From owner-chemistry@ccl.net Wed Sep 28 01:43:00 2011 From: "Brian Salter-Duke b_duke]^[bigpond.net.au" To: CCL Subject: CCL: Stuttgart Pseudopotentials in GAMESS Message-Id: <-45538-110928001151-17289-WzPAl+q2ObipMAJqZsUfWA|a|server.ccl.net> X-Original-From: Brian Salter-Duke Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Wed, 28 Sep 2011 14:11:30 +1000 MIME-Version: 1.0 Sent to CCL by: Brian Salter-Duke [b_duke.^^^.bigpond.net.au] On Tue, Sep 27, 2011 at 11:37:04PM -0400, Eli Lam elizabeth.shlam . gmail.com wrote: > > Sent to CCL by: "Eli Lam" [elizabeth.shlam-$-gmail.com] > Hi all, > > I've been facing the Stuttgart Pseudopotential problems in GAMESS and have > looked into the archive dated 3 Oct, 1995 "CCL:G:Stuttgart Pseudopotentials, summary". I'm not quite understand and > would like to ask for advice. I'm trying to use the Stuttgart ECP > for Pt atom in GAMESS but it seems cannot recognize the h-ul potential. How > may I modify the ECP so as to be readable by GAMESS? You can not yet. GAMESS does not handle h orbitals or potentials. It only goes to g. Soemday, perhaps not far off, the code will be extended to h and i. Brian. > Here's the input from EMSL basis set library for Pt ECP: > > PT-ECP GEN 60 5 > 1 ----- h-ul potential ----- > 0.00000000 2 1.00000000 > 2 ----- s-ul potential ----- > 429.64608700 2 14.60450000 > 73.15688400 2 7.21828700 > 4 ----- p-ul potential ----- > 88.02291700 2 11.57716200 > 175.99819600 2 10.88384300 > 13.68227400 2 6.42440300 > 27.41465100 2 5.22419800 > 4 ----- d-ul potential ----- > 43.55785200 2 7.69961000 > 65.36910800 2 7.55080800 > 7.01859600 2 3.96116400 > 11.39173300 2 3.87277700 > 2 ----- f-ul potential ----- > 10.71022000 2 3.37986900 > 14.27812500 2 3.32625500 > 2 ----- g-ul potential ----- > -11.65174900 2 5.45202000 > -14.37552500 2 5.41258500 > > Thank you! > Yours sincerely, > Eli> -- Brian Salter-Duke (Brian Duke) 626 Melbourne Rd, Spotswood, VIC, 3015, Australia. Email: b_duke^^^bigpond.net.au Phone: 03-93992847 Web: http://www.salter-duke.bigpondhosting.com/brian/index.htm From owner-chemistry@ccl.net Wed Sep 28 02:18:00 2011 From: "veera pandian ponnuchamy veera.pandi33 ~~ gmail.com" To: CCL Subject: CCL: Problem in TDDFT Calculation Message-Id: <-45539-110928014350-28513-HOOBU2q5+Jpmx7aTq4cD2A*|*server.ccl.net> X-Original-From: "veera pandian ponnuchamy" Date: Wed, 28 Sep 2011 01:43:47 -0400 Sent to CCL by: "veera pandian ponnuchamy" [veera.pandi33()gmail.com] Hi CCLrs, I have experienced a surprise case, while calculating the percentage of contribution in TDDFT calculation. This is the output Excited State 1: 2.066-A 1.1028 eV 1124.31 nm f=0.0003 =0.817 97B -> 98B 0.99625 This state for optimization and/or second-order correction. Total Energy, E(TD-HF/TD-KS) = -1221.52573888 Copying the excited state density for this state as the 1-particle RhoCI density. Excited State 2: 2.073-A 2.0309 eV 610.49 nm f=0.0003 =0.825 96B -> 98B 0.98993 Excited State 3: 3.476-A 2.0710 eV 598.68 nm f=0.0000 =2.771 95A ->103A 0.10782 96A ->102A -0.11015 98A ->100A 0.68284 94B ->105B -0.10218 95B ->103B -0.11202 96B ->101B 0.11454 97B ->100B -0.68191 98A <-100A 0.11802 97B <-100B -0.11806 Excited State 4: 2.852-A 2.5895 eV 478.80 nm f=0.0021 =1.783 98A -> 99A 0.99481 Excited State 5: 2.171-A 2.6627 eV 465.63 nm f=0.0193 =0.928 97A -> 99A 0.77986 97A ->104A 0.12398 90B -> 98B -0.25513 92B -> 98B 0.47858 93B -> 98B -0.13269 95B -> 98B -0.15685 The above state (excited state 5) is the most probable excited state, here when I calculate the percentage of contribution using C^2*2*100 formula. I get 121% how it is possible? or am I doing anything wrong? Your help will be appreciated. Thanks in advance... Yours Veerapandian.P From owner-chemistry@ccl.net Wed Sep 28 08:19:00 2011 From: "Jan Kuras jan.kuras-$-chemistrycentral.com" To: CCL Subject: CCL: Call for papers: ACS Spring Meeting 2012, Systems chemical biology Message-Id: <-45540-110928065640-6025-g+bOJAsHUFZje39bJoPcpg]=[server.ccl.net> X-Original-From: "Jan Kuras" Date: Wed, 28 Sep 2011 06:56:36 -0400 Sent to CCL by: "Jan Kuras" [jan.kuras/a\chemistrycentral.com] Call for papers Session title: Systems chemical biology and other "systems" approaches