From owner-chemistry@ccl.net Mon Oct 22 08:53:01 2007 From: "Gonzalo Jim nez-Os s gjimenez_-_unizar.es" To: CCL Subject: CCL: Parallel runs in Turbomole -Summary- Message-Id: <-35437-071022085205-7095-5GFurxzs5vQRM84ZKtpeZA*|*server.ccl.net> X-Original-From: "Gonzalo Jim nez-Os s" Date: Mon, 22 Oct 2007 08:52:01 -0400 Sent to CCL by: "Gonzalo Jim nez-Os s" [gjimenez+*+unizar.es] Dear CCL'ers, Fortunately, I`ve been able to run Turbomole in parallel with your help. It was simply a tricky problem with the environment variables, as many people suggested. Installing Turbomole outside the TmoleX folder and re-setting the parallel environment properly just made it work !!! It must be noted that no ssh password is now required and the N+1 processes starts immediately. I am currently testing the scaling ability of Turbomole on my machines, but in the meanwhile I must say that the code is really fast in serial mode (at least with the RI functionality enabled). I'm still a novel user, but it has been revealed as a really interesting QM package to me. Special thanks go to Uwe Huniar from COSMOLogic, who pointed exactly in the right direction, and to Jozsef Csontos, Mark Hahn and Jeff Hammond for their valuable comments. Here are their answers: *********************** Hi, your $TURBODIR setting points to a TmoleX installation and not to a non-GUI based installation. TmoleX does not contain the parallel version of Turbomole (not yet supported by the GUI), hence the shared libraries are usually not present - although it seems that the parallel version has been installed there in addition by hand, could that be? Replacing the serial binaries by the parallel ones might even work with TmoleX, but that has never been tested... Anyway, the problem stems from system settings or the installation. So please contact the Turbomole Support and/or your local Turbomole administrator. Parallel benchmarks have been done some time ago, but they are simply too old to be meaningful nowadays. We are planning to publish a white book about the parallel version of Turbomole together with HP, you will find the results on our web site (www.cosmologic.de) as soon as they are available. Regards, Uwe *********************** I'm not a Turbomole user, but this isn't a Turbomole problem. Your parallel nodes cannot find the MKL shared object libguide.so under MPI. Here's a few suggestions: 1. Have your job submission system export the environment when it submits. In PBS this is the -V flag I think. 2. Set LD_LIBRARY_PATH and LD_RUN_PATH appropriately or use the MKL environment script in ~/MKLDIR/tools with 'source mklvars.csh' 3. Link MKL statically. If MKL is on a part of the file system not visible to the compute nodes, then this is required. Try and check if /opt/... is visible to the compute nodes and that the environment variables are setup so that they know where to look. Best, Jeff *********************** Hi, I have no experience with turbomole at all but it seems to me that you don't have passwordless connection to the working nodes. (You said "when I launch the executable (e.g. jobex -ri) the calculation crashes after entering my ssh password") You should work on this issue. (for example: generate a public key with "ssh-keygen -t rsa" on the master node then put the content of the generated file into the authorized_keys file on the working nodes "cat ~/.ssh/id_rsa.pub | ssh hostname_of_your_working_node "cat- >> ~/.ssh/authorized_keys") However, this procedure strongly depends on your cluster configuration. I hope it helps, Jozsef *********************** as another followup mentioned, you should take a few minutes to set up passwordless ssh. the poster recommended a key-based approach, which I consider to be somewhat hazardous. I prefer to ensure that nodes in a cluster all trust the admin/login nodes (host-based trust, still fully secure, implemented using shosts.equiv). as you can see, the program hasn't even gotten close to setting up MPI mode. you have to explicitly provide the location of shared libraries, much like how $PATH has to be configured. your choice is either to do it system-wide (by altering /etc/ld.so.conf and re-running ldconfig, which updates /etc/ld.so.cache), or by setting LD_LIBRARY_PATH to include that directory. in either case, the point is simply to make sure that ld.so knows how to find the libraries. *********************** Best regards, Gonzalo From owner-chemistry@ccl.net Mon Oct 22 09:28:01 2007 From: "N. Sukumar nagams() rpi.edu" To: CCL Subject: CCL: Wavelet Analysis of Molecular Surface Properties. Message-Id: <-35438-071021195831-22587-yZM5MJ7CuxR8oUvQcY8Kpw{:}server.ccl.net> X-Original-From: "N. Sukumar" Content-Disposition: inline Content-Transfer-Encoding: binary Content-Type: text/plain Date: Sun, 21 Oct 2007 18:43:57 -0400 MIME-Version: 1.0 Sent to CCL by: "N. Sukumar" [nagams]-[rpi.edu] Perhaps this is the Powerpoint you refer to: http://www.drugmining.com/files/RECON/recondoc/ACS_Boston_PEST/ Slides 5-7 deal with Wavelets. More in the Rev. Comp. Chem. chapter that Curt referred to: C. Matthew Sundling; N. Sukumar; Hongmei Zhang; Mark J. Embrechts; Curt M. Breneman, "Wavelets in chemistry and cheminformatics." Reviews in Computational Chemistry (2006), 22 295-329. CODEN: RCCHEY ISSN:1069-3599. AN 2006:161999 N. Sukumar Associate Research Professor of Chemistry and Chemical Biology Center for Biotechnology and Interdisciplinary Studies Rensselaer Polytechnic Institute http://reccr.chem.rpi.edu/ ==============Original message text=============== On Sun, 21 Oct 2007 14:19:51 EDT "David Hose anthrax_brothers,+,hotmail.com" wrote: Sent to CCL by: "David Hose" [anthrax_brothers%hotmail.com] Hi Guys, Ive got a problem that you might be able to help me with, or at least point me in the right direction. Heres some background. As you all know, molecular surfaces are useful in explaining certain molecular phenomena. What I want to do, is take these 4D surfaces and compress them as a 2D graph, by dividing the surface up into tesserae, and then plotting a charge/frequency chart from them. This approach has been used by Liu at Virginia Tech to create sigma profiles using COSMO surfaces (http://www.design.che.vt.edu/VT-2005.html). If I recall correctly, regular contributor to this list, Andreas Klamt has also done something related to this as well. I came across a PowerPoint presentation some months ago that mentioned that these types property/ frequency charts can be compressed by using Wavelet analysis. Unfortunately, I cant find the presentation again. So my question is, how can I compress these property/frequency charts using Wavelet Analysis? If anyone can point me in the right direction of the maths / algorithms I would grateful. TIA. Dave.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt===========End of original message text=========== From owner-chemistry@ccl.net Mon Oct 22 11:20:01 2007 From: "Shirley Peng shirley,+,chemcomp.com" To: CCL Subject: CCL: =?us-ascii?Q?Chemical_Computing_Group_Releases_the_Molecular_Operating_En?= =?us-ascii?Q?vironment_for_the_SolarisT_10_Operating_System?= Message-Id: <-35439-071022111547-19677-r1xM0PObESvsYnftDmXmiw:server.ccl.net> X-Original-From: "Shirley Peng" Content-Type: multipart/alternative; boundary="----=_NextPart_000_0192_01C8149C.D734BAF0" Date: Mon, 22 Oct 2007 11:15:23 -0400 MIME-Version: 1.0 Sent to CCL by: "Shirley Peng" [shirley^^chemcomp.com] This is a multi-part message in MIME format. ------=_NextPart_000_0192_01C8149C.D734BAF0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit MONTREAL, October 22, 2007 - Chemical Computing Group Inc. (CCG) announces the general release of the 2007.09 version of the Molecular Operating Environment (MOE) for the SolarisT 10 Operating System (OS) > from Sun Microsystems Inc. running on UltraSPARCR and x86 architectures. Paul Labute, President and CEO of CCG said that "we have supported Sun's UltraSPARC platform for more than a decade and we are pleased to extend that support with the Solaris 10 OS to x86 servers and workstations platforms as well. We will be delivering the new executables for UltraSPARC and x86 to all MOE customers and we believe that the combination of MOE's flexibility with the reliability and scalability of the Solaris 10 OS will be of great benefit to our customers." Joerg Schwarz, Director, Heathcare and Life Sciences, of Sun Microsystems said "We're pleased that CCG, a leader in the Life Sciences industry, has chosen to extend their support of the Solaris 10 OS to the x86 platform. This decision offers the industry the opportunity to run Solaris on hundreds of systems from numerous suppliers as well as the latest high-performance systems from Sun Microsystems." About Chemical Computing Group Inc. Chemical Computing Group Inc. is a leading supplier of scientific software for Life Sciences and has been operating since 1994. Chemical Computing Group's software platform is the Molecular Operating Environment (MOE) that integrates visualization, simulation and methodology development in one package. MOE contains a wide variety of built-in applications in the fields of Cheminformatics, Bioinformatics, Computer-Aided Molecular Design and Molecular Modeling. MOE runs on a wide variety of computers including Windows, Linux, Macintosh and Unix systems both for the desktop and in parallel computing clusters. MOE is used by biologists, medicinal chemists and computational chemists in many pharmaceutical companies, biotechnology companies and universities throughout the world. Chemical Computing Group is headquartered in Montreal, Canada. Its web site is www.chemcomp.com. E-mail inquiries can be sent to info ~ chemcomp.com. Sun, Sun Microsystems and Solaris are trademarks of Sun Microsystems, Inc. in the United States and other countries. All SPARC trademarks are used under license and are trademarks or registered trademarks of SPARC, International, Inc. in the US and other countries. Products bearing SPARC trademarks are based upon an architecture developed by Sun Microsystems, Inc. ------=_NextPart_000_0192_01C8149C.D734BAF0 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

MONTREAL= , October 22, = 2007 – Chemical Computing Group Inc. (CCG) announces the general release of the 2007.09 version of the Molecular = Operating Environment (MOE) for the Solaris™ 10 Operating System (OS) from = Sun Microsystems Inc. running on UltraSPARC® = and x86 architectures.

<= o:p> 

P= aul Labute, President and CEO of CCG said that “we have supported = Sun's UltraSPARC platform for more than a decade and we = are pleased to extend that support with the Solaris 10 OS to x86 = servers and workstations platforms as well.  = We will be delivering the new executables for UltraSPARC and x86 to all MOE customers and we believe that the combination of MOE’s flexibility with the reliability and scalability of the Solaris 10 OS will be of great benefit to our customers.”

<= o:p> 

Joerg Schwarz, Director, Heathcare and Life = Sciences, of Sun Microsystems said "We're pleased that CCG, a leader in the Life Sciences industry, has chosen to extend their support of the Solaris 10 = OS to the x86 platform. This decision offers the = industry the opportunity to run Solaris on hundreds of systems from numerous = suppliers as well as the latest high-performance systems from Sun = Microsystems."

<= o:p> 

About Chemical Computing = Group Inc.

C= hemical Computing Group Inc. is a leading supplier of scientific software for = Life Sciences and has been operating since 1994.  Chemical Computing Group’s software platform is the = Molecular Operating Environment (MOE) that integrates visualization, simulation = and methodology development in one package.  MOE contains a wide variety of built-in applications in the = fields of Cheminformatics, Bioinformatics, Computer-Aided = Molecular Design and Molecular Modeling.  MOE runs on a wide variety of computers including Windows, Linux, Macintosh and = Unix systems both for the desktop and in parallel = computing clusters.  MOE is used by = biologists, medicinal chemists and computational chemists in many pharmaceutical = companies, biotechnology companies and universities throughout the = world.

<= o:p> 

C= hemical Computing Group is headquartered in = Montreal, Canada.  = Its web site is www.chemcomp.com.  E-mail inquiries can be sent to info ~ chemcomp.com.

<= o:p> 

Su= n, Sun Microsystems and Solaris are trademarks of Sun Microsystems, Inc. in = the United = States and other countries.  All SPARC trademarks are used = under license and are trademarks or registered trademarks of SPARC, International, = Inc. in the US and other countries.  Products bearing SPARC = trademarks are based upon an architecture developed by Sun Microsystems, Inc. =

 

