From owner-chemistry@ccl.net Wed Jan 25 02:08:00 2006 From: "Marc Baaden baaden#smplinux.de" To: CCL Subject: CCL: Assessment of the quality of a Homology Model Message-Id: <-30613-060125015914-10202-NTUNpc5PjXoJlHlL7cdmaA:-:server.ccl.net> X-Original-From: Marc Baaden Content-Type: text/plain; charset=us-ascii Date: Wed, 25 Jan 2006 07:10:39 +0100 Mime-Version: 1.0 Sent to CCL by: Marc Baaden [baaden^_^smplinux.de] Hi Christofer, if computing time is not critical, you could use molecular dynamics to try and distinguish between homology models. For an example comparison of several quality assessment methods and behaviour in molecular dynamics simulations, please have a look at [1]. Several experimental structures and homology models of membrane proteins were taken as a test set there. I also attach the abstract below. In particular in some cases MD simulation was able to distinguish between homology models where the protein quality checkers yielded inconclusive results. Regards, Marc Baaden [1] Membrane protein structure quality in molecular dynamics simulation Journal of Molecular Graphics and Modelling, 24 (2005) 157-165 Law, R.J.; Capener, C.; Baaden, M.; Bond, P.J.; Campbell, J.; Patargias, G.; Arinaminpathy, Y.; Sansom, M.S.P. Abstract: Our goal was to assess the relationship between membrane protein quality, output from protein quality checkers and output from molecular dynamics (MD) simulations. Membrane transport proteins are essential for a wide range of cellular processes. Structural features of integral membrane proteins are still under-explored due to experimental limitations in structure determination. Computational techniques can be used to exploit biochemical and medium resolution structural data, as well as sequence homology to known structures, and enable us to explore the structure?function relationships in several transmembrane proteins. The quality of the models produced is vitally important to obtain reliable predictions. An examination of the relationship between model stability in molecular dynamics (MD) simulations derived from RMSD (root mean squared deviation) and structure quality assessment from various protein quality checkers was undertaken. The results were compared to membrane protein structures, solved at various resolution, by either X-ray or electron diffraction techniques. The checking programs could predict the potential success of MD in making functional conclusions. MD stability was shown to be a good indicator for the quality of structures. The quality was also shown to be dependent on the resolution at which the structures were determined. >>> "Christofer Tautermann hannyho*_*yahoo.com" said: >> I am builing homology models of proteins (using different programs - e.g. M odeller, MOE) by comparative modeling. The output is a huge amount of mode ls for the same protein - but the difficulty is to find the "best" structu re which is closest to the target. I am using several protein-structure ch ecks (WhatCheck, procheck, ...) and they help to discard some unreasonable models, but they don't help finding the best model. >> Are there any proposals how to pick the model which is closest to the nativ e structure - or at least some of the "better" models? -- Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris mailto:baaden]=[smplinux.de - http://www.baaden.ibpc.fr FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217 From owner-chemistry@ccl.net Wed Jan 25 03:36:00 2006 From: "Georg Lefkidis lefkidis+/-physik.uni-kl.de" To: CCL Subject: CCL:G: AW: G: comparable software to Gaussian Message-Id: <-30614-060125033359-12758-KuhEjaYj32HnfSd5p9qGfQ::server.ccl.net> X-Original-From: "Georg Lefkidis" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 25 Jan 2006 09:30:03 +0100 MIME-Version: 1.0 Sent to CCL by: "Georg Lefkidis" [lefkidis|,|physik.uni-kl.de] Hi, MOLDEN, which is free, can be used to visualize results both from GAUSSIAN and GAMESS. Cheers Georg -- No virus found in this outgoing message. Checked by AVG Free Edition. Version: 7.1.375 / Virus Database: 267.14.22/239 - Release Date: 24/01/06 From owner-chemistry@ccl.net Wed Jan 25 05:15:00 2006 From: "Jens Thomas j.m.h.thomas.:.dl.ac.uk" To: CCL Subject: CCL:G: comparable software to Gaussian Message-Id: <-30615-060125045211-10939-rtT1OHlLGJVqBW7/EztKpA]~[server.ccl.net> X-Original-From: Jens Thomas Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 25 Jan 2006 09:03:55 +0000 MIME-Version: 1.0 Sent to CCL by: Jens Thomas [j.m.h.thomas%x%dl.ac.uk] Hi, GAMESS-UK has similar functionality to Gaussian. You can find out more at: http://www.cfs.dl.ac.uk The free CCP1GUI graphical interface can be used to drive GAMESS-UK, and can find out more about that here: http://www.cse.clrc.ac.uk/qcg/ccp1gui/index.shtml The CCP1GUI also serves as a basic GUI for Dalton, which is another very powerful QM code, which you can find out about: http://www.kjemi.uio.no/software/dalton/dalton.html I hope that helps. Best wishes, Jens H J Fan hjfan(_)pvamu.edu wrote: >Sent to CCL by: "H J Fan" [hjfan||pvamu.edu] >Hi, I once was a fan of Gaussian. Due to recent headache of License terms and extra long delay from Gaussian, I am seeking the advice on comparable software that I can purchase to do the similar calculations with a decent graphic interface. > >I am aware of free GAMESS but it lacks of graphic interface. Does MWCHEM have an interface? From Gaussian website, it has a price tag about 7,000 total for site license of both Gaussian and GView together. With that price, what kind of software can I buy? even better with site license though not necessary. > >Not to offend other Gaussian fan, here is the story: Gaussian basically reject my purchase order because there are some typical words on the back of the purchase order, called terms. They want my school to sign a blank agreement about license terms, and I am sure that freaks out my officials since normally, when they put in an order, nobody makes such a big fuss about what's written behind the purchase order, since the terms behind has no conflict with whatever the company wants. With this blank term asked by Gaussian, my purchase order has been stuck somewhere since Nov 26, last year. Unlike Spartan, once I scan the order to them, I got the software two days later, no questions asked. And I can assure everyone out there, I have no intention to do anything illegal about Spartan with or without terms behind the purchase order. > >Remembered a big hot discussion about Gaussian not so far ago. SIGH... I really should have listened. So I am looking for advice on the softare to spend this 7,000, probably more. Thanks in advance.