From owner-chemistry@ccl.net Tue May 19 00:09:01 2015 From: "Salter-Duke, Brian James - brian.james.duke]^[gmail.com" To: CCL Subject: CCL: Where is Spackman's geodesic derived charge implemented? Message-Id: <-51380-150519000803-32271-qwC6cT1GXHL44L9zY69Sig#,#server.ccl.net> X-Original-From: "Salter-Duke, Brian James -" Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Tue, 19 May 2015 14:07:51 +1000 MIME-Version: 1.0 Sent to CCL by: "Salter-Duke, Brian James -" [brian.james.duke. . .gmail.com] I think you will find it is also in GAMESS-US, where Spackman originally added his code, but I have no experience with it. Brian. On Mon, May 18, 2015 at 09:05:27PM -0300, André Farias de Moura moura(_)ufscar.br wrote: > Hi Italo, > > You can find it implemented in Firefly (formely PC-Gamess). > > best > > Andre > > On Mon, May 18, 2015 at 7:30 PM, Italo Anjos italocurvelo#,#gmail.com < > owner-chemistry*ccl.net> wrote: > > > Hi all, > > > > I would like to calculate point derived charges from the electrostatic > > potential using Spackman's geodesic algorithm but I couldn't find in which > > programs the method is implemented. > > > > Could anyone point me in the right direction? > > > > I appreciate any help. > > > > Italo Curvelo > > > > > > -- > _____________ > > Prof. Dr. André Farias de Moura > Department of Chemistry > Federal University of São Carlos > São Carlos - Brazil > phone: +55-16-3351-8090 -- Brian Salter-Duke (Brian Duke) Brian.Salter-Duke . monash.edu Adjunct Associate Professor Monash Institute of Pharmaceutical Sciences Monash University Parkville Campus, VIC 3052, Australia From owner-chemistry@ccl.net Tue May 19 03:41:01 2015 From: "Mark Andrew Blitz m.blitz]~[leeds.ac.uk" To: CCL Subject: CCL: Mesmer 4.0 Message-Id: <-51381-150519033828-14232-9aI+TdHefOa3avoPRmHMNQ(a)server.ccl.net> X-Original-From: "Mark Andrew Blitz" Date: Tue, 19 May 2015 03:38:27 -0400 Sent to CCL by: "Mark Andrew Blitz" [m.blitz.:.leeds.ac.uk] Dear Colleagues, On behalf of the MESMER team, I am delighted to announce that MESMER 4.0 (Master Equation Solver for Multi Energy-well Reactions) is now available for download. MESMER is designed to analyse and simulate reactions in the gas phase that take place on a potential energy surface that is characterised by having one or more potential wells, and which are typically described by rate coefficients that are concentration as well as temperature dependent. MESMER allows you to simulate systems over a wide range of pressures and temperatures, extract rate coefficients, analyse experimental data, fit model parameters and represent rate coefficients in formats that can be used directly in large scale simulations (e.g. Cantera). The Windows installer and Linux tar file are located at: http://sourceforge.net/projects/mesmer/files/mesmer/ The source can also be viewed and downloaded from this site. There are also bug and feature request tracking facilities which we encourage you to use. The following new features have been implemented: Internal rotor facility extended to, optionally, allow for an angle dependent internal moment of inertia term. Multiple control blocks. Limited support for second order bimolecular association reactions. Thermodynamic data from MESMER calculations can now be output in the form of NASA polynomials. Sensitivity analysis. Methods to perform a sensitivity analysis of MESMER outputs (rate coefficients) to key input parameters have been added. The accuracy of extended precision methods has been improved. If you have any comments or suggestions, please do not hesitate to let us know, either through the above site or by email (Mark Blitz(M.Blitz*leeds.ac.uk), Struan Robertson(struanhrobertson*gmail.com) and Robin Shannon( shannon.rj*gmail.com ) would be very happy to receive feedback). More information is available at the MESMER website: http://www.chem.leeds.ac.uk/mesmer.html