From owner-chemistry@ccl.net Wed Aug 17 11:05:03 2005 From: "CCL" To: CCL Subject: CCL: Problem runing job in G03. Message-Id: <-28972-050817110050-23238-jTKKlThOvCLwkE03HCXsVw!^!server.ccl.net> X-Original-From: Delwar Hossain Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-408457819-1124290841=:62309" MIME-Version: 1.0 Sent to CCL by: Delwar Hossain --0-408457819-1124290841=:62309 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear CCL members, I am facing problem to optimize structure in GO3. The structure optimize at B3LYP/6-311G. When I try to use 6-311G* and 6-311+G* I got the following error message: Search did not lower the energy significantly. No lower point found -- run aborted. Error termination via Lnk1e in /usr/local/appl/g03/l508.exe at Wed Aug 17 00:02:28 2005. Job cpu time: 0 days 9 hours 43 minutes 32.1 seconds. File lengths (MBytes): RWF= 37 Int= 0 D2E= 0 Chk= 11 Scr= 1 I used SCF=QC and OPT=CalcFC and still I got the same results. I therefore request you to send your valuale comments and suggestion. Thank you. Sincerely yours, Delwar Hossain hossaind2004!^!yahoo.com --------------------------------- Start your day with Yahoo! - make it your home page --0-408457819-1124290841=:62309 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
Dear CCL members,
I am facing problem to optimize structure in GO3. The structure optimize at B3LYP/6-311G. When I try to use 6-311G* and 6-311+G* I got the following error message:
 Search did not lower the energy significantly.
 No lower point found -- run aborted.
 Error termination via Lnk1e in /usr/local/appl/g03/l508.exe at Wed Aug 17 00:02:28 2005.
 Job cpu time:  0 days  9 hours 43 minutes 32.1 seconds.
 File lengths (MBytes):  RWF=     37 Int=      0 D2E=      0 Chk=     11 Scr=      1
I used SCF=QC and OPT=CalcFC and still I got the same results.
I therefore request you to send your valuale comments and suggestion.
Thank you.
Sincerely yours,
Delwar Hossain
hossaind2004!^!yahoo.com

Start your day with Yahoo! - make it your home page --0-408457819-1124290841=:62309-- From owner-chemistry@ccl.net Wed Aug 17 10:52:51 2005 From: "CCL" To: CCL Subject: CCL: FULLFILLED: PhD position in Computational Chemistry, ENS Lyon, Fr Message-Id: <-28971-050817105124-21374-jTKKlThOvCLwkE03HCXsVw%x%server.ccl.net> X-Original-From: Paul Fleurat-Lessard Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed MIME-Version: 1.0 Sent to CCL by: Paul Fleurat-Lessard Dear CCL'ers, Thank you for your help in providing very good applications for this position. The Ph.D. is now fullfilled. Regards, Paul. -- Fleurat-Lessard Paul, Lecturer e-mail: Paul.Fleurat-Lessard%x%ens-lyon.fr Laboratoire de Chimie Ecole Normale Supérieure de Lyon Tel: + 33 (0)4 72 72 81 54 46, Allée d'Italie Fax: + 33 (0)4 72 72 88 60 69364 Lyon Cedex 07 Si vous ne pouvez expliquer un concept à un enfant de six ans, c'est que vous ne le comprenez pas complètement. Albert Einstein From owner-chemistry@ccl.net Wed Aug 17 12:55:03 2005 From: "CCL" To: CCL Subject: CCL: how to plot Dials-Windows of DNA Message-Id: <-28973-050817123349-25583-jTKKlThOvCLwkE03HCXsVw#%#server.ccl.net> X-Original-From: jz7#%#duke.edu Content-Type: TEXT/PLAIN; charset=US-ASCII MIME-Version: 1.0 Sent to CCL by: jz7#%#duke.edu Dear all, I am looking for a free software that can plot the Dials and Windows for DNA MD simulation (or frames). I already got the output data from Curves program. But don't know how to visualize it. I googled on the web, and find that MxCurv from Univ. of Pune can do the plot. However, I don't know where to get the program. Any information would be appreciated! Thanks! Jeny From owner-chemistry@ccl.net Wed Aug 17 15:37:30 2005 From: "CCL" To: CCL Subject: CCL: New BioCoRE server released Message-Id: <-28974-050817133646-12271-jTKKlThOvCLwkE03HCXsVw-#-server.ccl.net> X-Original-From: Robert Brunner Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed Mime-Version: 1.0 (Apple Message framework v734) Sent to CCL by: Robert Brunner The Theoretical and Computational Biophysics Group at the University of Illinois is proud to announce the release of a completely new incarnation of the Biological Collaborative Research Environment (BioCoRE) Server software. BioCoRE is a tool-oriented web-based collaborative environment where users create project groups and can then share molecular views, messages, files, and more among the members of their projects. BioCoRE is freely available for use and testing on the Theoretical and Computational Biophysics Group's BioCoRE server and the server software is distributed free of charge. Development is supported by the NIH National Center for Research Resources. The Theoretical and Computational Biophysics Group (TCBG) has been developing the BioCoRE collaborative environment for several years and has completely redesigned the interface and underlying code structure. The new version of the server has a more modern look, previously unavailable features, such as a poll/quiz generation module, and is generally much more robust (particularly in the area of file sharing among collaborators). This new version, which was previously only available for testing on the TCBG's server, is now available for installation at remote locations. Installation of a BioCoRE server offers users potentially faster access and gives administrators increased customizability. BioCoRE Tour - Familiarize yourself with BioCoRE's features. http://www.ks.uiuc.edu/Research/biocore/tour/ BioCoRE Test Server - The TCBG BioCoRE server is available for testing and is always running the latest version. We encourage you to create and test an account on our server before installing your own server. http://www.ks.uiuc.edu/Research/biocore/ Server Software Download - For installing your own server. http://www.ks.uiuc.edu/Research/biocore/localServer/ The TCBG encourages BioCoRE users and server administrators to be closely involved in the development process through reporting bugs, contributing fixes, periodical surveys and via other means. Questions or comments may be directed to biocore-#-ks.uiuc.edu. We are eager to hear from you, and thank you for using our software! The BioCoRE Team From owner-chemistry@ccl.net Wed Aug 17 18:37:01 2005 From: "CCL" To: CCL Subject: CCL: W:Installing Tinker on Linux cluster Message-Id: <-28975-050817183002-9231-jTKKlThOvCLwkE03HCXsVw===server.ccl.net> X-Original-From: "Vanessa Oklejas" Sent to CCL by: "Vanessa Oklejas" Hi All, I want to install Tinker v 4.2 onto a file server so I can run MD simulations on a cluster running Linux. I copied the self-extracting installation kit into my directory, but I can't seem to launch the self-extracting file. A quick look at the permissions of the file shows that it is not executable. Can someone tell me how to launch the file? Also, could someone tell me what they think of using the new Tinker GUI (Force Field Explorer) on a Linux platform? Thanks, Vanessa voklejas===stanford.edu