> > > > > > From owner-chemistry@ccl.net Wed Jan 25 05:50:00 2006 From: "Joop van Lenthe joop[A]chem.uu.nl" To: CCL Subject: CCL:G: comparable software to Gaussian Message-Id: <-30616-060125052012-17079-+PuBWMeW6n3BXZDYsiUzyw||server.ccl.net> X-Original-From: Joop van Lenthe Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Wed, 25 Jan 2006 10:18:00 +0100 Mime-Version: 1.0 (Apple Message framework v623) Sent to CCL by: Joop van Lenthe [joop{}chem.uu.nl] GAMESS-UK (http://www.cfs.dl.ac.uk) is available, though it might be difficult to spend so much money on it (:)) There is a graphical interface; though not as smooth yet; GAMESS-US is also possible; MOLDEN can handle both (aLso GAUSSIAN) Joop On Jan 25, 2006, at 2:04, H J Fan hjfan(_)pvamu.edu wrote: > Sent to CCL by: "H J Fan" [hjfan||pvamu.edu] > Hi, I once was a fan of Gaussian. Due to recent headache of License > terms and extra long delay from Gaussian, I am seeking the advice on > comparable software that I can purchase to do the similar calculations > with a decent graphic interface. > > I am aware of free GAMESS but it lacks of graphic interface. Does > MWCHEM have an interface? From Gaussian website, it has a price tag > about 7,000 total for site license of both Gaussian and GView > together. With that price, what kind of software can I buy? even > better with site license though not necessary. > > Not to offend other Gaussian fan, here is the story: Gaussian > basically reject my purchase order because there are some typical > words on the back of the purchase order, called terms. They want my > school to sign a blank agreement about license terms, and I am sure > that freaks out my officials since normally, when they put in an > order, nobody makes such a big fuss about what's written behind the > purchase order, since the terms behind has no conflict with whatever > the company wants. With this blank term asked by Gaussian, my purchase > order has been stuck somewhere since Nov 26, last year. Unlike > Spartan, once I scan the order to them, I got the software two days > later, no questions asked. And I can assure everyone out there, I have > no intention to do anything illegal about Spartan with or without > terms behind the purchase order. > > Remembered a big hot discussion about Gaussian not so far ago. SIGH... > I really should have listened. So I am looking for advice on the > softare to spend this 7,000, probably more. Thanks in advance.> To recover the email address of the author of the message, please > change> > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+ > > > ========================================= Joop van Lenthe Theoretical Chemistry Group Debye Institute, Utrecht University Padualaan 8 3584 CH Utrecht -31-30-2532733 joop++chem.uu.nl ========================================= From owner-chemistry@ccl.net Wed Jan 25 06:24:00 2006 From: "alexAlex Allardyce aa+*+chemaxon.hu" To: CCL Subject: CCL: ChemAxon UGM - Changed dates - Now June 7-8th, 2006 Message-Id: <-30617-060125052802-21240-V2WeDp11svQWSImyjMy7BQ+/-server.ccl.net> X-Original-From: "alexAlex Allardyce" Sent to CCL by: "alexAlex Allardyce" [aa===chemaxon.hu] HI, Excuse the potential confusion (and cross postings) but due to a conflict with another event we have moved the dates of ChemAxon's User Group Meeting from May 30-31 to June 7-8th. The submission deadlines for oral and poster presentations have also been pushed back by a week or so. Sorry for the confusion this may have caused and look forward to seeing you here. Cheers Alex For more information please visit: http://www.chemaxon.com/UGM/06/index.html For registration and presentation submission form please visit: http://www.chemaxon.com/forum/ftopic272.html For guidance for presentations please visit: http://www.chemaxon.com/forum/ftopic295.html To review our 2005 meeting please visit: http://www.chemaxon.com/UGM/05/index.html -- Alex Allardyce Communications Director From owner-chemistry@ccl.net Wed Jan 25 06:59:01 2006 From: "Van Dam, HJJ \(Huub\) h.j.j.vandam%x%dl.ac.uk" To: CCL Subject: CCL:G: comparable software to Gaussian Message-Id: <-30618-060125061209-13127-tatV8gHZNRGipFY09pUyTA ~~ server.ccl.net> X-Original-From: "Van Dam, HJJ \(Huub\)" Content-Class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 25 Jan 2006 10:23:59 -0000 MIME-Version: 1.0 Sent to CCL by: "Van Dam, HJJ \(Huub\)" [h.j.j.vandam(~)dl.ac.uk] Hi, Indeed NWChem has a graphical user interface called ECCE. Have a look at http://ecce.emsl.pnl.gov/ for details. One of the particulary nice things about it is that once you have configured it to access your user accounts on various machines you can submit calculations directly from within ECCE to a wide variety of machines and batch systems and ECCE will keep track of the status of your job and bring back any results automatically as soon as they are available (i.e. while your job is running). This saves a lot of monkey work copying inputs and outputs all over the place and editing jobscripts. All this aside from the EMSL basis set library that comes with it and the visualisation capabilities. I think the package is well worth trying. Best wishes, Huub ========================================================== Huub van Dam (h.j.j.vandam\a/dl.ac.uk, +44-1925-603933) ========================================================== -----Original Message----- > From: owner-chemistry\a/ccl.net [mailto:owner-chemistry\a/ccl.net] Sent: 25 January 2006 01:16 To: Vandam, Huub Subject: CCL:G: comparable software to Gaussian Sent to CCL by: "H J Fan" [hjfan||pvamu.edu] Hi, I once was a fan of Gaussian. Due to recent headache of License terms and extra long delay > from Gaussian, I am seeking the advice on comparable software that I can purchase to do the similar calculations with a decent graphic interface. I am aware of free GAMESS