Also some of the implementation details of MESMER are described in Journal of Physical Chemistry A, 95459560, 116 (2012). It is also a pleasure to announce, that Dr. Xiaoqing You and colleagues of the University of Tsinghua, in collaboration with the MESMER team, have been developing a web based graphical user interface for creating MESMER input files. A prototype of this interface is available for testing and can be found at the following address: http://www.cce.tsinghua.edu.cn:8000/ Dr. You and the MESMER team would welcome feedback on this interface. The MESMER team also participate in the MEIC (Master Equation Inter- Comparison), details of which are available from Prof. John Barker (jrbarker*umich.edu). Please feel free to forward this email to other colleagues to whom it might be of interest. Regards, Mark Blitz From owner-chemistry@ccl.net Tue May 19 07:18:01 2015 From: "Ponnadurai Ramasami ramchemi%intnet.mu" To: CCL Subject: CCL: VCCC-2015: Call for abstracts-deadline extended Message-Id: <-51382-150519071358-3310-gckD6xZjvny/y/GQs9Dd1g##server.ccl.net> X-Original-From: "Ponnadurai Ramasami" Date: Tue, 19 May 2015 07:13:57 -0400 Sent to CCL by: "Ponnadurai Ramasami" [ramchemi#,#intnet.mu] Dear Sir/Madam, Greetings from Mauritius. A Virtual Conference (online conference) on Computational Chemistry will be organised by the Computational Chemistry Group of the University of Mauritius. The Virtual Conference will be held from 1st to 31st August 2015. You are invited to submit an abstract to be considered for the Virtual Conference. Deadline: 15th May 2015 (Extended to 1st June 2015). All topics related to Computational Chemistry may be considered. Please visit the website of the Conference and let me know if you need more details. http://sites.uom.ac.mu/vccc2015/ Looking forward for your participation. Prof Ponnadurai Ramasami Chairman of the Organising Committee From owner-chemistry@ccl.net Tue May 19 14:32:00 2015 From: "Lovija Meyer Lovija3\a/yahoo.de" To: CCL Subject: CCL: Relative energy Vs activation barrier Message-Id: <-51383-150519135534-754-7r6FFGf/Inj8HSTW2Nut7Q^-^server.ccl.net> X-Original-From: "Lovija Meyer" Date: Tue, 19 May 2015 13:55:33 -0400 Sent to CCL by: "Lovija Meyer" [Lovija3 _ yahoo.de] Dear Users ( and dear Andi U. who I hope to meet here...) The following part was an answer in 2011- but Is like to find an explanation here now...It was answered by Andi U. so I hope that hell read this to answer my question the way he did it years ago... The answer was: > > in multistep reactions the single activation barriers are unimportant and > the relative energies decide which pathway is favored. If you are interes= ted > in catalysis, I recommend that you have a look at the energetic span mode= l: > > A) Kozuch, S.; Shaik, S. *J. Am. Chem. Soc. **2006*, *128*, 3355-3365. > B) Kozuch, S.; Shaik, S. *J. Phys. Chem. A* *2008*, *112*, 6032-6041. > C) Uhe, A.; Kozuch, S.; Shaik, S. *J. Comp. Chem. **2011*, *32*, 978-985. > D) Kozuch, S.; Shaik, S. *Acc. **Chem. Res. **2011*, *44*, 101-110. > The model shows that the concept of a rate determining reaction step > (corresponding to a single activation barrier of a multistep reaction) is > misleading. It also allows to calculate the turnover frequency of a > catalytic system from relative energies e.g. obtained with DFT. Paper A > introduces the model, paper B extends its application to the reactant > concentrations, paper C further extends the model and introduces a small > computer program helping to apply the model and paper D reviews the model= From owner-chemistry@ccl.net Tue May 19 20:13:00 2015 From: "Ross C Walker rcw*_*sdsc.edu" To: CCL Subject: CCL: Computational Chemical Biology Conference - Abstract Deadline June 1st Message-Id: <-51384-150519160256-10830-/v+xx9bGiZCspVRx/QjS1g**server.ccl.net> X-Original-From: "Ross C Walker" Date: Tue, 19 May 2015 16:02:55 -0400 Sent to CCL by: "Ross C Walker" [rcw^^^sdsc.edu] Talk and Poster Abstract deadline extended to June 1st 2015. http://www.zingconferences.com/conferences/computational-chemical-biology/ Dear Colleagues, We invite you to attend the Zing conference on Computational Chemical Biology Conference (http://www.zingconferences.com/conferences/computational-chemical-biology/) that myself and Prof. Ian Gould are chairing. The meeting will take place at the Pullman Cairns International Hotel from 6th 9th August 2015. Sponsored by Takeda, DE Gruyter, Royal Society of Chemistry and OpenEye. We have a number of exciting plenary and invited speakers lined up including a number of young and dynamic innovators from both academia and industry: Prof. Darrin York (Rutgers) Prof. Jonathan Essex (Southampton) Prof. Qiang Cui (Wisconsin) Dr. Felice Lightstone (LLNL) Dr. Zoe Cournia (BRFA Athens) Prof. Ron Dror (Stanford) Dr. Scott Le Grand (NVIDIA Fellow) Dr. Andy Jennings (Takeda) Prof. Patricia Jennings (UCSD) Prof. Erik Lindahl (KTH Stockholm) Prof. Steven Schwartz (Arizona) Prof. Jeremy Tame (Yokohama) Dr. Elizabeth Brunk (UCSD) Prof. Oscar Ces (Imperial College) Prof. Laura Barter (Imperial College) Prof. Dave Winkler (CSIRO) Prof. Adrian Roitberg (UFL) Prof. David Minh (IIT) Prof. Thomas Cheatham (Utah) Prof. Alexey Onufriev (Virginia Tech) Prof. David Mobley (UCI) Dr. Tom Darden (OpenEye) Dr. Paul Hawkins (OpenEye) The conference will focus on multidisciplinary research that leverages computer simulation to address key questions crossing the physical sciences-life sciences/biomedical interface. In particular, the conference will feature sessions focusing on the development and application of novel and state-of-the-art computational tools and technology for solving major problems in the life and biomedical sciences. Topics will include advances in molecular dynamics simulation of enzymes; computational approaches to studying the interaction of drugs, drug transporters and signaling enzymes with lipid membranes; simulation of protein-protein interaction and multi-protein complex enzymatic systems; computational study of signaling pathways; new techniques in computational drug discovery as they apply to enzyme reactivity and dynamics; simulation of allosteric interactions; advances in multi-scale modeling; new techniques for direct simulation of reactivity in biological systems; and the impact of technological advances in computer hardware and software on the field of chemical biology. The conference will feature lectures by established leaders in the fields, as well as a specific focus on encouraging young and talented researchers to present both challenging questions and new ideas for solving them. The aim is to encourage a collegial atmosphere to promote stimulating and insightful discussion while enjoying the beauty of tropical Cairns, Australia. Deadlines for submissions is 1st June 2015 for both Oral and poster abstracts. For information on confirmed speakers, sponsors and how to register, please go to: http://www.zingconferences.com/conferences/computational-chemical-biology/ [http://tinyurl.com/nyblv7o] We hope you will be able to join us in Cairns. Kind Regards, Ross Walker & Ian Gould Chairs of the Computational Chemical Biology Conference 2015. /\ \/ |\oss Walker --------------------------------------------------------- | Associate Research Professor | | San Diego Supercomputer Center | | Adjunct Associate Professor | | Dept. of Chemistry and Biochemistry | | University of California San Diego | | NVIDIA Fellow | | http://www.rosswalker.co.uk | http://www.wmd-lab.org | | Tel: +1 858 822 0854 | EMail:- ross-,-rosswalker.co.uk | --------------------------------------------------------- Note: Electronic Mail is not secure, has no guarantee of delivery, may not be read every day, and should not be used for urgent or sensitive issues.