------=_NextPart_000_0192_01C8149C.D734BAF0-- From owner-chemistry@ccl.net Mon Oct 22 11:59:00 2007 From: "Ivanciuc, Ovidiu I. oiivanci|a|utmb.edu" To: CCL Subject: CCL: about program for molecular descriptor Message-Id: <-35440-071022115229-4115-8/D/dF8hDclIKDUE5T3HnA++server.ccl.net> X-Original-From: "Ivanciuc, Ovidiu I." Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Mon, 22 Oct 2007 10:47:28 -0500 MIME-Version: 1.0 Sent to CCL by: "Ivanciuc, Ovidiu I." [oiivanci-,-utmb.edu] >>>Does anybody know a "free" library or package to compute molecular >>>descriptors, beside CDK API, or a free program. Best free server: Parameter Client http://www.vcclab.org/lab/pclient/ http://146.107.217.178/lab/pclient/ E-Dragon http://www.vcclab.org/lab/edragon/ http://146.107.217.178/lab/edragon/ For QSAR papers that use DRAGON descriptors, see = http://biochempress.com/ Other free servers: MODEL - Molecular Descriptor Lab http://jing.cz3.nus.edu.sg/cgi-bin/model/model.cgi PreADMET http://preadmet.bmdrc.org/preadmet/index.php http://preadmet.bmdrc.org/preadmet/query/query1.php O. From owner-chemistry@ccl.net Mon Oct 22 12:40:01 2007 From: "Hu, Zengjian zhu:+:Howard.edu" To: CCL Subject: CCL: FW: Call for Papers: iCBBE 2008 (published by IEEE, indexed by EI ) Message-Id: <-35441-071022104419-6357-cMw7IeFldX/VvJnlzQbL5w=-=server.ccl.net> X-Original-From: "Hu, Zengjian" Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C814B5.3D117710" Date: Mon, 22 Oct 2007 10:10:02 -0400 MIME-Version: 1.0 Sent to CCL by: "Hu, Zengjian" [zhu!^!Howard.edu] This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. ------_=_NextPart_001_01C814B5.3D117710 Content-Type: text/plain; charset="iso-2022-jp" Subject: Call for Papers: iCBBE 2008 (published by IEEE, indexed by EI) 2008 International Conference on Bioinformatics and Biomedical Engineering (iCBBE) Submission Deadline: Dec. 10th, 2007 May 16th to 18th, 2008, Shanghai, China http://www.icbbe.org 　 　 Dear Collegue, The 1st International Conference on Bioinformatics and Biomedical Engineering (iCBBE2007) was held susessfully from July 7th to 9th, 2007 at RAMADA hotel, Wuhan, China. More than 250 authors coming from 15 countries attended the conference. Now all the accepted papers are included in IEEE Xplore and EI Inspec, and will be indexed by EI Compendex soon. 　 The 2nd International Conference on Bioinformatics and Biomedical Engineering (iCBBE2008: www.icbbe.org ) will be held > from May 16th to 18th, 2008 in Shanghai, China. iCBBE2008 will bring together top researchers from Asian Pacific areas, North America, Europe and around the world to exchange research results and address open issues in all aspects of bioinformatics and biomedical engineering. As we did in iCBBE 2007, All accepted papers in iCBBE 2008 will be published by IEEE, AND will be indexed by EI Compendex. 　 The conference is soliciting state-of-the-art research papers in the following areas of interest: * Bioinformatics and Computational Biology * Sequence analysis and sequence alignment * Gene finding and gene function recognition * Genome assembly and genome annotation * Analysis of gene expression * Analysis of regulation * Computational evolutionary biology * Measuring biodiversity * Protein structure alignment * Protein structure prediction and structure based drug design * Protein-protein interactions and protein-protein docking * Comparative genomics * Modeling biological systems * High-throughput image analysis * Gene Ontology and taxonomy study * Biological and biomedical data integration, mining and visualization * Genetic and biochemical networks and regulation * High performance bio-computing * Modelling software and makeup language in systems biology * Computational genomics and proteomics * 3-D modeling related to biology * Any novel mathematical and physical approaches to bioinformatics problems * Other topics related to bioinformatics * Biomedical Engineering * Bioelectrical and neural engineering * Biomedical imaging, image processing, visualization and biomedical optics * Biomaterials * Biomedical modeling * Biomechanics and biotransport * Biomedical devices, instrumentation, sensors, artificial organs, and nano technologies * Molecular, cellular and tissue engineering * Systems and integrative engineering * Biochemical, cellular, molecular and tissue engineering * Medical data storage and compression techniques * Biomedical effects of electromagnetic radiation * Experimental and computational mobile phone dosimetry * Special ICES sessions on mobile phone safety * Medical data storage and compression techniques * Biomedical robotics and mechanics * Rehabilitation engineering * Clinical engineering, surgical planning, wearable and real-time health monitoring systems * Mobile and wireless technologies in healthcare systems * Biomedical education * Biomedicine in industry and society * Physiological signal processing * NMR/CT/ECG technologies and electromagnetic field simulation in biomedical engineering * Structure-based drug design * Pattern recognition and machine learning techniques in biomedical engineering * Medical signal and imaging processing * Artificial heart, artificial heart valve, artificial limb, artificial pacemaker, and automated external defibrillator * Other topics related to biomedical engineering * Topics Related to Bioinformatics and Biomedical Engineering * Biostatics * Protein Engineering * Gene Engineering * Biology Engineering * System Biology * Biochemistry * Biophysics * Biomathematics * Biomeasurement * Biomechanics * Biometrics Prospective authors are encouraged to submit a full paper for review by Dec 10, 2007, in PDF or Word format. Only original papers that have not been published or submitted for publication elsewhere will be considered. The submission process is carried through iCBBE conference management system (www.icbbe.org ). The manuscripts must follow the IEEE two-column format with single-spaced, 10-point font in the text. A standard paper should not succeed 4 pages. All accepted papers will be presented in oral sessions or poster sessions. 　 For more information please visit the conference web page: www.icbbe.org , or send your request to icbbe2008/./icbbe.org . 　 IMPORTANT DATES Papers Due: Dec 10, 2007 Notification of Acceptance: Feb 28, 2008 Registration deadline: March 20, 2008 Conference: May 16--18,2008 　 CONFERENCE SPONSORS * IEEE EMBS (Engineering in Medicine and Biology Society), USA * Gordon Life Science Institute, San Diego, California, USA * College of Life Science and Technology, Shanghai Jiaotong University, China * Advanced Research Center for Science and Technology, Wuhan University, China * The Center for Bioinformatics and Computational Biology, University of Iowa, USA * Center for Devices and Radiological Health, U.S. Food and Drug Administration, USA 　 CONFERENCE CO-CHAIRS * Dr. Ji Chen (Dept. of Electrical and Computer Engineering, University of Houston, USA), jchen18/./uh.edu * Dr. Huaibei Zhou (Dean of International School of Software, Wuhan University, China), bzhou/./whu.edu.cn * Dr. Dongqing Wei (College of Life Science and Technology, Shanghai Jiaotong University, China), dqwei2000/./gmail.com * Dr. Kuo-Chen Chou (Chief Scientist, Gordon Life Science Institute, San Diego, CA, USA), kchou/./san.rr.com * Dr. Thomas Casavant (Director of the Center for Bioinformatics and Computational Biology, University of Iowa, USA), tomc/./eng.uiowa.edu * Dr. Gert Lubec (Medical University of Vienna, Austria; Chief Editor, Amino Acids), gert.lubec/./meduniwien.ac.at * Dr. Jun Zhang ( Director of Laboratory for Computational Medical Imaging & Data Analysis,University of Kentucky, USA ), * Dr. Zengjian Hu (Research Center in Minority Institutions, Howard University, USA), huzengjian/./yahoo.com * Dr. Wolfgang Kainz (Senior Scientist, U.S. Food and Drug Administration, Center for Devices and Radiological Health, USA), wolfgang.kainz/./fda.hhs.gov ) ------_=_NextPart_001_01C814B5.3D117710 Content-Type: text/html; charset="iso-2022-jp" Content-Transfer-Encoding: quoted-printable 2008 International Conference on

Subject: Call = for Papers: iCBBE 2008 (published by IEEE, indexed by = EI)

 

2008 International Conference on Bioinformatics and Biomedical Engineering (iCBBE)

Submission Deadline: Dec. 10th, = 2007

May 16th to 18th, 2008, Shanghai, China

=1B$B!!=1B(J=

=1B$B!!=1B(J=

Dear Collegue,

 

The 1st International Conference on Bioinformatics and = Biomedical Engineering (iCBBE2007) was held susessfully from July 7th to 9th, = 2007 at RAMADA hotel, Wuhan, China. More than 250 = authors coming > from 15 countries attended the conference. Now all the accepted papers = are included in IEEE Xplore and EI Inspec, and will be indexed by EI = Compendex soon.


