry@ccl.net Mon Mar 31 21:14:00 2008 From: "Guanna Li gnli ~ dicp.ac.cn" To: CCL Subject: CCL: emission spectrum Message-Id: <-36603-080331021741-1695-AQDUuR9hH5kaAmUZ4I0wOA^server.ccl.net> X-Original-From: "Guanna Li" Content-Transfer-Encoding: base64 Content-Type: text/plain; charset="gb2312" Date: Mon, 31 Mar 2008 14:16:16 +0800 Mime-Version: 1.0 Sent to CCL by: "Guanna Li" [gnli{=}dicp.ac.cn] RGVhciBSYWppo6wNCnlvdSB0YWxrZWQgYWJvdXQgdGhlIHN0ZXAgdG8gY2FsY3VsYXRlIGVtaXNz aW9uIHNwZWN0cnVtLg0KSWYgZ2F1c3NpYW52aWV3IGNhbiBkcmF3IHRoZSBzcGVjdHJ1bSBkaXJl Y3RseT8NCm9yIHNob3VsZCB3ZSBuZWVkIG90aGVyIHByb2dyYW0gdG8gZGVhbCB3aXRoIHRoZSBk YXRhPw0KVGhhbmsgeW91ISANCiAJCQkJDQpCZXN0IHdpc2hlcyANCkd1YW5uYSBMaQ0KIA0K