in chemistry and biology research 243rd ACS National Meeting, San Diego, California, March 25-29, 2012 CINF Division We are accepting submission of abstracts for consideration for an ACS Division of Chemical Information (CINF) Symposium on systems-based approaches in chemistry and biology research. A systems approach to science aims to study complex networks rather than isolated entities. This goal of this symposium is to review recent developments in systems chemical biology, systems biology and systems chemistry, and examine links between them. In systems biology large networks describing the regulation of entire genomes, metabolic pathways and signal transduction pathways are analyzed in their totality at different levels of biological organization. The development of cheminformatics tools that can integrate chemical knowledge with this biological data has created an interest in systems chemical biology. Systems chemistry provides another new research area moving beyond single molecular entities to multi-component, multi-functional chemical systems to create new functions from molecular components at different hierarchical levels or via molecular networks with emergent properties. The development of these integrated systems-based approaches could improve our understanding of complex chemical and biological networks in areas as diverse as drug discovery and materials science. Presentations will be 25-30 minutes, including time for questions. The deadline for submitting an abstract for consideration is October 17, 2011. Abstracts may be submitted via: http://abstracts.acs.org. Please contact the co-organizers if you have any questions or to discuss a paper. Thank you, Tudor Oprea, Professor Biochemistry and Molecular Biology, University of New Mexico (toprea a salud.unm.edu) Jan Kuras, Journal Publisher, Chemistry Central (jan.kuras a chemistrycentral.com) ______________________ Jan Kuras Chemistry Central 236 Gray's Inn Road London WC1X 8HB, UK www.chemistrycentral.com From owner-chemistry@ccl.net Wed Sep 28 10:30:01 2011 From: "Shirley Peng speng##chemcomp.com" To: CCL Subject: CCL: Chemical Computing Group Announces the New Version of PSILO Message-Id: <-45541-110928101841-1378-jbP6fTte9h0bTMdhUivkUQ ~ server.ccl.net> X-Original-From: "Shirley Peng" Date: Wed, 28 Sep 2011 10:18:37 -0400 Sent to CCL by: "Shirley Peng" [speng-x-chemcomp.com] MONTREAL, Canada September 27, 2011 Chemical Computing Group (CCG) today announces a new version of its structure database and visualization system, PSILO, featuring new analytical tools and enhanced search capabilities. PSILO is an integrated repository for public and in-house structural data that allows easy collaboration and data sharing across organizational departments. Using a standard web browser interface, PSILOs structural data can be searched, visualized, registered, annotated and tracked. The new and enhanced features in PSILO 2011.09 include: 3D query statistical analysis tools Ligand-independent pocket similarity searches Export protein families to common reference frame Metal ion treatment as ligands The new additions demonstrate our ongoing commitment to lead the structural repository and visualization market, commented Paul Labute, president and CEO of CCG. PSILO 2011.09 incorporates an automatic process for ligand-independent pocket detection, thereby expanding the space of the searchable pocket database. Paul Labute explained, We eliminated previous pocket search constraints by implementing a pocket detection algorithm, thus providing richer query results. With a greater pool of potential binding sites, researchers are now in a better position, for example, to identify potential drug side effects or new therapeutic areas. PSILO has a simple yet powerful Google-like search bar in which multiple search criteria, such as combinations of text, sequence, 2D substructure and 3D geometry specifications, can be expressed. In PSILO 2011.09, new statistical analysis tools are available to investigate the significance of defined 3D geometric constraints within PDB and in-house structural data. Paul Labute said, The ability to understand the statistical relevance of protein-ligand