but it lacks of graphic interface. Does MWCHEM have an interface? From owner-chemistry@ccl.net Wed Jan 25 08:01:00 2006 From: "John McKelvey jmmckel_+_attglobal.net" To: CCL Subject: CCL:G: comparable software to Gaussian Message-Id: <-30619-060125071519-27578-RskwDL5m84iMU4+dJSUSIw/a\server.ccl.net> X-Original-From: John McKelvey Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 25 Jan 2006 07:10:49 -0500 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel(-)attglobal.net] Hello, There is an additional free very good QM code available that might suit some of your needs, ORCA. It follows many of the concepts in Turbomole, and is _very_ easy to use, is fast, and the documentation is good. Do a Google on 'Frank Neese' who wrote ORCA. John McKelvey H J Fan hjfan(_)pvamu.edu wrote: >Sent to CCL by: "H J Fan" [hjfan||pvamu.edu] >Hi, I once was a fan of Gaussian. Due to recent headache of License terms and extra long delay from Gaussian, I am seeking the advice on comparable software that I can purchase to do the similar calculations with a decent graphic interface. > >I am aware of free GAMESS but it lacks of graphic interface. Does MWCHEM have an interface? From Gaussian website, it has a price tag about 7,000 total for site license of both Gaussian and GView together. With that price, what kind of software can I buy? even better with site license though not necessary. > >Not to offend other Gaussian fan, here is the story: Gaussian basically reject my purchase order because there are some typical words on the back of the purchase order, called terms. They want my school to sign a blank agreement about license terms, and I am sure that freaks out my officials since normally, when they put in an order, nobody makes such a big fuss about what's written behind the purchase order, since the terms behind has no conflict with whatever the company wants. With this blank term asked by Gaussian, my purchase order has been stuck somewhere since Nov 26, last year. Unlike Spartan, once I scan the order to them, I got the software two days later, no questions asked. And I can assure everyone out there, I have no intention to do anything illegal about Spartan with or without terms behind the purchase order. > >Remembered a big hot discussion about Gaussian not so far ago. SIGH... I really should have listened. So I am looking for advice on the softare to spend this 7,000, probably more. Thanks in advance.> > > > > > From owner-chemistry@ccl.net Wed Jan 25 08:36:00 2006 From: "Pradipta Bandyopadhyay pradipta_._iitg.ernet.in" To: CCL Subject: CCL: Experience with SGI Prism ! Message-Id: <-30620-060125081818-21345-dSTmc4k7q7/tZkHuJp78Ew(!)server.ccl.net> X-Original-From: "Pradipta Bandyopadhyay" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Wed, 25 Jan 2006 18:32:01 +0530 (IST) MIME-Version: 1.0 Sent to CCL by: "Pradipta Bandyopadhyay" [pradipta#,#iitg.ernet.in] Hello, Does anyone have experience with the performance with SGI prism (dual processor) as a number cruncher? Also, I am looking for some multiple processor machine with a budget of about US $25,000 - I will do both QM and MD. I would greatly appreciate any suggestion. thanks, Pradipta Dr. Pradipta Bandyopadhyay Assistant Professor Dept. of Biotechnology Indian Institute of Technology, Guwahati Phone: 91-361-258-2213 (office) e-mail: pradipta]=[iitg.ernet.in web: http://202.141.80.5/~pradipta/Pradipta.htm ----------------------------------------------------------------------------------- This email was sent from IIT Guwahati Webmail. If you are not the intended recipient, please contact the sender by email and delete all copies; your cooperation in this regard is appreciated. http://www.iitg.ernet.in From owner-chemistry@ccl.net Wed Jan 25 09:10:00 2006 From: "zhendong zhao zzhao_-_olemiss.edu" To: CCL Subject: CCL:G: comparable software to Gaussian Message-Id: <-30621-060125021003-13085-0vQ6yv7Ss0c1s1uTl02vTQ_._server.ccl.net> X-Original-From: zhendong zhao Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Tue, 24 Jan 2006 23:40:54 -0600 Mime-Version: 1.0 (Apple Message framework v746.2) Sent to CCL by: zhendong zhao [zzhao:-:olemiss.edu] Which program suite is suitable for you depends on your specific research purpose. Now gamess does has a GUI, which is called ghemical- gms. the GUI has win/linux/mac distributions. Please check gamess web for more information. On Jan 24, 2006, at 6:49 PM, H J Fan hjfan(_)pvamu.edu wrote: > Sent to CCL by: "H J Fan" [hjfan||pvamu.edu] > Hi, I once was a fan of Gaussian. Due to recent headache of License > terms and extra long delay from Gaussian, I am seeking the advice > on comparable software that I can purchase to do the similar > calculations with a decent graphic interface. > > I am aware of free GAMESS but it lacks of graphic interface. Does > MWCHEM have an interface? From Gaussian website, it has a price tag > about 7,000 total for site license of both Gaussian and GView > together. With that price, what kind of software can I buy? even > better with site license though not necessary. > > Not to offend other Gaussian fan, here is the story: Gaussian > basically reject my purchase order because there are some typical > words on the back of the purchase order, called terms. They want my > school to sign a blank agreement about license terms, and I am sure > that freaks out my officials since normally, when they put in an > order, nobody makes such a big fuss about what's written behind the > purchase order, since the terms behind has no conflict with > whatever the company wants. With this blank term asked by Gaussian, > my purchase order has been stuck somewhere since Nov 26, last year. > Unlike Spartan, once I scan the order to them, I got the software > two days later, no questions asked. And I can assure everyone out > there, I have no intention to do anything illegal about Spartan > with or without terms behind the purchase order. > > Remembered a big hot discussion about Gaussian not so far ago. > SIGH... I really should have listened. So I am looking for advice > on the softare to spend this 7,000, probably more. Thanks in advance. > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, please > change> Conferences: http://server.ccl.net/chemistry/announcements/ > conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+-+ > > > > From owner-chemistry@ccl.net Wed Jan 25 09:45:00 2006 From: "Anastasios Papadopoulos anastp,,chem.auth.gr" To: CCL Subject: CCL:G: UV calculations with Gaussian Message-Id: <-30622-060125050434-12241-Y9sSeX/zCIETYgGBO1XmDA#server.ccl.net> X-Original-From: Anastasios Papadopoulos Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-7 Date: Wed, 25 Jan 2006 11:17:55 +0200 MIME-Version: 1.0 Sent to CCL by: Anastasios Papadopoulos [anastp,+,chem.auth.gr] Dear CCL users, I am running UV calculations of Ag,Cu clusters in Gaussian 03,using BP86/lanl2dz method. All calculations abnormally end during link l914 without any error message. Could anybody inform me about the causes of this problem? Yours, Tasos G. Papadopoulos From owner-chemistry@ccl.net Wed Jan 25 10:20:00 2006 From: "Delphine Picot delphine[]dcmr.polytechnique.fr" To: CCL Subject: CCL:G: Fukui Indices Message-Id: <-30623-060125055238-2751-61ExEcgEI6Yy2M6+alOZKA!A!server.ccl.net> X-Original-From: "Delphine Picot" Sent to CCL by: "Delphine Picot" [delphine- -dcmr.polytechnique.fr] Hello, I am interested in the calculation of condensed-to-atom Fukui functions for small molecules calculated with Gaussian 03. The literature reports the modification of the MulPop link 601 of the software to have them directly reported in the outputs (R.R.Contreras et al., Chem. Phys. Lett. 1999, 304,405) This seems a little difficult for me and I was wondering if anyone has found another way to calculate them (use of another software compatible with gaussian outputs, Perl Script...) I would be grateful about any idea and help on this. Delphine Picot From owner-chemistry@ccl.net Wed Jan 25 10:55:00 2006 From: "neese|a|dsa.mpi-muelheim.mpg.de neese|a|dsa.mpi-muelheim.mpg.de" To: CCL Subject: CCL:G: comparable software to Gaussian Message-Id: <-30624-060125022458-26576-TSDWckBdIQD+18WJ0711Mw%server.ccl.net> X-Original-From: "neese~!~dsa.mpi-muelheim.mpg.de" Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=iso-8859-1 Date: Wed, 25 Jan 2006 01:28:25 -0500 MIME-Version: 1.0 Sent to CCL by: "neese-#-dsa.mpi-muelheim.mpg.de" [neese-#-dsa.mpi-muelheim.mpg.de] Dear H J Fan, you are invited to use the ORCA software which will cost you nothing. It can be downloaded from the homepage of the Max Planck institute for bioinorganic chemistry (http://ewww.mpi-muelheim.mpg.de/bac/index_en.php go to "download area"). It is easy to use and connects to several free graphics programs. It does not, however, have everything that gaussian has. All the best, Frank Original Message: ----------------- > From: H J Fan hjfan(_)pvamu.edu owner-chemistry||ccl.net Date: Tue, 24 Jan 2006 20:03:45 -0500 To: neese||mpi-muelheim.mpg.de Subject: CCL:G: comparable software to Gaussian Sent to CCL by: "H J Fan" [hjfan||pvamu.edu] Hi, I once was a fan of Gaussian. Due to recent headache of License terms and extra long delay from Gaussian, I am seeking the advice on comparable software that I can purchase to do the similar calculations with a decent graphic interface. I am aware of free GAMESS but it lacks of graphic interface. Does MWCHEM have an interface? From Gaussian website, it has a price tag about 7,000 total for site license of both Gaussian and GView together. With that price, what kind of software can I buy? even better with site license though not necessary. Not to offend other Gaussian fan, here is the story: Gaussian basically reject my purchase order because there are some typical words on the back of the purchase order, called terms. They want my school to sign a blank agreement about license terms, and I am sure that freaks out my officials since normally, when they put in an order, nobody makes such a big fuss about what's written behind the purchase order, since the terms behind has no conflict with whatever the company wants. With this blank term asked by Gaussian, my purchase order has been stuck somewhere since Nov 26, last year. Unlike Spartan, once I scan the order to them, I got the software two days later, no questions asked. And I can assure everyone out there, I have no intention to do anything illegal about Spartan with or without terms behind the purchase order. Remembered a big hot discussion about Gaussian not so far ago. SIGH... I really should have listened. So I am looking for advice on the softare to spend this 7,000, probably more. Thanks in advance.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt-------------------------------------------------------------------- mail2web - Check your email from the web at http://mail2web.com/ . From owner-chemistry@ccl.net Wed Jan 25 11:30:05 2006 From: "Angel Rubio arubio{=}ehu.es" To: CCL Subject: CCL: TDDFT school and workshop, 27th-Aug-11th Sep (2006), Benasque (SPAIN) Message-Id: <-30625-060125063350-30337-AreCK9YjsV+Rt9KGX3AzSg_+_server.ccl.net> X-Original-From: "Angel Rubio" Sent to CCL by: "Angel Rubio" [arubio%ehu.es] SECOND: Psi-k/NANOQUANTA SCHOOL + WORKSHOP PROPOSAL Time-Dependent Density-Functional Theory: Prospects and Applications August 27th to September 11th 2006 Benasque Center for Physics, Spain http://benasque.ecm.ub.es/2006tddft/2006tddft.htm Organizers: *) E. K. U. Gross Institut fuer Theoretische Physik, Freie Universitaet Berlin Arnimallee 14, D-14195 Berlin, Germany *) Miguel A. L. Marques and Fernando Nogueira Dep. de Fsica, Faculdade de Cincias e Tecnologia, Universidade de Coimbra and Centro de Fsica Computacional Rua Larga, 3004-516 Coimbra, Portugal *) Angel Rubio Dpto. Fisica de Materiales, Facultad de Quimicas U. Pais Vasco, 20018 San Sebastian/Donostia, Spain History and Scientific motivation: --------------------------------- The first School and workshop was hosted by the Benasque Center for Science, Spain from August 28th to September 12th, 2004. The aim of the school was to introduce theoretical, practical, and numerical aspects of time-dependent density-functional theory (TDDFT) to young graduate students, post-docs and even older scientists that are envisaging a project for which TDDFT would be the tool of choice. The use of TDDFT is increasing, and it is fast becoming one of the tools of choice to get accurate and reliable predictions for excited-state properties in solid state physics, chemistry and biophysics, both in the linear and non-linear regimes. This interest has been motivated by the recent developments of TDDFT (and time-dependent current functional theory) and include the description of photo-absorption cross section of molecules and nanostructures, electron-ion dynamics in the excited state triggered by either a small or high intense laser fields, van der Waals interactions, development of new functionals coping with memory and non-locality effects, applications to biological systems (chromophores), transport phenomena, optical spectra of solids and low-dimensional structures (as nanotubes, polymers, surfaces...). Following our previous experience, the most efficient scheme for training of young researchers in these techniques is to have a school where the basic theory is taught followed by a workshop that introduces them to the forefront research in the field. The school should have an equal share of theoretical and practical classes. This would ease the learning of the techniques and would provide the students with the practical knowledge of the numerical aspects and difficulties, while also introducing them to well-established open source numerical codes. At the end of the school, students should have sufficient working knowledge to pursue their projects at their home institution. The school will be followed by an international workshop, where the new developments of TDDFT and Many-Body Techniques for the calculation of excitations will be discussed. Students attending the school will be encouraged to attend the workshop, so they can get in contact with state of the art research in the field. The purpose of the workshop is to bring together leading experts in all these fields with different backgrounds, like density functional, many-body, nuclear physics and quantum chemists. This will allow the exchange of ideas between the different fields and the creation of links between the traditionally separated communities. We believe that the intense and informal discussion which is possible in this kind of workshops can contribute to the formation of a strong community in the field of TDDFT. Location/Timing --------------- We plan to organize this event at the ``Benasque Center for Science'', Benasque, Spain, from August 27, 2006 to September 10, 2006. Benasque is a beautiful town in the heart of the Pyrenees. The school will take place from August 27 (Day 0 - arrival of students for the school) to September 6, and the workshop will start September 6 (arrival of participants to the workshop) and finish on September 11 (departure of all participants). See http://benasque.ecm.ub.es/. Participants ------------ The call for participation will be mainly directed to students and scientists specialized on computational physics, quantum chemistry and biophysics. We will limit the number of students to the school to 35 and participants to the workshop to less than 100, in order to ensure a maximum interaction between all the scientists participating. Attendance of graduate students and postdocs will be strongly encouraged through the inclusion of short contributed talks and a poster session. Furthermore, we will award to PhD students who present an outstanding poster short oral presentations. Applications/Support: -------------------- School/Workshop: All persons who wish to participate should fill out the application form at http://benasque.ecm.ub.es/2006tddft/2006tddft.htm In the comments section, please indicate if you wish to participate in the Summer Summer School or in the Workshop (or in both). School only: As we have a very limited number of places for the school (35), students will be selected from among an open pool of applicants who have demonstrated a strong interest in computational sciences, applied to chemistry, physics, materials science and biology. Therefore, in order that we can make a reasonable selection, we ask that *all* candidates include in the comments section the following information: *) Date of birth *) Sex *) Motivation/Why they want to come (just a couple of lines is enough) *) What is their current and previous positions (if PhD or Post- doc state your supervisor). We will *not* accept applications that do not include this information. Furthermore, we will give priority to students willing to participate in both the Summer School and the Workshop. We also have a certain number of grants available that cover traveling and part of the stay in Benasque. If you want to apply for a grant, please indicate explicitly that you wish to be supported in the comments section, and explain why (just a couple of lines is enough). For participants coming from the USA, please check the following address for support: http://www.mcc.uiuc.edu/travel/ ------------------------ P.S: Our apologies if you have received multiple copies of this announcement. From owner-chemistry@ccl.net Wed Jan 25 12:05:01 2006 From: "andras.borosy#,#givaudan.com" To: CCL Subject: CCL: Experience with SGI Prism ! Message-Id: <-30626-060125094953-7334-XOLLN/gG9BpZo48+6BN/FQ^_^server.ccl.net> X-Original-From: andras.borosy---givaudan.com Content-Type: multipart/alternative; boundary="=_alternative 005174E1C1257101_=" Date: Wed, 25 Jan 2006 15:49:43 +0100 MIME-Version: 1.0 Sent to CCL by: andras.borosy\a/givaudan.com This is a multipart message in MIME format. --=_alternative 005174E1C1257101_= Content-Type: text/plain; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable Dear Pradipta, >=20 > Does anyone have experience with the performance with SGI prism (dual > processor) as a number cruncher? Also, I am looking for some multiple > processor machine with a budget of about US $25,000 - I will do both QM > and MD. I would greatly appreciate any suggestion. I think Parallel Quantum Solution has the best price/perofrmance ratio=20 (http://www.pqs-chem.com). Regards, Dr. Andr=E1s Borosy Seniour Scientist Delivery Systems, Fragrance Research Givaudan Schweiz AG Ueberlandstr. 138 8600 D=FCbendorf Switzerland tel: + 41-1-8242164 fax: +41-1-8242926 e-mail: andras.borosy|*|givaudan.com --=_alternative 005174E1C1257101_= Content-Type: text/html; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable

Dear Pradipta,

>
>  Does anyone have experience with the performance with SGI prism (dual
> processor) as a number cruncher? Also, I am looking for some multiple<= br> > processor machine with a budget of about US $25,000 - I will do both QM
> and MD. I would greatly appreciate any suggestion.

I think Parallel Quant= um Solution has the best price/perofrmance ratio (http://www.pqs-chem.com).

Regards,

Dr. Andr=E1s Borosy
Seniour Scientist
Delivery Systems, Fragrance Research
Givaudan Schweiz AG
Ueberlandstr. 138
8600 D=FCbendorf
Switzerland
tel: + 41-1-8242164
fax: +41-1-8242926
e-mail: andras.borosy|*|givaudan.com --=_alternative 005174E1C1257101_=-- From owner-chemistry@ccl.net Wed Jan 25 13:01:00 2006 From: "Goedele Roos groos-#-vub.ac.be" To: CCL Subject: CCL:G: Fukui Indices Message-Id: <-30627-060125122243-6904-rGpBYstNKShNqp4m6kf/3Q##server.ccl.net> X-Original-From: Goedele Roos Date: Wed, 25 Jan 2006 18:22:32 +0100 (CET) Sent to CCL by: Goedele Roos [groos^^vub.ac.be] Hello, You can calculate them : Within a finite difference approximation combined with the idea of integrating the Fukui function over atomic regions one finds the condensed Fukui functions for nucleophilic and electrophilic attack on atom A having N electrons: (5) f- = qA(N0) - qA(N0-1) (6)f+ = qA(N0+1) - qA(N0) qA(N0), qA(N0+1) and qA(N0-1) are the atomic populations for atom A in the neutral molecule (N0 electrons) and the corresponding anion (N0 + 1) or cation (N0 - 1), all evaluated at the neutral (as reference) molecular geometry (cf. the demand for constant extern potential in (2)). I usually use the NPa population analysis. You can find everything in A Computational and Conceptual DFT Study of the Reactivity of Anionic Compounds: Implications for Enzymatic Catalysis G. Roos, S. Loverix F. De Proft, L. Wyns, and P. Geerlings J. Phys. Chem. A 2003, 107, 6828-6836 Best regards, Goedele >Sent to CCL by: "Delphine Picot" [delphine- -dcmr.polytechnique.fr] >Hello, > >I am interested in the calculation of condensed-to-atom Fukui functions for small molecules calculated with Gaussian 03. > >The literature reports the modification of the MulPop link 601 of the software to have them directly reported in the outputs (R.R.Contreras et al., Chem. Phys. Lett. 1999, 304,405) >This seems a little difficult for me and I was wondering if anyone has found another way to calculate them (use of another software compatible with gaussian outputs, Perl Script...) > >I would be grateful about any idea and help on this. > > >Delphine Picot> > > > Drs. Goedele Roos Dienst Algemene Chemie (ALGC) Vrije Universiteit Brussel (VUB) Pleinlaan 2 B-1050 Brussels Tel: 0032-2-629 35 16 Fax: 0032-2-629 33 17 From owner-chemistry@ccl.net Wed Jan 25 13:36:01 2006 From: "john furr john.furr[A]gmail.com" To: CCL Subject: CCL: Dynamol Update Message-Id: <-30628-060125111327-6561-/ZxpWnhJm1+i0bjWcj837w_+_server.ccl.net> X-Original-From: john furr Content-Type: multipart/alternative; boundary="----=_Part_837_9052651.1138205595542" Date: Wed, 25 Jan 2006 11:13:15 -0500 MIME-Version: 1.0 Sent to CCL by: john furr [john.furr__gmail.com] ------=_Part_837_9052651.1138205595542 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline It has been brought to my attention that I have not included install instructions for the Linux versions of Dynamol. For those that are interested: right click on the download link and choose save as: gunzip dynamol-install.gz chmod +x dynamol-install ./dynamol-intstall **Note the archive is self installing and it is important to preserve the exact name "dynamol-install" Run the last step as root to install system wide...or as a normal user for a local install. Cheers John Furr Dynamol Inc. http://www.dynamol.com john.furr * gmail.com ------=_Part_837_9052651.1138205595542 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline It has been brought to my attention that I have not included install instru= ctions for the Linux versions of Dynamol. 

For those that are interested:

right click on the download link and choose save as:

gunzip dynamol-install.gz
chmod +x dynamol-install
./dynamol-intstall

**Note the archive is self installing and it is important to preserve the exact name "dynamol-install"  Run the last step as root = to install system wide...or as a normal user for a local install.

Cheers

John Furr
Dynamol Inc.
http://www.dynamol.com
john.furr * gmail.com
------=_Part_837_9052651.1138205595542-- From owner-chemistry@ccl.net Wed Jan 25 14:11:01 2006 From: "Steve Williams willsd%appstate.edu" To: CCL Subject: CCL:G: comparable software to Gaussian Message-Id: <-30629-060125123053-21936-kZSL/ekuTsPnuIaPx8pX7A^^^server.ccl.net> X-Original-From: Steve Williams Content-transfer-encoding: 7bit Content-type: text/plain; format=flowed; charset=ISO-8859-1 Date: Wed, 25 Jan 2006 12:06:22 -0500 MIME-version: 1.0 Sent to CCL by: Steve Williams [willsd+*+appstate.edu] neese|a|dsa.mpi-muelheim.mpg.de neese|a|dsa.mpi-muelheim.mpg.de wrote: >Sent to CCL by: "neese-#-dsa.mpi-muelheim.mpg.de" [neese-#-dsa.mpi-muelheim.mpg.de] >Dear H J Fan, > >you are invited to use the ORCA software which will cost you nothing. It >can be downloaded from the homepage of the Max Planck institute for >bioinorganic chemistry (http://ewww.mpi-muelheim.mpg.de/bac/index_en.php go >to "download area"). It is easy to use and connects to several free >graphics programs. It does not, however, have everything that gaussian has. >All the best, >Frank > > Hello Frank, I'd like to try your ORCA program. What is the usual turn around time > from registering to reciept of email with the needed login and password to get to the ORCA download area? I've registered but not gotten a email with this information; I am wondering if I made some error with my registration. Steve Williams > >Original Message: >----------------- > > >>From: H J Fan hjfan(_)pvamu.edu owner-chemistry[*]ccl.net >> >> >Date: Tue, 24 Jan 2006 20:03:45 -0500 >To: neese[*]mpi-muelheim.mpg.de >Subject: CCL:G: comparable software to Gaussian > > >Sent to CCL by: "H J Fan" [hjfan||pvamu.edu] >Hi, I once was a fan of Gaussian. Due to recent headache of License terms >and extra long delay from Gaussian, I am seeking the advice on comparable >software that I can purchase to do the similar calculations with a decent >graphic interface. > >I am aware of free GAMESS but it lacks of graphic interface. Does MWCHEM >have an interface? From Gaussian website, it has a price tag about 7,000 >total for site license of both Gaussian and GView together. With that >price, what kind of software can I buy? even better with site license >though not necessary. > >Not to offend other Gaussian fan, here is the story: Gaussian basically >reject my purchase order because there are some typical words on the back >of the purchase order, called terms. They want my school to sign a blank >agreement about license terms, and I am sure that freaks out my officials >since normally, when they put in an order, nobody makes such a big fuss >about what's written behind the purchase order, since the terms behind has >no conflict with whatever the company wants. With this blank term asked by >Gaussian, my purchase order has been stuck somewhere since Nov 26, last >year. Unlike Spartan, once I scan the order to them, I got the software two >days later, no questions asked. And I can assure everyone out there, I have >no intention to do anything illegal about Spartan with or without terms >behind the purchase order. > >Remembered a big hot discussion about Gaussian not so far ago. SIGH... I >really should have listened. So I am looking for advice on the softare to >spend this 7,000, probably more. Thanks in advance.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt-------------------------------------------------------------------- >mail2web - Check your email from the web at >http://mail2web.com/ .> > > > > From owner-chemistry@ccl.net Wed Jan 25 14:46:01 2006 From: "errol lewars elewars{=}trentu.ca" To: CCL Subject: CCL:G: Fukui Indices Message-Id: <-30630-060125125422-27991-LsWdQ0RdKr34w4VoLTgh4Q-,-server.ccl.net> X-Original-From: errol lewars Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii; format=flowed Date: Wed, 25 Jan 2006 11:56:58 -0500 MIME-Version: 1.0 Sent to CCL by: errol lewars [elewars,trentu.ca] 2006 Jan 25 The calculaton and use of the Fukui functions using ordinary Gaussian output is described in "Computational Chemistry", E. Lewars, pp 431-436. E. Lewars === Delphine Picot delphine[]dcmr.polytechnique.fr wrote: >Sent to CCL by: "Delphine Picot" [delphine- -dcmr.polytechnique.fr] >Hello, > >I am interested in the calculation of condensed-to-atom Fukui functions for small molecules calculated with Gaussian 03. > >The literature reports the modification of the MulPop link 601 of the software to have them directly reported in the outputs (R.R.Contreras et al., Chem. Phys. Lett. 1999, 304,405) >This seems a little difficult for me and I was wondering if anyone has found another way to calculate them (use of another software compatible with gaussian outputs, Perl Script...) > >I would be grateful about any idea and help on this. > > >Delphine Picot> > > > > > > From owner-chemistry@ccl.net Wed Jan 25 15:21:01 2006 From: "S.I.Gorelsky gorelsky++stanford.edu" To: CCL Subject: CCL:G: Fukui Indices Message-Id: <-30631-060125132737-22044-ND5QMa9A0JucFBORaK/eFA,,server.ccl.net> X-Original-From: "S.I.Gorelsky" Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Wed, 25 Jan 2006 09:46:29 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: "S.I.Gorelsky" [gorelsky]~[stanford.edu] condensed-to-atom Fukui functions can be calculated using AOMix (http://www.sg-chem.net/aomix) from Gaussian (and other QC software) output files and visualized using UCSF Chimera. Check the AOMix manual for details. Regards, S. Gorelsky On Wed, 25 Jan 2006, Delphine Picot delphine[]dcmr.polytechnique.fr wrote: > Sent to CCL by: "Delphine Picot" [delphine- -dcmr.polytechnique.fr] > Hello, > > I am interested in the calculation of condensed-to-atom Fukui functions for small molecules calculated with Gaussian 03. > > The literature reports the modification of the MulPop link 601 of the software to have them directly reported in the outputs (R.R.Contreras et al., Chem. Phys. Lett. 1999, 304,405) > This seems a little difficult for me and I was wondering if anyone has found another way to calculate them (use of another software compatible with gaussian outputs, Perl Script...) > > I would be grateful about any idea and help on this. > > > Delphine Picot> > > ---------------------------------------------------------------- Dr S.I. Gorelsky, Department of Chemistry, Stanford University Box 155, 333 Campus Drive, Stanford, CA 94305-5080 USA Phone: (650) 723-0041. Fax: (650) 723-0852. ---------------------------------------------------------------- From owner-chemistry@ccl.net Wed Jan 25 15:55:00 2006 From: "SANDEEP KUMAR skumar23/a\jhem.jhu.edu" To: CCL Subject: CCL: Experience with SGI Prism ! Message-Id: <-30632-060125143604-6605-Dm3cfycScGxCrnSNt5I9mQ(-)server.ccl.net> X-Original-From: SANDEEP KUMAR Content-Disposition: inline Content-Language: en Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Wed, 25 Jan 2006 13:35:49 -0500 MIME-Version: 1.0 Sent to CCL by: SANDEEP KUMAR [skumar23^_^jhem.jhu.edu] Hello Pradipta: It all depends upon what kind of calculations you wish to do and also how many people you have in your group. For example, when I needed to buy a machine with multiple processors for a single user doing multiple MM/MD claculations and some QM but not very extensive, I chose a Dell Workstation instead of an SGI, mainly because its about 5X cheaper than SGI and still gives very good graphics etc. As for number crunching depends upon processor speed and here too Dell Workstation came out to be much faster. The only caveat is that Dell comes with Windows pre-installed and for our kind of work, its better to install Linux on it. So instead of one $25,000 SGI machine, one could buy 3 -5 Dell workstations, each of which perfroms better than an SGI workstation. Also, if you have bit of more money than 10 -12 lacs, its better to go with Linux clusters. You can get ~20 node linux cluster for about the same price in India. Sincerely, Sandeep ------------------------------------------------------------------- Dr. Sandeep Kumar, Associate Research Scientist, Johns Hopkins University Department of Biology, 106 Mudd Hall, 3400 N. Charles Street, Baltimore, MD 21218, USA. Phone: 410-516-8433, Email: kumarsan(-)jhu.edu. URL: http://myprofile.cos.com/Kumarsan. or https://jshare.johnshopkins.edu/skumar23/public_html/ ----- Original Message ----- > From: "Pradipta Bandyopadhyay pradipta_._iitg.ernet.in" Date: Wednesday, January 25, 2006 8:58 am Subject: CCL: Experience with SGI Prism ! > Sent to CCL by: "Pradipta Bandyopadhyay" [pradipta#,#iitg.ernet.in] > Hello, > > Does anyone have experience with the performance with SGI prism (dual > processor) as a number cruncher? Also, I am looking for some multiple > processor machine with a budget of about US $25,000 - I will do > both QM > and MD. I would greatly appreciate any suggestion. > > thanks, > > Pradipta > > > Dr. Pradipta Bandyopadhyay > Assistant Professor > Dept. of Biotechnology > Indian Institute of Technology, Guwahati > Phone: 91-361-258-2213 (office) > e-mail: pradipta ~ iitg.ernet.in > web: http://202.141.80.5/~pradipta/Pradipta.htm > > > -------------------------------------------------------------------- > --------------- > This email was sent from IIT Guwahati Webmail. If you are not the > intended recipient, please contact the sender by email and delete > all copies; your cooperation in this regard is appreciated. > http://www.iitg.ernet.in > > > > -= 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 Wed Jan 25 19:46:00 2006 From: "Dr. Peter Bladon cbas25###strath.ac.uk" To: CCL Subject: CCL: Fukui indices Message-Id: <-30633-060125184414-9890-02uYUYMEdxl9IV8LaaCfyw[*]server.ccl.net> X-Original-From: "Dr. Peter Bladon" Content-Type: multipart/alternative; boundary="------------030700030407070703020309" Date: Wed, 25 Jan 2006 22:36:49 +0000 MIME-Version: 1.0 Sent to CCL by: "Dr. Peter Bladon" [cbas25%x%strath.ac.uk] This is a multi-part message in MIME format. --------------030700030407070703020309 Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Dear Delphine, I think that what you want to calculate are the quantities such as Nucleophilic superdelocalizabities etc. The fact is that some time ago I wrote some extra code that is incorporated into MOPAC. You can get the modified MOPAC from my ftp site at: 81.178.7.83 (logon as anonymous and use your email address as password). The same ftp site is also accessible from my website (http://www.interprobe.co.uk/inter/interprobe.html) about three quarters down the home page. The MOPAC is available both for SGI machines and for Windows platforms. The calculation is initiated by putting an extra keyword (PROPER) in the keyword line. The modelling programs INTERCHEM (for SGI) and INTERCHEM-PC allow the construction of the input structures (in various ways) and direct submission to MOPAC. All this software is available from the web/ftp site and is free to academics. Yours sincerely Peter Bladon --------------030700030407070703020309 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Delphine,

I think that what you want to calculate are the quantities such as Nucleophilic superdelocalizabities etc. The fact is that some time ago I wrote some extra code that is incorporated into MOPAC.  You can get the modified MOPAC from my ftp site at: 81.178.7.83 (logon as anonymous and use your email address as password).  The same ftp site is also accessible from my website (http://www.interprobe.co.uk/inter/interprobe.html) about three quarters down the home page.

The MOPAC is available both for SGI machines and for Windows platforms.  The calculation is initiated by putting an extra keyword (PROPER) in the keyword line.

The modelling programs INTERCHEM (for SGI) and INTERCHEM-PC allow the construction of the input structures (in various ways) and direct submission to MOPAC.

All this software is available from the web/ftp site and is free to academics.

Yours sincerely

Peter Bladon

 --------------030700030407070703020309--