=1B$B!!=1B(J

The 2nd International Conference on Bioinformatics and = Biomedical Engineering (iCBBE2008: www.icbbe.org) will be held from May 16th to 18th, 2008 in Shanghai, China. iCBBE2008 will bring together top researchers from Asian Pacific areas, = North America, Europe and around the world = to exchange research results and address open issues in all  aspects = of bioinformatics and biomedical engineering. As we did in iCBBE 2007, All accepted papers in iCBBE 2008 will be published by IEEE, AND = will be indexed by EI Compendex.


=1B$B!!=1B(J

The conference is soliciting state-of-the-art = research papers in the following areas of interest:

  • Bioinformatics and Computational Biology
  • Sequence = analysis and sequence alignment    =
  • Gene = finding and gene function recognition =
  • Genome = assembly and genome annotation =
  • Analysis = of gene expression =
  • Analysis = of regulation =
  • Computational evolutionary biology =
  • Measuring biodiversity =
  • Protein = structure alignment =
  • Protein = structure prediction and structure based drug = design
  • Protein-protein= interactions and protein-protein = docking =
  • Comparative = genomics =
  • Modeling = biological systems =
  • High-throughput= image analysis =
  • Gene = Ontology and taxonomy study =
  • Biological and biomedical data integration, mining and = visualization =
  • Genetic = and biochemical networks and regulation =
  • High = performance bio-computing =
  • Modelling = software and makeup language in systems = biology =
  • Computational genomics and proteomics =
  • 3-D = modeling related to biology =
  • Any novel mathematical and physical approaches to bioinformatics = problems =
  • Other = topics related to bioinformatics
  • Biomedical Engineering
  • Bioelectrical = and neural engineering
  • Biomedical = imaging, image processing, visualization and biomedical optics =
  • Biomaterials =
  • Biomedical = modeling =
  • Biomechanics = and biotransport
  • Biomedical = devices, instrumentation, sensors, artificial organs, and nano technologies =
  • Molecular, = cellular and tissue engineering
  • Systems = and integrative engineering
  • Biochemical, cellular, molecular and tissue = engineering =
  • Medical = data storage and compression techniques =
  • Biomedical = effects of electromagnetic radiation =
  • Experimental = and computational mobile phone dosimetry =
  • Special = ICES sessions on mobile phone safety =
  • Medical = data storage and compression techniques =
  • Biomedical = robotics and mechanics =
  • Rehabilitation engineering =
  • Clinical engineering, surgical planning, wearable and real-time health = monitoring systems =
  • Mobile = and wireless technologies in healthcare systems =
  • Biomedical = education =
  • Biomedicine in industry and society =
  • Physiological signal processing =
  • NMR/CT/ECG technologies and electromagnetic field simulation in biomedical engineering
  • Structure-based= drug design
  • Pattern = recognition and machine learning techniques in biomedical = engineering  =
  • Medical = signal and imaging processing =
  • Artificial = heart, artificial heart valve, artificial limb, artificial pacemaker, and automated external defibrillator =
  • Other = topics related to biomedical engineering
  • Topics Related to Bioinformatics and Biomedical = Engineering
  • Biostatics =
  • Protein = Engineering =
  • Gene = Engineering =
  • Biology = Engineering =
  • System = Biology =
  • Biochemistry
  • Biophysics =
  • Biomathematics<= /span> =
  • Biomeasurement<= /span> =
  • Biomechanics =
  • Biometrics

Prospective authors are encouraged to submit a full = paper for review by Dec 10, 2007, in PDF or Word format. Only original = papers that have not been published or submitted for publication elsewhere will be considered. The submission process is carried through iCBBE conference management system (www.icbbe.org). The manuscripts must follow the IEEE two-column format with single-spaced, = 10-point font in the text. A standard paper should not succeed 4 pages. All = accepted papers will be presented in oral sessions or poster = sessions.


=1B$B!!=1B(J

For more information please visit the conference web = page: www.icbbe.org,  or send your = request to icbbe2008/./icbbe.org. =


=1B$B!!=1B(J

IMPORTANT = DATES

Papers Due:           &n= bsp;          Dec 10, 2007

Notification of Acceptance: Feb 28, = 2008

Registration = deadline:         March 20, 2008

Conference:       =             =     May 16--18,2008

=1B$B!!=1B(J=

CONFERENCE = SPONSORS

  • IEEE EMBS (Engineering in Medicine and = Biology Society), USA 
  • Gordon Life Science Institute, = San Diego, California, USA =
  • College of Life Science and Technology, = Shanghai Jiaotong = University, China =
  • Advanced Research Center for Science and Technology, Wuhan = University, China =
  • The Center for Bioinformatics and = Computational Biology, University = of Iowa, USA =
  • Center for Devices and Radiological = Health, U.S. Food and Drug Administration, USA

=1B$B!!=1B(J=

CONFERENCE = CO-CHAIRS

  • Dr. Ji Chen (Dept. of Electrical and = Computer Engineering, University of Houston, = USA), jchen18/./uh.edu =
  • Dr. Huaibei Zhou (Dean of International = School of Software, Wuhan University, = China<= /st1:place>), bzhou/./whu.edu.cn<= /font> =
  • Dr. Dongqing Wei (College of Life Science and = Technology, Shanghai Jiaotong = University, China), dqwei2000/./gmail.com =
  • Dr. Kuo-Chen Chou (Chief Scientist, = Gordon Life Science Institute, San Diego, = CA, USA), kchou/./san.rr.com =
  • Dr. Thomas Casavant (Director of the = Center for Bioinformatics and Computational Biology, University of = Iowa, USA), tomc/./eng.uiowa.edu
  • Dr. Gert Lubec (Medical University of = Vienna, Austria; Chief Editor, Amino Acids), gert.lubec/./meduniwien.ac.at =
  • Dr. Jun Zhang ( Director of Laboratory = for Computational Medical Imaging & Data Analysis,University of Kentucky, = USA ), =
  • Dr. Zengjian Hu (Research Center in Minority = Institutions, Howard University, USA), huzengjian/./yahoo.com  =
  • Dr. Wolfgang = Kainz (Senior Scientist, U.S. Food and Drug Administration, Center for = Devices and Radiological Health, USA), wolfgang.kainz/./fda.hhs.gov)
------_=_NextPart_001_01C814B5.3D117710-- From owner-chemistry@ccl.net Mon Oct 22 13:11:01 2007 From: "Roman D. Gorbunov rgorbuno|,|aecom.yu.edu" To: CCL Subject: CCL: Gaussian is unable to allocate space. Message-Id: <-35442-071022120802-13092-AIwzPg531ro+fQfej27yzA[#]server.ccl.net> X-Original-From: "Roman D. Gorbunov" Date: Mon, 22 Oct 2007 12:07:57 -0400 Sent to CCL by: "Roman D. Gorbunov" [rgorbuno^^^aecom.yu.edu] Dear all, my calculations dies with the following message: Symmetrizing basis deriv contribution to polar: IMax=3 JMax=2 DiffMx= 0.00D+00 Unable to allocate space to process matrices in G2DrvN: NAtomX= 58 NBasis= 762 NBas6D= 762 MDV1= 6291106 MinMem= 105955841. Does anybody know what happens and if this problem can be solved by with the usage of some keywords? Thank you in advance, Roman From owner-chemistry@ccl.net Mon Oct 22 14:17:00 2007 From: "venkatramaiah nutalapati nvenkat83(0)yahoo.co.in" To: CCL Subject: CCL:G: effect of external heavy atom effect in gaussian Message-Id: <-35443-071022141049-1776-AhQ092k8fVcoKMEhYbtBzA- -server.ccl.net> X-Original-From: "venkatramaiah nutalapati" Date: Mon, 22 Oct 2007 14:10:45 -0400 Sent to CCL by: "venkatramaiah nutalapati" [nvenkat83^^^yahoo.co.in] dear all, i need to find external heavy atom effect on porphyrin molecules. in order to do this theoritically in gaussian any commands are avaialable. kindly suggest me any such commands available in gaussian? From owner-chemistry@ccl.net Mon Oct 22 14:49:01 2007 From: "David Hose anthrax_brothers||hotmail.com" To: CCL Subject: CCL: Wavelet Analysis of Molecular Surface Properties. Message-Id: <-35444-071022143814-12476-rNabDCjNpjqL7SYZZ8JKWQ..server.ccl.net> X-Original-From: "David Hose" Date: Mon, 22 Oct 2007 14:38:10 -0400 Sent to CCL by: "David Hose" [anthrax_brothers],[hotmail.com] Thanks to everyone who sent me a reply regarding Wavelet analysis. It's greatly appreciated. It sounds like Curt's aforementioned Review will be a good starting point. Cheers. Dave From owner-chemistry@ccl.net Mon Oct 22 15:25:00 2007 From: "Igor Filippov Contr igorf,,helix.nih.gov" To: CCL Subject: CCL: Gaussian is unable to allocate space. Message-Id: <-35445-071022142647-7726-G5+60m8nkCGU4+XslxiZag]=[server.ccl.net> X-Original-From: "Igor Filippov [Contr]" Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Mon, 22 Oct 2007 14:26:34 -0400 Mime-Version: 1.0 Sent to CCL by: "Igor Filippov [Contr]" [igorf(!)helix.nih.gov] Try to run this calculation with a smaller basis set. Or, if you have an access to a computer with bigger RAM try running it there. By the by - what %mem setting and what basis set you used ? If you've set up a small %mem I'd suggest setting it to about 80% of your available RAM. Igor On Mon, 2007-10-22 at 12:07 -0400, Roman D. Gorbunov rgorbuno|,| aecom.yu.edu wrote: > Sent to CCL by: "Roman D. Gorbunov" [rgorbuno^^^aecom.yu.edu] > Dear all, > > my calculations dies with the following message: > > Symmetrizing basis deriv contribution to polar: > IMax=3 JMax=2 DiffMx= 0.00D+00 > Unable to allocate space to process matrices in G2DrvN: > NAtomX= 58 NBasis= 762 NBas6D= 762 MDV1= 6291106 MinMem= 105955841. > > Does anybody know what happens and if this problem can be solved by with the usage of some keywords? > > Thank you in advance, > Roman From owner-chemistry@ccl.net Mon Oct 22 16:09:01 2007 From: "Cristian V. Diaconu cvdiaconu*lanl.gov" To: CCL Subject: CCL:G: Gaussian is unable to allocate space. Message-Id: <-35446-071022155357-22908-gZJoBjGIGD4icAwnUznqHQ%%server.ccl.net> X-Original-From: "Cristian V. Diaconu" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 22 Oct 2007 13:16:08 -0600 MIME-Version: 1.0 Sent to CCL by: "Cristian V. Diaconu" [cvdiaconu,+,lanl.gov] MDV1 = 6291106 says gaussian has 6MW (48MB) of memory available, but it needs MinMem= 105955841 = 101.05 MW (808.38MB) put the line: %mem=1024MB before the route section (hopefully the machine you are running on has that much memory). I hope this helps--Chris Roman D. Gorbunov rgorbuno|,|aecom.yu.edu wrote: > Sent to CCL by: "Roman D. Gorbunov" [rgorbuno^^^aecom.yu.edu] > Dear all, > > my calculations dies with the following message: > > Symmetrizing basis deriv contribution to polar: > IMax=3 JMax=2 DiffMx= 0.00D+00 > Unable to allocate space to process matrices in G2DrvN: > NAtomX= 58 NBasis= 762 NBas6D= 762 MDV1= 6291106 MinMem= 105955841. > > Does anybody know what happens and if this problem can be solved by with the usage of some keywords? > > Thank you in advance, > Roman> > > > -- Cristian V. Diaconu Postdoctoral Research Associate Los Alamos National Laboratory Theoretical Division Theoretical Chemistry & Molecular Physics Group (T-12) From owner-chemistry@ccl.net Mon Oct 22 16:42:00 2007 From: "Jeff Woodford jwoodfor===eou.edu" To: CCL Subject: CCL: vibronic coupling constants Message-Id: <-35447-071022163115-9315-IdwwST7Z5mJR9wy+WDCrRQ : server.ccl.net> X-Original-From: "Jeff Woodford" Content-Type: multipart/alternative; boundary="----=_NextPart_000_00A5_01C814B0.04F4A280" Date: Mon, 22 Oct 2007 13:32:40 -0700 MIME-Version: 1.0 Sent to CCL by: "Jeff Woodford" [jwoodfor]![eou.edu] This is a multi-part message in MIME format. ------=_NextPart_000_00A5_01C814B0.04F4A280 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit All: Do you have a recommendation for software (preferably free!) that is capable of calculating nonadiabatic coupling constants? Specifically, I'd like to calculate linear and quadratic vibronic coupling constants using the methods of Bersuker. Any suggestions would be helpful. Thanks in advance! Best, -Jeff Jeffrey N. Woodford Associate Professor of Chemistry Eastern Oregon University Tel: 541-962-3321 Fax: 541-962-3873 ------=_NextPart_000_00A5_01C814B0.04F4A280 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

