From owner-chemistry@ccl.net Wed Mar 2 13:01:00 2011 From: "Neranjan Perera neranjan007^^gmail.com" To: CCL Subject: CCL:G: software to visualize Gaussian cube files Message-Id: <-44033-110302125850-11874-S2R2pJz31VFfUZ6qLDToow#%#server.ccl.net> X-Original-From: "Neranjan Perera" Date: Wed, 2 Mar 2011 12:58:48 -0500 Sent to CCL by: "Neranjan Perera" [neranjan007++gmail.com] Hi all, I would like to know is there any software that can be used to visualize gaussian cube files which can show molecular orbitals? I am using 09 and tried using gopenmol and molden to visualize but it doesn't work at all. In gopenmol, I created the *.plt file and the *.crd files and tried to visualize it but when i tried to import the *.plt file , the program crashed. thanks for the help. neranjan From owner-chemistry@ccl.net Wed Mar 2 13:49:00 2011 From: "Mike Edmund Miller really_mike###yahoo.com" To: CCL Subject: CCL: Boron NT fails with "Diagonalization in DiagDN via DSPEV failed" Message-Id: <-44034-110302113018-4509-YpTkGrkpK+OLp4Fhu0z+dw^^server.ccl.net> X-Original-From: "Mike Edmund Miller" Date: Wed, 2 Mar 2011 11:30:16 -0500 Sent to CCL by: "Mike Edmund Miller" [really_mike{:}yahoo.com] Dear CCL members, A boron nanotube which I am trying to optimize fails as indicated in subject header. The route line for that job is: #T Opt Freq=raman b3lyp/6-31g(d) scf=(NoVarAcc,maxcyc=9999) I included the "NoVarAcc" keyword in an attempt to solve the original error of "Inaccurate quadrature in CalDSu". Other unsuccessful attempts to deal with the inaccurate quadrature error included 1) another WF guess, i.e., "Guess=INDO" and 2) an ultrafine grid together with a opt=tight. I have also tried tweaking the input coordinates manually. Thank you for your ideas / guidance you could provide in this matter. Mike From owner-chemistry@ccl.net Wed Mar 2 14:24:00 2011 From: "Wendy A Warr wendy]_[warr.com" To: CCL Subject: CCL: Three reports Message-Id: <-44035-110302100151-28784-Jk4LJqnQ/mUw6F1yBxONZw++server.ccl.net> X-Original-From: "Wendy A Warr" Date: Wed, 2 Mar 2011 10:01:49 -0500 Sent to CCL by: "Wendy A Warr" [wendy.]![.warr.com] Two free reports Report on JCIM 50th Anniversary Symposium and Celebrating the history of chemical information are freely accessible at http://www.warr.com. On a larger scale, the latest issue of our ACS report is going to press right now: Chemical Information and Computation 2010, Number Two 240th ACS National Meeting and Exposition: Boston, MA, August 22-26, 2010 Our 36th ACS report has transcripts of: * papers from the 50th anniversary symposium of the Journal of Chemical Information and Modeling * some of the papers in Tony Hopfinger's Herman Skolnik Award symposium on molecular simulation, modelling and QSAR * papers on data-intensive drug design * papers on recent progress in chemical structure representation. plus six months' worth of news from about 75 companies. Contents list and order form at http://www.warr.com. Half price to academia and government. Commercial organizations will find the multi-site license beneficial. Wendy Dr. Wendy A. Warr Wendy Warr & Associates 6 Berwick Court, Holmes Chapel Cheshire, CW4 7HZ, England Tel./Fax +44 (0)1477 533837 wendy]![warr.com http://www.warr.com From owner-chemistry@ccl.net Wed Mar 2 15:09:00 2011 From: "Ol Ga eurisco1- -pochta.ru" To: CCL Subject: CCL:G: software to visualize Gaussian cube files Message-Id: <-44036-110302150801-7462-QO7nW/TN2E2pZaIukKysoQ(0)server.ccl.net> X-Original-From: "Ol Ga" Date: Wed, 2 Mar 2011 15:07:58 -0500 Sent to CCL by: "Ol Ga" [eurisco1---pochta.ru] Dear Neranjan Perera, ChemCraft works. Sincerely, Ol Ga > > Sent to CCL by: "Neranjan Perera" [neranjan007++gmail.com] > Hi all, > I would like to know is there any software that can be used to visualize gaussian cube files which can show molecular orbitals? > > I am using 09 and tried using gopenmol and molden to visualize but it doesn't work at all. In gopenmol, I created the *.plt file and the *.crd files and tried to visualize it but when i tried to import the *.plt file , the program crashed. > > thanks for the help. > > neranjan> From owner-chemistry@ccl.net Wed Mar 2 16:34:00 2011 From: "Christophe Morell cmorell^^ujf-grenoble.fr" To: CCL Subject: CCL:G: software to visualize Gaussian cube files Message-Id: <-44037-110302150552-6049-RZCF51FZ6O/rBzJkAXRXQQ###server.ccl.net> X-Original-From: Christophe Morell Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Wed, 02 Mar 2011 21:05:30 +0100 MIME-Version: 1.0 Sent to CCL by: Christophe Morell [cmorell:-:ujf-grenoble.fr] Hi Neranjan I'm using an old version of molekel (4.3) which works fine with gaussian cub files. In my opinion molekel is one of the best software to visualize gaussian cube and outputs. You can download the latest version for free at : http://molekel.cscs.ch/wiki/pmwiki.php/Main/DownloadBinary best regards, Christophe Morell Neranjan Perera neranjan007^^gmail.com a écrit : > Sent to CCL by: "Neranjan Perera" [neranjan007++gmail.com] > Hi all, > I would like to know is there any software that can be used to visualize gaussian cube files which can show molecular orbitals? > > I am using 09 and tried using gopenmol and molden to visualize but it doesn't work at all. In gopenmol, I created the *.plt file and the *.crd files and tried to visualize it but when i tried to import the *.plt file , the program crashed. > > thanks for the help. > > neranjan> > > > > -- Christophe Morell Directeur des Etudes Formation Continue et Apprentissage _________________________________________________________ Département Mesures Physiques IUT 1 – Quai Claude Bernard 38000 Grenoble (France) tel : 00 (33) 4 76 57 50 27 christophe.morell{=}ujf-grenoble.fr _________________________________________________________ Commissariat à l’Energie Atomique (CEA) INAC/SCIB/LAN 17, Rue des Martyrs 38017 GRENOBLE CEDEX tel : 00 (33) 4 38 78 53 76 christophe.morell{=}cea.fr _________________________________________________________ “Contrary to what is sometimes supposed, the theoretical chemist is not a mathematician, thinking mathematically, but a chemist, thinking chemically.” C.A. Coulson http://inac.cea.fr/scib/Phocea/Pisp/visu.php?id=98&uid=christophe.morell From owner-chemistry@ccl.net Wed Mar 2 17:09:00 2011 From: "angela bruneau amb458(a)cornell.edu" To: CCL Subject: CCL: Molden question: How to change plot sizes? Message-Id: <-44038-110302164128-5679-cISwCrpdtj1+sFWQsg6kXg .. server.ccl.net> X-Original-From: "angela bruneau" Date: Wed, 2 Mar 2011 16:41:22 -0500 Sent to CCL by: "angela bruneau" [amb458 a cornell.edu] Hi there, I need to change the size of an energy vs point plot in order to expand the x axis as there were too many points to avoid overlap in a plot of ~8x8cm. There does not appear to be any way to change this by dragging, is there a way to do this at all? I am running this on Mac, fyi. Thanks! From owner-chemistry@ccl.net Wed Mar 2 17:44:00 2011 From: "Secretariat{=}isast.org secretariat{=}isast.org" To: CCL Subject: CCL: 3rd-round submissions DLMC2011 Digital Library Conference and QQML2011 International Conference Message-Id: <-44039-110301203553-4036-DOWqUG5CRXFnaL53ml8LOQ]|[server.ccl.net> X-Original-From: "Secretariat++isast.org" Content-Type: multipart/alternative; boundary="----=_NextPart_000_2880_01CBD88A.EB83C900" Date: Wed, 2 Mar 2011 03:35:47 +0200 MIME-Version: 1.0 Sent to CCL by: "Secretariat||isast.org" [secretariat||isast.org] This is a multi-part message in MIME format. ------=_NextPart_000_2880_01CBD88A.EB83C900 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Dear Colleagues, Don't miss the 3rd-round submissions to the 3rd QQML2011 International Conference and the DLMC2011 Digital Library Conference that starts now until 15 March 2011. Please think of abstract or paper submission and disseminate this Call for Papers to your colleagues. [Those of you who have already email your abstract(s) or paper(s) during the last call, please ignore this announcement] The Qualitative and Quantitative Methods in Libraries International Conference (QQML2011, http://www.isast.org/qqml2011.html ) and the Digital Library International Conference (DLMC2011, http://www.isast.org/dlmcconference.html ) aim to bring together researchers and scientists from academia, libraries, archives, museums, from governmental and non government organizations to present new results and identify future research interests. All papers will be published in the QQML2011 and the DLMC2011 proceedings and/or in scientific journals. The proceedings of the 2009 QQML International conference are published by World Scientific and the 2010 QQML proceedings will be published soon by the same publisher. To fulfill QQML and DLMC goals and success we are inviting proposals for: * Conference Presentations: 20- 25 minute presentations. * Conference Workshops: 4 - 5 hour workshops. * New researchers' research results. We would like to remind you the sub-themes that are listed at: www.isast.org . Perhaps you have another topic relevant to the library theory and practice. We would like to tell us about! The deadline for proposals is 15th March 2011. If you have any questions concerning the Call for Proposals, please contact: Anthi Katsirikou, anthi**asmda.com and secretariat**isast.org Looking forward to meeting you in Athens, Kind regards, Dr. Anthi Katsirikou Conference co-chair Deputy Director, University of Piraeus Library European Documentation Center Adjunct Lecturer at TEI of Athens Member of the Board of the Association of Greek Librarians and Information Professionals If you don't like to receive information regarding the QQML and DLMC conferences and our publications and meetings please: unsubscribe ------=_NextPart_000_2880_01CBD88A.EB83C900 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Dear Colleagues,

Dear = Colleagues,

 

Don’t miss the 3rd-round submissions to the 3rd QQML2011 = International Conference and the DLMC2011 Digital Library Conference that starts now = until 15 March 2011<= /b>.

Please think of abstract or paper submission and disseminate this Call for = Papers to your colleagues.

[Those of you who have already email your abstract(s) or paper(s) during the = last call, please ignore this announcement]

The Qualitative and Quantitative Methods in Libraries International = Conference (QQML2011, http://www.isast.org/qqml2011= .html ) and the Digital Library International Conference (DLMC2011, http://www.isast.org/dl= mcconference.html ) aim to bring together researchers and scientists from academia, = libraries, archives, museums, from governmental and non government organizations to present new results and identify future research interests. =

All papers will be published in the QQML2011 and the DLMC2011 proceedings = and/or in scientific journals. The proceedings of the 2009 QQML International conference are published by World Scientific and the 2010 = QQML proceedings will be published soon by the = same publisher.

To fulfill QQML and DLMC goals and success we are inviting = proposals for:

 

  • Conference Presentations: 20- 25 minute presentations.
  • Conference Workshops: 4 – 5 hour = workshops.
  • New researchers’ research = results.

 

We would like to = remind you the sub-themes that are listed at: www.isast.org.

 

Perhaps you have = another topic relevant to the library theory and practice. We would like to tell us = about!

 

The deadline for = proposals is 15th March 2011.

 

If you have any = questions concerning the Call for Proposals, please contact: =

Anthi Katsirikou, anthi**asmda.com and secretariat**isast.org =

 

Looking forward to = meeting you in Athens,

Kind = regards,

 

Dr. Anthi = Katsirikou

Conference = co-chair

Deputy Director,<= o:p>

University of Piraeus = Library

European Documentation Center

Adjunct Lecturer at = TEI of Athens

Member of the = Board of the Association of Greek Librarians and Information = Professionals

 

 

 

 

 

 

 

 

If you don’t = like to receive information regarding the QQML and = DLMC conferences and our publications and meetings = please: unsubscribe

 

 

 

------=_NextPart_000_2880_01CBD88A.EB83C900-- From owner-chemistry@ccl.net Wed Mar 2 18:19:00 2011 From: "James Gary Prudhomme jprudhomme%x%healthtech.com" To: CCL Subject: CCL: Course: Druggable Sites for Protein-Protein Interaction Targets Message-Id: <-44040-110302152651-28007-ZbkFe/8ZcJbPugo9kFNaLg,+,server.ccl.net> X-Original-From: "James Gary Prudhomme" Date: Wed, 2 Mar 2011 15:26:49 -0500 Sent to CCL by: "James Gary Prudhomme" [jprudhomme_._healthtech.com] Cambridge Healthtech Institute & Bio-IT World Announce Upcoming Dinner Short Course: Identification of Druggable Sites for Protein-Protein Interaction Targets June 8, 2011 (6:00 9:00 p.m.) Royal Sonesta Hotel Boston, Cambridge, MA Register at https://chidb.com/register/2011/sbd/reg.asp Course topics: * The problem of disrupting protein-protein interactions * Predicting the structure of protein-protein complexes using fragment-based identification of binding hot spots * Druggability of binding sites determined by the hot spots * Identification of functional groups with preferential binding to hot spots * Comparison of computational and experimental approaches. Course Instructors: Sandor Vajda, Ph.D., Professor, Departments of Biomedical Engineering and Chemistry, Boston University Dima Kozakov, Ph.D., Research Assistant Professor, Departments of Biomedical Engineering, Boston University Additional information and registration details for this course and conference is available at http://www.healthtech.com/sbd or call CHI at 781-972-5400. A separate registration is required to attend the Structure-Based Drug Design conference that is scheduled for June 6-8, 2011. If you would like to also attend the Structure-Based Drug Design conference, you can save up to $350 if you register by Friday, March 11. Contact: James Prudhomme Cambridge Healthtech Institute 250 First Avenue, Suite 300 Needham, MA 02494 Phone: 781-972-5400 Fax: 781-972-5425 www.healthtech.com From owner-chemistry@ccl.net Wed Mar 2 18:54:00 2011 From: "Brian Austin brianmaustin||gmail.com" To: CCL Subject: CCL:G: software to visualize Gaussian cube files Message-Id: <-44041-110302172300-7665-ZMWjUcuCXa3k/S3ADrfR/g!=!server.ccl.net> X-Original-From: Brian Austin Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 2 Mar 2011 14:22:32 -0800 MIME-Version: 1.0 Sent to CCL by: Brian Austin [brianmaustin===gmail.com] Hi Neranjan, I've used gabedit to do this. http://gabedit.sourceforge.net/ -Brian On Wed, Mar 2, 2011 at 9:58 AM, Neranjan Perera neranjan007^^gmail.com wrote: > > Sent to CCL by: "Neranjan  Perera" [neranjan007++gmail.com] > Hi all, > I would like to know is there any software that can be used to visualize gaussian cube files which can show molecular orbitals? > > I am using 09 and tried using gopenmol and molden to visualize but it doesn't work at all. In gopenmol, I created the *.plt file and the *.crd files and tried to visualize it but when i tried to import the *.plt file , the program crashed. > >  thanks for the help. > > neranjan>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml>      http://www.ccl.net/spammers.txt> > >