From owner-chemistry@ccl.net Tue May 5 08:01:01 2015 From: "David A Case case---biomaps.rutgers.edu" To: CCL Subject: CCL: Announcement: Release of AmberTools15 Message-Id: <-51342-150504205430-20540-4vw3tshjYPrkJt/g9cYzgg . server.ccl.net> X-Original-From: David A Case Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Mon, 4 May 2015 20:54:24 -0400 Mime-Version: 1.0 Sent to CCL by: David A Case [case * biomaps.rutgers.edu] The Amber development team is pleased to announce the release of AmberTools15. This is a significant update to AmberTools: http://ambermd.org/#AmberTools. Among the new features: * New generalized Born solvation parameters for nucleic acids * New ("OPC") explicit water model * New parameters for monatomic ions * Generation of an API for sander and mdgx, allowing their functionality to be accessed by third-party programs * Support for implicit membrane models in PB and FEW (free energy workbench) * Major updates and extensions to the cpptraj program for trajectory analysis * Improved workflow for system preparation and validation Please note: If you already have AmberTools14, you do not need to download anything. Simply type "./update_amber --upgrade" in your AMBERHOME directory. (Follow the instructions: you will need to type this twice.) You then need to re-run the configure script and re-compile. If you are a new user, click on the "Download AmberTools15" link at http://ambermd.org. Follow the installation instructions in the Reference Manual. (Special shout-out to Jason Swails and Scott Brozell for help in preparing the release. See http://ambermd.org/contributors.html for a fuller list of who has contributed.) ...dave case From owner-chemistry@ccl.net Tue May 5 11:05:01 2015 From: "Peter Kraus p.kraus12~!~imperial.ac.uk" To: CCL Subject: CCL: Calculating Transport Properties Message-Id: <-51343-150505102921-26604-s7+WoDWt1ZmoLwJORpTQSw*server.ccl.net> X-Original-From: "Peter Kraus" Date: Tue, 5 May 2015 10:29:20 -0400 Sent to CCL by: "Peter Kraus" [p.kraus12*imperial.ac.uk] Dear colleagues, I would like to calculate transport properties for a set of species for application in kinetic modelling, namely the following: Lennard-Jones sigma and epsilon, rotational collision number (Zrot), rotational heat capacoty (Crot), gas phase (vapour) viscosity, I have tried using Reaction Mechanism Generator, but I am having difficulty with larger aromatic species, and it doesn't provide all of the required data. I have accurate thermodynamic properties in the form of JANAF polynomials for the species in question, if that helps. Thanks a lot in advance, Peter Kraus From owner-chemistry@ccl.net Tue May 5 13:10:01 2015 From: "Ross C Walker rcw]~[sdsc.edu" To: CCL Subject: CCL: Computational Chemical Biology Conference - Abstract deadline May 15th Message-Id: <-51344-150505123348-12869-PCFf1l9MLlz1wLVHiHpC2Q|,|server.ccl.net> X-Original-From: "Ross C Walker" Date: Tue, 5 May 2015 12:33:47 -0400 Sent to CCL by: "Ross C Walker" [rcw ~ sdsc.edu] Abstract deadline extended to May 15th 2015. 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) Prof. Carlos Simmerling (Stony Brook) Dr. Andy Jennings (Takeda) Prof. Patricia Jennings (UCSD) Prof. Erik Lindahl (KTH Stockholm) Prof. Knut Teigen (Bergen) Prof. Steven Schwartz (Arizona) Prof. Jeremy Tame (Yokohama) Prof. Oscar Ces (Imperial College) Dr. Daniel Ormsby (Dotmatics) 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 15th May 2015 for Oral abstracts and 1st June 2015 for 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. From owner-chemistry@ccl.net Tue May 5 18:16:00 2015 From: "Safiya Ess Amer amersaf85 ~~ yahoo.com" To: CCL Subject: CCL:G: Potential Energy Scan Message-Id: <-51345-150505170749-12801-IHVngzbU4JVZXOCmxO0efg(-)server.ccl.net> X-Original-From: "Safiya Ess Amer" Date: Tue, 5 May 2015 17:07:48 -0400 Sent to CCL by: "Safiya Ess Amer" [amersaf85|a|yahoo.com] Hello, all I have a system of H2-MgO(001) I want to find Potential Energy Surface (PES) for this system. I am using G03 and GaussView 3.07. creating input file with help of Gaussview #p B3LYP 6-31G(d) popt=z-matrix Theta=0 / H2-MgO 0 1 Mg Mg 1 B1 Mg 1 B2 A1 Mg 3 B3 1 A2 2 D1 Mg 1 B4 3 A3 2 D2 Mg 4 B5 3 A4 1 D3 Mg 5 B6 1 A5 3 D4 Mg 1 B7 5 A6 7 D5 Mg 8 B8 1 A7 5 D6 O 2 B9 1 A8 5 D7 O 4 B10 3 A9 1 D8 O 4 B11 3 A10 1 D9 O 3 B12 1 A11 5 D10 O 4 B13 3 A12 1 D11 O 4 B14 3 A13 1 D12 O 1 B15 13 A14 3 D13 O 6 B16 4 A15 3 D14 O 6 B17 4 A16 3 D15 X 1 B18 16 A17 5 D16 H 1 B19 16 A18 5 D17 H 1 B20 16 A19 5 D18 B1 4.20021428 f B2 2.97000000 f B3 2.97000000 f B4 2.97000000 f B5 2.97000000 f B6 2.97000000 f B7 2.97000000 f B8 2.97000000 f B9 2.10010714 f B10 2.10010714 f B11 2.10010714 f B12 2.10010714 f B13 2.10010714 f B14 2.10010714 f B15 2.10010714 f B16 2.10010714 f B17 2.10010714 f B18 2.00000000 S 1 0.1 B19 2.37000000 S 1 0.1 B20 1.63000000 S 1 0.1 A1 45.00000000 f A2 90.00000000 f A3 90.00000000 f A4 90.00000000 f A5 90.00000000 f A6 90.00000000 f A7 90.00000000 f A8 90.00000000 f A9 45.00000000 f A10 135.00000000 f A11 45.00000000 f A12 45.00000000 f A13 135.00000000 f A14 90.00000000 f A15 135.00000000 f A16 135.00000000 f A17 90.00000000 f A18 90.00000000 f A19 90.00000000 f D1 180.00000000 f D2 0.00000000 f D3 0.00000000 f D4 180.00000000 f D5 0.00000000 f D6 180.00000000 f D7 180.00000000 f D8 180.00000000 f D9 180.00000000 f D10 0.00000000 f D11 0.00000000 f D12 0.00000000 f D13 180.00000000 f D14 0.00000000 f D15 180.00000000 f D16 90.00000000 f D17 90.00000000 f D18 90.00000000 f ********************************************* hydrogen molecule must be moved above Mg1 atom which is at origin. Can I make variables B18, B19, and B20 scanned from 2 to 8 Angstrom by 0.1 increments at the same time. Thanks in advance Safiya Amer amersas85++yahoo.com