From owner-chemistry@ccl.net Wed Feb 9 03:27:00 2011 From: "Allouche Abdul-rahman allouche . lasim.univ-lyon1.fr" To: CCL Subject: CCL:G: Gabedit version 2.3.5 released. Message-Id: <-43921-110209021728-19287-ImJI+MLUsLk8Ad/+oL+cbA|*|server.ccl.net> X-Original-From: Allouche Abdul-rahman Content-Type: multipart/alternative; boundary="------------090905040305000609010907" Date: Wed, 09 Feb 2011 08:13:16 +0100 MIME-Version: 1.0 Sent to CCL by: Allouche Abdul-rahman [allouche|lasim.univ-lyon1.fr] This is a multi-part message in MIME format. --------------090905040305000609010907 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit Dear CCLers, Release 2.3.5 of Gabedit is now available from http://gabedit.sf.net . Gabedit is a free open-source graphical user interface for computational chemistry packages. It's work under Windows, Linux, Mac OSX11 and other UNIX OS. Computational chemistry packages supported ((to date) by Gabedit are : Gamess-US , Gaussian , Molcas , Molpro , MPQC , OpenMopac < http://www.openmopac.net > , ORCA FireFly and Q-Chem . ADF, Turbomole, and other softwares (through the gabedit and molden format files) are partially supported by Gabedit. Gabedit makes using Computational Chemistry Packages (CCP) simple and straightforward : * Sketch in molecules using its advanced 3D Structure Builder, or load in molecules from standard files. * Set up and submit CCP jobs right from the interface, and monitor their progress as they run. * Examine calculation results graphically via state-of-the-art visualization features: display molecular orbitals and other surfaces, view spectra, animate normal modes, geometry optimizations and reaction paths. * Simulated Annealing with Molecular Dynamics is implemented in Gabedit, using the Amber MM or a Semi-empirical (like AM1, PM6, PM6-DH2, PM6-Sparkle (http://www.sparkle.pro.br/),...) potential. * A conformational search tool using a molecular mechanics (Amber) or a semi-empirical potential is implemented in Gabedit. Major features * Gabedit can creates input file for GAMESS(US), GAUSSIAN, MOLCAS, MOLPRO , MPQC, OpenMopac, ORCA, FireFly, and Q-Chem. * Gabedit can graphically display a variety of Gamess-US, Gaussian, Molcas, Molpro, MPQC, OpenMopac, ORCA, FireFly, Q-Chem and (partially) ADF calculation results, including the following * Molecular orbitals, * Surfaces from the electron density, electrostatic potential, NMR shielding density, and other properties. * Surfaces may be displayed in solid, translucent and wire mesh modes. they are can be colorcoded by a separate property. * Contours (colorcoded), Planes colorcoded, Dipole. XYZ axes and the molecular principal axes. * Animation of the normal modes corresponding to vibrational frequencies. * Animation of the rotation of geometry, surfaces, contours, planes colorcoded, xyz and the molecular principal axes. * Animation of contours, Animation of planes colorcoded. * Gabedit can generate a povray file for geometry (including hydrogen's bond),surfaces (including colorcoded surfaces), contours, planes colorcoded. * Gabedit can export picture in PDF, PS, EPS, and SVG format * Gabedit can save picture in BMP, JPEG, PNG and PPM format. * Gabedit can generate automatically a series of pictures for animation (vibration, geometry convergence, rotation, contours, planes colorcoded). * More quantities can be calculated before visualization : Molecular electrostatic potential (MEP), orbitals, electronic density, difference density, Laplacian of the density, AIM charges, Fukui functions, ELF, SAS, Coulomb integrals, transition matrix elements. * Volumetric data can be scaled, squared or subtracted. * The peak IR, UV, Raman, ECD spectra can be convoluted with a Gaussian or a Lorentzian profile. * NMR spectra can be calculated from chemical shift and spin--spin coupling constants. * The isotope distribution for a molecule can be calculated by Gabedit. You can download this new version from : http://gabedit.sf.net If you find any bugs or have any problems, please contact me ( allouchear at users.sourceforge.net). Best regards A.R. Allouche Université Claude Bernard Lyon 1 LASIM, UMR 5579 Villeurbanne France --------------090905040305000609010907 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit

Dear CCLers,

Release 2.3.5 of Gabedit is now available from  http://gabedit.sf.net .

Gabedit is a free open-source graphical user interface for computational chemistry packages.
It's work under Windows, Linux, Mac OSX11 and other UNIX OS. 

Computational chemistry packages supported ( (to date) by Gabedit are :
Gamess-US <http://www.msg.ameslab.gov/GAMESS/>,
Gaussian  <http://www.gaussian.com>,
Molcas <http://www.teokem.lu.se/molcas/>,
Molpro <http://www.molpro.net>,
MPQC <http://www.mpqc.org>,
OpenMopac <http://www.openmopac.net>,
ORCA <http://www.thch.uni-bonn.de/tc/orca/>
FireFly  <http://classic.chem.msu.su/gran/gamess/index.html> and
Q-Chem  <http://www.q-chem.com/>.
ADF, Turbomole, and other softwares (through the gabedit and molden format files)  are partially supported by Gabedit.

Gabedit makes using Computational Chemistry Packages (CCP) simple and straightforward :
* Sketch in molecules using its advanced 3D Structure Builder, or load in molecules from standard files.
* Set up and submit CCP jobs right from the interface, and monitor their progress as they run.
* Examine calculation results graphically via state-of-the-art visualization features: display molecular orbitals and other surfaces, view spectra, animate normal modes, geometry optimizations and reaction paths.
* Simulated Annealing with Molecular Dynamics is implemented in Gabedit, using the Amber <http://amber.scripps.edu/> MM or a Semi-empirical (like AM1, PM6, PM6-DH2, PM6-Sparkle (http://www.sparkle.pro.br/),...) potential.
* A conformational search tool using a molecular mechanics (Amber) or a semi-empirical potential is implemented in Gabedit.


Major features
   * Gabedit can creates input file for GAMESS(US), GAUSSIAN, MOLCAS, MOLPRO , MPQC, OpenMopac, ORCA, FireFly, and Q-Chem.
   * Gabedit can graphically display a variety of Gamess-US, Gaussian, Molcas, Molpro, MPQC, OpenMopac, ORCA, FireFly, Q-Chem and (partially) ADF calculation results, including the following
   * Molecular orbitals,
   * Surfaces from the electron density, electrostatic potential, NMR shielding density, and other properties.
   * Surfaces may be displayed in solid, translucent and wire mesh modes. they are can be colorcoded by a separate property.
   * Contours (colorcoded), Planes colorcoded, Dipole. XYZ axes and the molecular principal axes.
   * Animation of the normal modes corresponding to vibrational frequencies.
   * Animation of the rotation of geometry, surfaces, contours, planes colorcoded, xyz and the molecular principal axes.
   * Animation of contours, Animation of planes colorcoded.
   * Gabedit can generate a povray file for geometry (including hydrogen's bond),surfaces (including colorcoded surfaces), contours, planes colorcoded.
   * Gabedit can export picture in PDF, PS, EPS, and SVG format
   * Gabedit can save picture in BMP, JPEG, PNG and PPM format.
   * Gabedit can generate automatically a series of pictures for animation (vibration, geometry convergence, rotation, contours, planes colorcoded).
   * More quantities can be  calculated  before  visualization : Molecular electrostatic potential (MEP),  orbitals, electronic density, difference density, Laplacian of the density, AIM  charges, Fukui functions, ELF, SAS, Coulomb integrals, transition matrix elements.
   *  Volumetric data can be scaled, squared or subtracted.
   * The peak IR, UV, Raman, ECD spectra can be convoluted with  a Gaussian or a Lorentzian profile.
   * NMR  spectra can be calculated from chemical  shift and spin–spin coupling constants.
   * The isotope distribution for a molecule can be calculated by Gabedit.

You can download this new version from : http://gabedit.sf.net


If you find any bugs or have any problems,
please contact me ( allouchear at users.sourceforge.net).

Best regards

A.R. Allouche
Université Claude Bernard Lyon 1
LASIM, UMR 5579
Villeurbanne
France

--------------090905040305000609010907-- From owner-chemistry@ccl.net Wed Feb 9 06:45:01 2011 From: "eurisco1|,|pochta.ru" To: CCL Subject: CCL: different symmetries of FMO in output and chk files Message-Id: <-43922-110209032653-8979-rGpBYstNKShNqp4m6kf/3Q::server.ccl.net> X-Original-From: Content-Transfer-Encoding: 8bit Content-Type: text/plain; format=flowed; charset="koi8-r"; reply-type=original Date: Wed, 9 Feb 2011 11:26:40 +0300 MIME-Version: 1.0 Sent to CCL by: [eurisco1+*+pochta.ru] Dear Mr.Mi, According your route card #p b3lyp/6-311g(d) polar=analytic nosymm test the NOSYMM directive is used. It removes all symmetry constraints in calculations and output. I suggest that you need to use #p b3lyp/6-311g(d) polar=analytic Sincerely, Ol Ga -----éÓÈÏÄÎÏÅ ÓÏÏÂÝÅÎÉÅ----- > From: mi yang agri_chemist(0)yahoo.com Sent: Wednesday, February 09, 2011 6:11 AM To: Ga, Ol Subject: CCL: different symmetries of FMO in output and chk files Sent to CCL by: "mi yang" [agri_chemist++yahoo.com] Dear colleagues, I am dealing with chemical system having C3v symmetry like a plate. Although in output file its shows the C3v point group but when I tried to make its Frontier Molecular orbitals in GaussView these always come out in Cs symmetry. I have re-optimized the structure and tried several ways but in vain. Any suggestion to get FMO in same symmetry as in output file. I am using G09 and DFT method. Any helpful suggestion will be encouraging! Mr.Mi a part from output file: Alpha occ. igenvalues -- -0.48784 -0.48784 -0.46675 -0.44940 -0.44691 Alpha occ. igenvalues -- -0.44690 -0.44242 -0.44242 -0.43899 -0.43899 Alpha occ. igenvalues -- -0.41038 -0.40828 -0.39120 -0.39120 -0.38593 Alpha occ. igenvalues -- -0.37357 -0.35441 -0.35419 -0.35418 -0.34288 Alpha occ. igenvalues -- -0.34287 -0.32547 -0.32547 -0.28832 -0.27704 Alpha occ. eigenvalues -- -0.27704 -0.23662 -0.21098 -0.21097 Alpha virt. eigenvalues -- -0.03768 -0.03767 -0.03728 0.00683 0.00683 Alpha virt. eigenvalues -- 0.04035 0.05491 0.05835 0.05836 0.06365 Alpha virt. eigenvalues -- 0.06365 0.08320 0.09521 0.09521 0.10413 Alpha virt. eigenvalues -- 0.11858 0.12443 0.12443 0.13176 0.13177 Alpha virt. eigenvalues -- 0.17000 0.17000 0.17742 0.18838 0.19880 \#p b3lyp/6-311g(d) polar=analytic nosymm test\\Title Card Required\\0,1\C ,0,-1.408554,0.013779,-0.693819\C,0,0.71621,1.212954,-0.693819\C,0,0.6 92344,-1.226733,-0.693819\C,0,-0.71621,1.212954,-0.693819\C,0,1.408554 ,0.013779,-0.693819\C,0,-0.692344,-1.226733,-0.693819\C,0,-1.212199,2. 359685,-0.069039\C,0,2.649646,-0.130047,-0.069039\C,0,-1.437447,-2.229 637,-0.069039\C,0,0.,3.295111,0.186393\C,0,2.85365,-1.647556,0.186393\ C,0,-2.85365,-1.647556,0.186393\C,0,1.212199,2.359685,-0.069039\C,0,1. 437447,-2.229637,-0.069039\C,0,-2.649646,-0.130047,-0.069039\C,0,2.507 054,2.272296,0.446881\C,0,0.714339,-3.307321,0.446881\C,0,-3.221393,1. 035025,0.446881\C,0,3.221393,1.035025,0.446881\C,0,-0.714339,-3.307321 ,0.446881\C,0,-2.507054,2.272296,0.446881\H,0,0.,3.688705,1.206282\H,0 ,3.194512,-1.844352,1.206282\H,0,-3.194512,-1.844352,1.206282\H, 0,0.,4 .160611,-0.487291\H,0,3.603195,-2.080306,-0.487291\H,0,-3.603195,-2.08 0306,-0.487291\H,0,2.952936,3.109228,0.977189\H,0,1.216203,-4.111931,0 .977189\H,0,-4.169138,1.002703,0.977189\H,0,4.169138,1.002703,0.977189 \H,0,-1.216203,-4.111931,0.977189\H,0,-2.952936,3.109228,0.977189\\Ver sion=AM64L-G09RevA.02\HF=-807.5873872\RMSD=6.825e-09\Dipole=0.,-0.0000 201,0.9889751\Polar=272.6983144,0.,272.7016946,0.,0.0016419,110.797517 9\HyperPolar=0.,-66.4222618,0.,66.3907597,78.7765546,0.,78.7714524,0., -0.0033505,70.8747214\Quadrupole=2.8881437,2.8873016,-5.7754453,0.,0., 0.0002\PG=C03V [3SGV(C1H2),X(C18H6)]\\##http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Wed Feb 9 07:56:00 2011 From: "Andrea Lombardi Lombardi ebiu2005**gmail.com" To: CCL Subject: CCL: CECAM workshop "Spin Networks in Atomic and Molecular Physics, Quantum Message-Id: <-43923-110209041421-19933-IhCkAlT4jLoABb9QFowPwg^server.ccl.net> X-Original-From: "Andrea Lombardi Lombardi" Date: Wed, 9 Feb 2011 04:14:19 -0500 Sent to CCL by: "Andrea Lombardi Lombardi" [ebiu2005*gmail.com] We are pleased to announce the CECAM workshop "Spin Networks in Atomic and Molecular Physics, Quantum Chemistry and Quantum Computing " to be held at ETH Zurich, June 27-29 2011. The workshop will consist of invited lectures, contributed talks, and posters. Therample time for discussions. For full information and application see the workshop website : http://www.cecam.org/workshop-521.html We are looking forward for oral and poster contributions. Please use the application form available at the workshop website to submit your contribution. The formal registration deadline is May 15th, but we invite you to contact informally one of the organizers at your earliest convenience. We would appreciate if you could also bring the workshop to the attention of colleague researchers that might be interested. Sincerely, Andrea Lombardi (ebiu2005() gmail.com) VIncenzo Aquilanti (vincenzoaquilanti() yahoo.it) Annalisa Marzuoli (annalisa.marzuoli() pv.infn.it) Robert Littlejohn (robert() wigner.berkeley.edu) Roger Anderson (anderso() chemistry.ucsc.edu) ============================================ Andrea Lombardi Dipartimento di Chimica, Universit di Perugia Via Elce di Sotto 8, 06121 Perugia, ITALY e-mail: abulafia() dyn.unipg.it; ebiu2005() gmail.com phone: +39 075 5855511 fax: +39 075 5855606 ============================================ From owner-chemistry@ccl.net Wed Feb 9 12:18:00 2011 From: "marutheeswaran srinivasan maruthees.waran]=[gmail.com" To: CCL Subject: CCL:G: second hyperpolarizability Message-Id: <-43924-110209121032-8700-/skAWjy8bnoM1S8PLeKpsw%%server.ccl.net> X-Original-From: "marutheeswaran srinivasan" Date: Wed, 9 Feb 2011 12:10:30 -0500 Sent to CCL by: "marutheeswaran srinivasan" [maruthees.waran^gmail.com] I am doing theoretical study on two photon absorption for that i need to calculate imaginary part of second hyperpolarizability.So, Please anybody tell me what keyword to use for calculating the same in G09 or G03 and where i will see the second hyperpolarizability in the output result. thank you Marutheeswaran.S Chemical information science lab Dept.of Chemistry Pondicherry university From owner-chemistry@ccl.net Wed Feb 9 15:52:01 2011 From: "Markus Dittrich markusle()gmail.com" To: CCL Subject: CCL: Computational Biophysics Workshop using NAMD and VMD Message-Id: <-43925-110209132446-947-XUQEXHVlfzNF6nv+aLCCkQ_-_server.ccl.net> X-Original-From: "Markus Dittrich" Date: Wed, 9 Feb 2011 13:24:44 -0500 Sent to CCL by: "Markus Dittrich" [markusle/a\gmail.com] Dear Colleagues, The National Resource for Biomedical Supercomputing (www.nrbsc.org) at the Pittsburgh Supercomputing Center (www.psc.edu) and Carnegie Mellon University (www.cmu.edu) will organize an "Computational Biophysics Workshop using NAMD and VMD" to be held May 16-20, 2011 at the Pittsburgh Supercomputing Center in Pittsburgh, Pennsylvania. The workshop will be presented by members of the Theoretical and Computational Biophysics Group (www.ks.uiuc.edu) from the University of Illinois at Urbana-Champaign and will explore a wide range of physical models and computational approaches for the simulation of biological systems. The workshop is based on case studies including the properties of membranes and membrane proteins, mechanism of molecular motors, trafficking in the living cell through water and ion channels, and signaling pathways. Physical concepts, mathematical techniques, and computational methods required will be introduced, including force fields and algorithms used in molecular modeling, molecular dynamics simulations on parallel computers, and steered molecular dynamics simulations. The workshop is designed for graduate students and postdoctoral researchers in computational and/or biophysical fields who seek to extend their research skills to include computational and theoretical expertise, as well as other researchers interested in theoretical and computational biophysics. Theory sessions in the morning will be followed by hands-on computer labs in the afternoon in which students will be able to set up and run simulations. Applications to the workshop are due by March 26, 2011. Selection and notification of participants from the application pool will be completed by April 4th, 2011. Registration will be free of charge for attendees from non-profit academic institutions, and, in addition, the National Resource for Biomedical Supercomputing will cover housing costs. Participants are, however, required to cover their own travel expenses. Due to space and equipment constraints, the workshop is limited to 25 participants. For on-line application, go to We look forward to receiving your application. For more information, please contact NRBSC Administrator Christal Banks at cbanks.at.psc.edu. From owner-chemistry@ccl.net Wed Feb 9 17:36:01 2011 From: "Guenter Grethe ggrethe],[att.net" To: CCL Subject: CCL: CINF Scholarship for Scientific Exccellence Sponsored by FIZ CHEMIE Message-Id: <-43926-110209162130-7805-vubtWp1KYZ30HoLa17L1tw(~)server.ccl.net> X-Original-From: "Guenter Grethe" Date: Wed, 9 Feb 2011 16:21:24 -0500 Sent to CCL by: "Guenter Grethe" [ggrethe+*+att.net] 2011 CINF Scholarship for Scientific Excellence Sponsored by FIZ Chemie Berlin The scholarship program of the Division of Chemical Information (CINF) of the American Chemical Society (ACS) funded by FIZ Chemie Berlin is designed to reward graduate and postdoctoral students in chemical information and related sciences for scientific excellence and to foster their involvement in CINF. Up to three scholarships valued at $1,000 each will be presented at the 242th ACS National Meeting in Denver, CO, August 28 September 1, 2011. Applicants must be enrolled at a certified college or university, and they will present a poster during the Welcoming Reception of the division on Sunday evening at the National Meeting. Additionally, they will have the option to also show their poster at the Sci-Mix session on Monday night. Abstracts for the poster must be submitted electronically through PACS, the abstract submission system of ACS. To apply, please inform the Chair of the selection committee, Guenter Grethe at ggrethe(_)att.net, that you are applying for a scholarship. Submit your abstract to http://abstracts.acs.org using your ACS ID. If you do not have an ACS ID, follow the registration instructions and submit your abstract for CINF Scholarship for Scientific Excellence. The deadline for submitting an abstract to PACS is April 1, 2011. Additionally, please send a 2,000-word abstract describing the work to be presented in electronic form to the Chair of the selection committee by June30, 2010. Any questions related to applying for one of the scholarships should be directed to the same e-mail address. Winners will be chosen based on contents, presentation and relevance of the poster and they will be announced during the reception. The contents shall reflect upon the students work and describe research in the field of cheminformatics and related sciences. Winning posters will be marked Winner of FIZ Chemie-CINF Scholarship for Scientific Excellence at the poster session. Guenter Grethe