All:

Do you have a recommendation for software (preferably = free!) that is capable of calculating nonadiabatic coupling constants? =  Specifically, I’d like to calculate linear and quadratic vibronic coupling = constants using the methods of Bersuker.  Any suggestions would be = helpful.  Thanks in advance!

 

Best,

-Jeff

 

Jeffrey N. Woodford

Associate Professor of Chemistry

Eastern Oregon University

Tel: 541-962-3321

Fax: 541-962-3873

 

------=_NextPart_000_00A5_01C814B0.04F4A280-- From owner-chemistry@ccl.net Mon Oct 22 17:17:00 2007 From: "Yasset Perez Riverol yasset.perez[-]biocomp.cigb.edu.cu" To: CCL Subject: CCL: about program for molecular descriptor Message-Id: <-35448-071022164650-19144-mx7/zdeHAjw+cfpaSTCQpQ%%server.ccl.net> X-Original-From: Yasset Perez Riverol Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Mon, 22 Oct 2007 16:10:53 -0400 MIME-Version: 1.0 Sent to CCL by: Yasset Perez Riverol [yasset.perez:_:biocomp.cigb.edu.cu] On Monday 22 October 2007 11:47:28 am you wrote: > Sent to CCL by: "Ivanciuc, Ovidiu I." [oiivanci-,-utmb.edu] > > >>>Does anybody know a "free" library or package to compute molecular > >>>descriptors, beside CDK API, or a free program. > > Best free server: > > Parameter Client > http://www.vcclab.org/lab/pclient/ > http://146.107.217.178/lab/pclient/ > > E-Dragon > http://www.vcclab.org/lab/edragon/ > http://146.107.217.178/lab/edragon/ > > For QSAR papers that use DRAGON descriptors, see http://biochempress.com/ > > Other free servers: > > MODEL - Molecular Descriptor Lab > http://jing.cz3.nus.edu.sg/cgi-bin/model/model.cgi > > PreADMET > http://preadmet.bmdrc.org/preadmet/index.php > http://preadmet.bmdrc.org/preadmet/query/query1.php > > O. > > > > -=3DThis is automatically added to each message by the mailing script =3D-Thanks for your quick answer, but I would like to be able to compute these= =20 descriptors for a file with 10.000 molecules. For this reason the online=20 service for me isn't a possible idea. =20 =2D-=20 Ing. Yasset P=E9rez Riverol. Grupo de Bioinform=E1tica. CIGB, La Habana, Cuba. =2D------------------------ "Si supiera que el mundo se acaba ma=F1ana, yo, hoy todav=EDa, plantar=EDa un =E1rbol." Martin Luther King =20 =20 From owner-chemistry@ccl.net Mon Oct 22 20:08:01 2007 From: "Shina Kamerlin skamerli:_:usc.edu" To: CCL Subject: CCL:G: Problem with Gaussian opt(EF,TS) Message-Id: <-35449-071022152708-23242-MB2qhHBMN7i+opuXdNrUiQ^server.ccl.net> X-Original-From: "Shina Kamerlin" Date: Mon, 22 Oct 2007 15:27:04 -0400 Sent to CCL by: "Shina Kamerlin" [skamerli],[usc.edu] Hello all, I am having problems using Gaussian's opt(EF,TS), in that I get the following error message: ************************************************ ** ERROR IN INITEF. NUMBER OF VARIABLES (111) ** ** INCORRECT (SHOULD BE BETWEEN 1 AND 50) ** ************************************************ I have gotten variations of this before for other structures where then I got NUMBER OF VARIABLES (0) instead of 111. This is a problem I have only had with G03 (which my new research group uses), never with G98, and it occurs mainly with larger structures, in this case 40 atoms. I'm using B3LYP/6-31+G*. I did a More O'Ferrall-Jencks plot in solution, so I am fairly sure that this structure is almost at the transition state. Someone posted this previously and it was suggested that they use ZMAT rather than Cartesian coordinates. I have tried both and get the same error message. I have tried other alternatives, like for instance using just TS or trying GDIIS, but its a difficult structure and I am fairly sure the only way to get this TS is using EF. Has anyone had this problem before, and does anyone know what is going on? I have never had this problem using EF before. Thanks, Shina Lynn Kamerlin From owner-chemistry@ccl.net Mon Oct 22 22:22:01 2007 From: "Jeff Woodford jwoodfor{:}eou.edu" To: CCL Subject: CCL:G: Problem with Gaussian opt(EF,TS) Message-Id: <-35450-071022221919-10724-9u4y63jukxpa1sb35jZX1g%a%server.ccl.net> X-Original-From: "Jeff Woodford" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="US-ASCII" Date: Mon, 22 Oct 2007 19:20:34 -0700 MIME-Version: 1.0 Sent to CCL by: "Jeff Woodford" [jwoodfor]-[eou.edu] Hi, I have gotten this error message before when using EF. The Z-matrix has to be in the following format in order for EF to work: C C 1 r1 C 2 r2 1 a1 ... Variables: r1=1.500 r2=1.500 a1=120.0 etc. I have not tried it with TS so I can't help you there. Good luck! -Jeff Jeffrey N. Woodford Associate Professor of Chemistry Eastern Oregon University Tel: 541-962-3321 Fax: 541-962-3873 -----Original Message----- > From: owner-chemistry^^ccl.net [mailto:owner-chemistry^^ccl.net] Sent: Monday, October 22, 2007 12:27 PM To: Woodford, Jeffrey N Subject: CCL:G: Problem with Gaussian opt(EF,TS) Sent to CCL by: "Shina Kamerlin" [skamerli],[usc.edu] Hello all, I am having problems using Gaussian's opt(EF,TS), in that I get the following error message: ************************************************ ** ERROR IN INITEF. NUMBER OF VARIABLES (111) ** ** INCORRECT (SHOULD BE BETWEEN 1 AND 50) ** ************************************************ I have gotten variations of this before for other structures where then I got NUMBER OF VARIABLES (0) instead of 111. This is a problem I have only had with G03 (which my new research group uses), never with G98, and it occurs mainly with larger structures, in this case 40 atoms. I'm using B3LYP/6-31+G*. I did a More O'Ferrall-Jencks plot in solution, so I am fairly sure that this structure is almost at the transition state. Someone posted this previously and it was suggested that they use ZMAT rather than Cartesian coordinates. I have tried both and get the same error message. I have tried other alternatives, like for instance using just TS or trying GDIIS, but its a difficult structure and I am fairly sure the only way to get this TS is using EF. Has anyone had this problem before, and does anyone know what is going on? I have never had this problem using EF before. Thanks, Shina Lynn Kamerlinhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt