From owner-chemistry@ccl.net Thu May 11 07:49:00 2006 From: "D. Boyd boyd\a/chem.iupui.edu" To: CCL Subject: CCL: Program for similarity index calculation Message-Id: <-31744-060510221102-14700-QWK3VOPT87CDVAjjVg7Yjg]*[server.ccl.net> X-Original-From: "D. Boyd" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 10 May 2006 21:10:50 -0400 Mime-Version: 1.0 (Apple Message framework v623) Sent to CCL by: "D. Boyd" [boyd---chem.iupui.edu] Dear Anderson, Another nice free service is Guha's CDK Web Services: Similarity Calculator, http://blue.chem.psu.edu/~rajarshi/code/java/cdkws.html. Don Boyd Editor Emeritus, Reviews in Computational Chemistry From owner-chemistry@ccl.net Thu May 11 10:20:00 2006 From: "Roger Kevin Robinson r.robinson(!)imperial.ac.uk" To: CCL Subject: CCL:G: Gaussian Segmentation Fault termination via Lnk1e in /opt/gaussian03/g03/l9999.exe Message-Id: <-31745-060511101754-30381-QTSK6M3f/1F8NgNs+FMNPg{:}server.ccl.net> X-Original-From: Roger Kevin Robinson Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 11 May 2006 15:18:09 +0100 MIME-Version: 1.0 Sent to CCL by: Roger Kevin Robinson [r.robinson]|[imperial.ac.uk] Hi, I keep getting segmentation faults with gaussian. Its on TS jobs and some G3B3 calculations. Its when the program is passed to l9999.exe deireclty after a quote. Im pretty sure the complilation is sound. this is the error in the shell **** Segmentation fault! Fault address: 0x3ec00003bb5 Fault address is 4312054295477 bytes above the nearest valid mapping boundary, which is at 0x5895000. You can obtain a view of your program's memory map at the time of the crash by rerunning with the F90_DUMP_MAP environment variable set to a non-empty string. and this in the shell UPON WHICH ONE COULD HAVE BUILT. -- A.EINSTEIN Error termination request processed by link 9999. Error termination via Lnk1e in /opt/gaussian03/g03/l9999.exe at Thu May 11 13:35:32 2006. Job cpu time: 0 days 0 hours 0 minutes 7.0 seconds. File lengths (MBytes): RWF= 19 Int= 0 D2E= 0 Chk= 10 Scr= I've tried uping the memory using 1 processor uptime the size of the scratch directory. I cant even do the TS job example from Exploring chemistry with electronic structure methods 2ed. - Foresman, Frisch I've ran plenty of other G3B3 jobs with out error it mainly seems to be a fault locating Transistion States. Any ideas ? Thanks Roger From owner-chemistry@ccl.net Thu May 11 11:03:01 2006 From: "Joseph T Golab joseph.golab-,-innovene.com" To: CCL Subject: CCL: FOMMS 2006 Early Registration Deadline -- 15-May-2006 Message-Id: <-31746-060511105945-20858-IsfkCl91h8TfjxjPbVaTMg^server.ccl.net> X-Original-From: "Joseph T Golab" Date: Thu, 11 May 2006 10:59:41 -0400 Sent to CCL by: "Joseph T Golab" [joseph.golab(_)innovene.com] We take this opportunity to remind you that the deadline for FOMMS 2006 Early Registration is May 15! 3rd International Conference on the Foundations of Molecular Modeling and Simulation (FOMMS 2006), Semiahmoo Resort, Blaine, WA, USA, July 9th - 14th, 2006 >> Deadline for Early Registration May 15 2006 << The 3rd International Conference on the Foundations of Molecular Modeling and Simulation (FOMMS), will be held July 9th - 14th, 2006, at Semiahmoo Resort (www.semiahmoo.com), in Blaine, WA, USA. FOMMS 2006 is a scientific meeting balanced between the methods of quantum mechanics, atomistic simulation, mesoscale methods and beyond, with application areas in chemistry, biology, and materials. FOMMS is the only focused conference that brings together such a broad modeling community and emphasizes integration from atomistic to meso- & macro-scale modeling. A detailed conference agenda as well as housing and travel information are available at the FOMMS 2006 website (www.fomms.org). You are encouraged to take advantage of the early registration fee before the May 15 deadline! FOMMS 2006 Program Keynote Address Professor Mark A. Ratner Nanoscience & Nanotechnology Professor Glenn Fredrickson Professor Katsumi Kaneko Professor Jerzy Bernholc Contributed Poster Session A Education Dr. Warren Hehre Professor Michael Allen Polymeric Materials Professor Kurt Kremer Dr. Shi-aki Hyodo Professor Mark W. Matsen Advances in Modeling & Simulation Dr. Philippe Ungerer Professor Denis Evans Biological Applications Professor Carol K. Hall Professor Shekhar Garde Professor Gerhard Hummer Methods & Applications for Materials Modeling Professor Gregory A. Voth Professor C. Richard A. Catlow Reaction Engineering Professor Emily A. Carter Professor Randall Q. Snurr Professor Rutger A. van Santen Contributed Poster Session B Future Vision Professor Vijay Pande Dr. Patricia T. Sparrell Dr. Thom Dunning For additional information about the conference please visit our web site or contact us directly at chair]^[fomms.org. Joe Golab (Ineos Technoloiges) & Clare McCabe (Vanderbilt University) FOMMS 2006 Conference Chairs, chair]^[fomms.org From owner-chemistry@ccl.net Thu May 11 12:54:01 2006 From: "Thomas H Dr Pierce TPierce _ rohmhaas.com" To: CCL Subject: CCL: Ask help for launching autodock tools in Vmware Message-Id: <-31747-060511124117-22431-zW95GSHmqSYjdt5f1Jy4+Q|a|server.ccl.net> X-Original-From: Thomas H Dr Pierce Content-Type: multipart/alternative; boundary="=_alternative 005BA6AC8525716B_=" Date: Thu, 11 May 2006 12:41:06 -0400 MIME-Version: 1.0 Sent to CCL by: Thomas H Dr Pierce [TPierce]^[rohmhaas.com] This is a multipart message in MIME format. --=_alternative 005BA6AC8525716B_= Content-Type: text/plain; charset="US-ASCII" Edit /etc/X11/XFree86Config and select in the module section DRI ------ Sincerely, Tom Pierce Bldg 7/ Rm 207D - Spring House, PA 215-641-7475 - Office owner-chemistry__ccl.net wrote on 05/10/2006 07:26:50 PM: > Sent to CCL by: "Bo Li" [liboqd .. gmail.com] > Hi: > > I installed Redhat 9 in Vmware 5, in order to run Autodock on it. I have > successfully installed Autodock Tools(ADT), but everytime I launched PMV, > I received the following message and PMV paused: > > Run PMV from /usr/local/lib/python2.4/site-packages/Pmv > Xlib: extension "XFree86-DRI" missing on display ":0.0". --=_alternative 005BA6AC8525716B_= Content-Type: text/html; charset="US-ASCII"
Edit /etc/X11/XFree86Config
and select in the module section DRI

------
Sincerely,

  Tom Pierce
   Bldg 7/ Rm 207D - Spring House, PA
   215-641-7475 - Office  

owner-chemistry__ccl.net wrote on 05/10/2006 07:26:50 PM:

> Sent to CCL by: "Bo  Li" [liboqd .. gmail.com]
> Hi:
>
> I installed Redhat 9 in Vmware 5, in order to run Autodock on it. I have
> successfully installed Autodock Tools(ADT), but everytime I launched PMV,
> I received the following message and PMV paused:
>
> Run PMV from  /usr/local/lib/python2.4/site-packages/Pmv
> Xlib:  extension "XFree86-DRI" missing on display ":0.0".

 --=_alternative 005BA6AC8525716B_=-- From owner-chemistry@ccl.net Thu May 11 15:20:00 2006 From: "Alex A. Granovsky gran[A]classic.chem.msu.su" To: CCL Subject: CCL: The final PC GAMESS v. 7.0 release announcement Message-Id: <-31748-060511151325-27647-cgfmENv67ypODjQzet08IA(-)server.ccl.net> X-Original-From: "Alex A. Granovsky" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="koi8-r" Date: Thu, 11 May 2006 21:43:43 +0400 MIME-Version: 1.0 Sent to CCL by: "Alex A. Granovsky" [gran++classic.chem.msu.su] Dear GAMESS users, I am glad to inform you that the final, official version of the PC GAMESS v. 7.0 was released today and is available from the PC GAMESS download site at ISU: http://www.msg.ameslab.gov/GAMESS/pcgamess.shtml The PC GAMESS page at MSU was updated as well: http://classic.chem.msu.su/gran/gamess/ Our big thanks to all testers of the intermediate PC GAMESS releases! As compared with the previous public release v. 6.4, PC GAMESS v. 7.0 includes the following enhancements and new features: much faster MCQDPT code with SMP support and optional semidirect integral transformation for large-scale jobs, newly developed 2-electron integral code package, faster direct HF/DFT code, Quantum Fast Multipole Method and Linear Exchange for linear scaling HF and DFT, support of spherical basis functions, support of general contraction basis sets, large-scale direct and conventional parallel MCSCF program, Configuration Interaction Singles (CIS), Time-dependent Hartree-Fock (TDHF) and density functional theory (TDDFT) for excited states with full support of any point group molecular symmetry, static and dynamic (hyper)polarizabilities via TDDFT, unified support of different MPI implementations under Windows, improved Linux compatibility, initial optimization for Intel Core (Woodcrest/Conroe/Merom processors) microarchitecture, and many other improvements and performance enhancements. We are strongly encouraging all PC GAMESS users to upgrade to the most recent binaries. Beta testers, please upgrade as well, as there are several known bugs in the intermediate releases. Best regards, Alex Granovsky ------------------------- Dr. Alex A. Granovsky The PC GAMESS project, Laboratory of Chemical Cybernetics, Moscow State University From owner-chemistry@ccl.net Thu May 11 20:37:00 2006 From: "rodrigo souza souzarod21~~yahoo.com.br" To: CCL Subject: CCL:G: Logic error in SftOpn Message-Id: <-31749-060511145315-24924-EDolp6xFEdhrvX2yTttO7w^^server.ccl.net> X-Original-From: rodrigo souza Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-1657153092-1147369987=:31910" Date: Thu, 11 May 2006 14:53:07 -0300 (ART) MIME-Version: 1.0 Sent to CCL by: rodrigo souza [souzarod21 a yahoo.com.br] --0-1657153092-1147369987=:31910 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hi, Somebody can help me with this error in gaussian calculations? Logic error in SftOpn. Error termination via Lnk1e in /usr/local/bin/g03/l502.exe at Sat Jul 29 07:50:53 2000. Job cpu time: 0 days 0 hours 3 minutes 34.5 seconds. File lengths (MBytes): RWF= 43 Int= 0 D2E= 0 Chk= 2 Scr= 1 Thank you Rodrigo Souza --------------------------------- Novidade no Yahoo! Mail: receba alertas de novas mensagens no seu celular. Registre seu aparelho agora! --0-1657153092-1147369987=:31910 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
Hi,

     Somebody can help me with this error in gaussian calculations?

Logic error in SftOpn.
 Error termination via Lnk1e in /usr/local/bin/g03/l502.exe at Sat Jul 29 07:50:53 2000.
 Job cpu time:  0 days  0 hours  3 minutes 34.5 seconds.
 File lengths (MBytes):  RWF=     43 Int=      0 D2E=      0 Chk=      2 Scr=      1

Thank you

Rodrigo Souza

Novidade no Yahoo! Mail: receba alertas de novas mensagens no seu celular. Registre seu aparelho agora! --0-1657153092-1147369987=:31910--