From owner-chemistry@ccl.net Thu Nov 17 10:11:00 2011 From: "Saman Mandegar mandegar_saman::yahoo.com" <owner-chemistry*server.ccl.net> To: CCL Subject: CCL: StateAveraged CASSCF calculations Message-Id: <-45891-111117100816-9216-1UUDijLvccfrVJX/Tu2A2Q*server.ccl.net> X-Original-From: "Saman Mandegar" <mandegar_saman..yahoo.com> Date: Thu, 17 Nov 2011 10:08:13 -0500 Sent to CCL by: "Saman Mandegar" [mandegar_saman[]yahoo.com] Dear All, I would be very happy to have the ideas about state average calculations in CASSCF. I am not pretty sure why state average calculations are done. What is the reason? Why it is necessary for excited state computations? And how we determine the weighting factor for each state for example in SA3-CAS(4,3) calculation? Any help and pointer to literature is greatly appreciated. Regards, Saman From owner-chemistry@ccl.net Thu Nov 17 11:56:01 2011 From: "Yavuz Dede dede|,|gazi.edu.tr" <owner-chemistry|a|server.ccl.net> To: CCL Subject: CCL: StateAveraged CASSCF calculations Message-Id: <-45892-111117115325-21398-s6+p1fC1wbMPMvr+t8SAow|a|server.ccl.net> X-Original-From: Yavuz Dede <dede*o*gazi.edu.tr> Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 17 Nov 2011 18:53:06 +0200 MIME-Version: 1.0 Sent to CCL by: Yavuz Dede [dede_-_gazi.edu.tr] Saman, I've recently given the very first reference by Ruedenberg at CCL. See http://www.ccl.net/cca/archived-messages/11/11/03 Also on SA checking work of Jurgen Hinze can help. Moreover reviews of late Prof. Bj�rn O. Roos, In Adv. Chem. Phys. are nice sources for CASSCF and CASPT2. As to the weighing factor, there is no exact answer, it needs experimentation; however one usually has no idea about proper weights beforehand and in those cases equal weights for all states is the first choice. But you have to be consistent in SAing among different species; i.e. use the same weight for all. BTW 4e in 3o is too small of an active space. Best, Yavuz On 17.11.2011 17:08, Saman Mandegar mandegar_saman::yahoo.com wrote: > Sent to CCL by: "Saman Mandegar" [mandegar_saman[]yahoo.com] > > Dear All, > > I would be very happy to have the ideas about state average calculations in CASSCF. I am not pretty sure why state average calculations are done. What is the reason? Why it is necessary for excited state computations? And how we determine the weighting factor for each state for example in SA3-CAS(4,3) calculation? Any help and pointer to literature is greatly appreciated. > > Regards, > Saman> > > From owner-chemistry@ccl.net Thu Nov 17 12:53:01 2011 From: "Yawen Li yl6c2|a|mail.missouri.edu" <owner-chemistry*|*server.ccl.net> To: CCL Subject: CCL: a question about making a parm file containing damino acids with LEaP Message-Id: <-45893-111117125007-30282-lbfEz6gawauIZ6g78jPxAA*|*server.ccl.net> X-Original-From: "Yawen Li" <yl6c2[a]mail.missouri.edu> Date: Thu, 17 Nov 2011 12:50:04 -0500 Sent to CCL by: "Yawen Li" [yl6c2-#-mail.missouri.edu] Hi, I am a beginner of the AMBER program. In the molecule I want to study, there is several D amino acids. But it seems to me that "source leaprc.ff99SB" do not have any D amino acids. How can I fix this problem and generate AMBER topology and coordinate files correctly? By the way, I have to run the AMBER program on a university server, which means I have limited authority to modify the program. If it's possible, can anyone tell me how to fix this under my working directory. Thanks a lot, Yawen Li Email: yl6c2~~mail.missouri.edu From owner-chemistry@ccl.net Thu Nov 17 13:27:00 2011 From: "Partha P Kundu partha1kundu[A]yahoo.com" <owner-chemistry()server.ccl.net> To: CCL Subject: CCL:G: Fragment calculation Message-Id: <-45894-111117131216-31274-swQmpcoCH44LJO6MEE4Amw()server.ccl.net> X-Original-From: "Partha P Kundu" <partha1kundu[]yahoo.com> Date: Thu, 17 Nov 2011 13:12:13 -0500 Sent to CCL by: "Partha P Kundu" [partha1kundu=-=yahoo.com] Dear All, I want to optimize a structure with different charge on different parts of system. Is it possible to do in Gaussian 03? Thanks in advance. Partha. From owner-chemistry@ccl.net Thu Nov 17 14:03:00 2011 From: "Johannes Hachmann jh .. chemistry.harvard.edu" <owner-chemistry---server.ccl.net> To: CCL Subject: CCL: StateAveraged CASSCF calculations Message-Id: <-45895-111117120650-5040-DLlIbQYtBjb3CmQ29WzH5w---server.ccl.net> X-Original-From: "Johannes Hachmann" <jh##chemistry.harvard.edu> Content-Language: en-us Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 17 Nov 2011 12:06:32 -0500 MIME-Version: 1.0 Sent to CCL by: "Johannes Hachmann" [jh(-)chemistry.harvard.edu] Hi Saman, If you try to obtain an excited state in a variational method you often get root-flipping, i.e., your optimization collapses down to the ground state. In certain cases you can utilize spin or spatial symmetry constraints to prevent this but otherwise this is a touch problem. If you take a ground state result and assume that the higher roots are the excited states it leads to bad excitation energies because the expansion is tailored towards one state and may not represent the other states well, which leads to an unbalanced description. Therefore, the weights should be chosen according to what you want to get out of your calc. There is a way around root-flipping which is described here: http://jcp.aip.org/resource/1/jcpsa6/v127/i8/p084109_s1 This paper also contains useful references. Helgaker's 'Molecular Electronic-Structure Theory' book discusses this in some technical detail as well, if I remember correctly. Best wishes Johannes ----------------------------------------------- Dr. Johannes Hachmann Postdoctoral Fellow Aspuru-Guzik Research Group Harvard University Department of Chemistry and Chemical Biology 12 Oxford St, Rm M104A Cambridge, MA 02138 USA eMail: jh _ chemistry.harvard.edu ----------------------------------------------- > -----Original Message----- > From: owner-chemistry+jh==chemistry.harvard.edu _ ccl.net > [mailto:owner-chemistry+jh==chemistry.harvard.edu _ ccl.net] On Behalf > Of Saman Mandegar mandegar_saman::yahoo.com > Sent: Thursday, November 17, 2011 10:08 > To: Hachmann, Johannes > Subject: CCL: StateAveraged CASSCF calculations > > > Sent to CCL by: "Saman Mandegar" [mandegar_saman[]yahoo.com] > > Dear All, > > I would be very happy to have the ideas about state average > calculations in CASSCF. I am not pretty sure why state average > calculations are done. What is the reason? Why it is necessary for > excited state computations? And how we determine the weighting > factor for each state for example in SA3-CAS(4,3) calculation? Any > help and pointer to literature is greatly appreciated. > > Regards, > Saman > > > > -= 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/ From owner-chemistry@ccl.net Thu Nov 17 21:09:01 2011 From: "Jan Labanowski janl-x-speakeasy.net" <owner-chemistry * server.ccl.net> To: CCL Subject: CCL: Therapeutic applications of computational chemistry and biology (TACBAC) Message-Id: <-45896-111117210735-369-y2RAov7lXznk/RfsddWfXw * server.ccl.net> X-Original-From: Jan Labanowski <janl . speakeasy.net> Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Thu, 17 Nov 2011 21:07:27 EST MIME-Version: 1.0 Sent to CCL by: Jan Labanowski [janl^speakeasy.net] Subject: Fwd: Therapeutic applications of computational chemistry and biology (TACBAC) Wellcome Trust meeting on Therapeutic applications of computational chemistry and biology (TACBAC) WT Conference Centre, near Cambridge (UK) 12-14 March 2012 https://registration.hinxton.wellcome.ac.uk/display_info.asp?id=263 The conference will take place at the WT Conference Centre, near Cambridge (UK) on the 12-14 March 2012. This conference will bring together leading researchers investigating computational chemistry and biology techniques as applied to advancing our ability to predict, diagnose and modulate human disease. This broad and multidisciplinary meeting will explore the major challenges in drug discovery and development where innovation in computational approaches and tools can really make a significant and tangible contribution towards novel treatments. Each of the sessions, which progress from identifying disease mechanisms to implementing new therapeutic and diagnostic approaches in the clinic, will bring together experts in both the biomedical and the computational aspects of the topic under discussion. Session topics * Clinical implications of individual genomes * Metabolism and biomarkers * Computational systems biology * Discovery of chemical probes * Modelling xenobiotic metabolism Scientific Programme Committee: Lee Harland, Pfizer, UK John Overington, EMBL-European Bioinformatics Institute, Hinxton, UK Christoph Steinbeck, EMBL-European Bioinformatics Institute, Hinxton, UK Speakers include: Chas Bountra, Structural Genomics Consortium, UK Paul Flicek, EMBL-European Bioinformatics Institute, Hinxton, UK Ronald Frank, Helmholtz Centre for Infection Research, Germany Bobby Glen, University of Cambridge, UK Roy Goodacre, University of Manchester, UK Jules Griffin, University of Cambridge, UK Lee Harland, Pfizer, UK Aroon Hingorani, University College London, UK John Overington, EMBL-European Bioinformatics Institute, Hinxton, UK Julio Saez-Rodriguez, EMBL-European Bioinformatics Institute, Hinxton, UK Christoph Steinbeck, EMBL-European Bioinformatics Institute, Hinxton, UK Olivier Tabourieau, Center for Biological Sequence Analysis, Denmark For more details, please view the the conference website: https://registration.hinxton.wellcome.ac.uk/display_info.asp?id=263