or protein-protein interaction motifs using scatter plots, histograms, or sorting by constraint values will allow researchers to make more informed decisions about critical interactions and to facilitate drug design. In this new version of PSILO, metal ions are treated as ligands making it possible to visualize ligand interaction diagrams for metals and to perform 3D/2D metal ion searches. Non-standard amino acids can also be searched. Another addition to PSILO 2011.09 is the ability to choose a family reference frame when exporting hit lists. This ability to select reference orientations allows scientists to easily compare project structures, helping identify relevant interactions to be considered in drug development. For additional information about PSILO please contact: sales+/-chemcomp.com About Chemical Computing Group Chemical Computing Group (CCG) is a leading supplier of software solutions for life sciences. CCG has been in business since 1994, always providing state of the art applications in drug discovery to pharmaceutical, biotechnology and academic researchers. CCGs products and services are used by biologists, medicinal chemists and computational chemists throughout the world. Chemical Computing Group has a proven track record in scientific innovation, consistently producing releases and upgrades for their products. CCG has a very strong reputation for collaborative scientific support, maintaining support offices in both Europe and North America. CCG headquarters is in Montreal, Canada. For more information visit: www.chemcomp.com For additional information please contact: Raul Alvarez | Senior Marketing Manager | (514) 393-1055 | Info+/-chemcomp.com From owner-chemistry@ccl.net Wed Sep 28 14:02:00 2011 From: "Van Dam, Hubertus J HubertusJJ.vanDam-,-pnnl.gov" To: CCL Subject: CCL: Problem in TDDFT Calculation Message-Id: <-45542-110928140044-17092-M1MiMgXOKAYoHhZlu/pFeA|*|server.ccl.net> X-Original-From: "Van Dam, Hubertus J" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 28 Sep 2011 10:59:48 -0700 MIME-Version: 1.0 Sent to CCL by: "Van Dam, Hubertus J" [HubertusJJ.vanDam[*]pnnl.gov] Hi Veerapandian, The output lists every excitation separately (excitations of alpha electrons are labeled "A" and beta electrons "B"). Hence the excitation 97A -> 99A contributes only once and not twice. So adapting your description you should use the formula C^2*100 which gives you approximately 61% and your mystery is resolved. Best wishes, Huub -----Original Message----- > From: owner-chemistry+hubertus.vandam==pnnl.gov!=!ccl.net [mailto:owner-chemistry+hubertus.vandam==pnnl.gov!=!ccl.net] On Behalf Of veera pandian ponnuchamy veera.pandi33 ~~ gmail.com Sent: Tuesday, September 27, 2011 10:44 PM To: Van Dam, Hubertus J Subject: CCL: Problem in TDDFT Calculation Sent to CCL by: "veera pandian ponnuchamy" [veera.pandi33()gmail.com] Hi CCLrs, I have experienced a surprise case, while calculating the percentage of contribution in TDDFT calculation. This is the output Excited State 1: 2.066-A 1.1028 eV 1124.31 nm f=0.0003 =0.817 97B -> 98B 0.99625 This state for optimization and/or second-order correction. Total Energy, E(TD-HF/TD-KS) = -1221.52573888 Copying the excited state density for this state as the 1-particle RhoCI density. Excited State 2: 2.073-A 2.0309 eV 610.49 nm f=0.0003 =0.825 96B -> 98B 0.98993 Excited State 3: 3.476-A 2.0710 eV 598.68 nm f=0.0000 =2.771 95A ->103A 0.10782 96A ->102A -0.11015 98A ->100A 0.68284 94B ->105B -0.10218 95B ->103B -0.11202 96B ->101B 0.11454 97B ->100B -0.68191 98A <-100A 0.11802 97B <-100B -0.11806 Excited State 4: 2.852-A 2.5895 eV 478.80 nm f=0.0021 =1.783 98A -> 99A 0.99481 Excited State 5: 2.171-A 2.6627 eV 465.63 nm f=0.0193 =0.928 97A -> 99A 0.77986 97A ->104A 0.12398 90B -> 98B -0.25513 92B -> 98B 0.47858 93B -> 98B -0.13269 95B -> 98B -0.15685 The above state (excited state 5) is the most probable excited state, here when I calculate the percentage of contribution using C^2*2*100 formula. I get 121% how it is possible? or am I doing anything wrong? Your help will be appreciated. Thanks in advance... Yours Veerapandian.Phttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt