From richard@tc.cornell.edu Mon Mar 10 09:28:23 1997 Received: from theory.tc.cornell.edu for richard@tc.cornell.edu by www.ccl.net (8.8.3/950822.1) id IAA14554; Mon, 10 Mar 1997 08:30:00 -0500 (EST) Received: from ren.tc.cornell.edu (REN.TC.CORNELL.EDU [128.84.244.22]) by theory.tc.cornell.edu (8.8.4/8.8.3/CTC-1.0) with SMTP id IAA37295; Mon, 10 Mar 1997 08:30:00 -0500 Sender: richard@TC.Cornell.EDU Message-ID: <33240CD9.52BF@tc.cornell.edu> Date: Mon, 10 Mar 1997 08:30:01 -0500 From: Richard Gillilan X-Mailer: Mozilla 3.0 (X11; I; IRIX 5.3 IP22) MIME-Version: 1.0 To: chemistry@www.ccl.net CC: richard@TC.Cornell.EDU Subject: CTC Docking Workshop Content-Type: multipart/mixed; boundary="------------623163DE6956" This is a multi-part message in MIME format. --------------623163DE6956 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit (submitted by richard@tc.cornell.edu) --------------623163DE6956 Content-Type: text/plain; charset=us-ascii; name="final_annouc" Content-Transfer-Encoding: 7bit Content-Disposition: inline; filename="final_annouc" ******************************************* CORNELL THEORY CENTER WORKSHOP Flexible Ligand Docking for Drug Design April 24 - 26, 1997 ******************************************* http://www.tc.cornell.edu/~richard The Cornell Theory Center (CTC) will hold a workshop on the use of Monte Carlo methods for predicting the conformations of small ligands bound to proteins. Class size will be limited to 12 to allow each participant to work on an SGI workstation. The workshop will be highly practical in nature, focusing on how to run the RESEARCH docking package, a Monte Carlo-based docking code created at the University of Alberta. The RESEARCH algorithm was highly successful at the recent CASP2 competition for structure prediction (http://PredictionCenter.llnl.gov/). The format will be short lectures delivered by the authors of RESEARCH interspersed with periods of laboratory time. Worked examples will be provided for those who do not wish to bring their own data. A huge variety of test ligands will be available via the NCI 3D structural database (http://epnws1.ncifcrf.gov:2345/dis3d/3Ddatabase/dis3d.html). An experimental virtual reality interface to RESEARCH will be available for use in CTC's Visual Insight Zone, a state-of-the-art immersive interactive graphics environment. Speakers: Trevor Hart and Steven Ness Department of Medical Microbiology and Immunology Univeristy of Alberta, Canada Richard Gillilan Cornell Theory Center Ithaca, NY The workshop will cover o Molecular force fields: a practical guide (including an intro to CTC's automatic assignment library for the recently published MMFF94 force field) o Introduction to molecular docking o Analysis of data and prediction o Docking with genetic algorithms o Database screening o Virtual reality (hands-on) Participants are encouraged to bring their own data sets. Consulting staff will be available to assist researchers in their projects. The licenses for home-institution or corporate use of the RESEARCH package may be purchased from the authors. Contact Trevor Hart (hart@ualberta.ca) for details. Accommodations Attendees are responsible for their own hotel reservations and meals. Paid parking is available on campus, but walking or use of the shuttle or bus service, where available, is strongly recommended. We have reserved a block of rooms at the Best Western. If you want one, tell them you are with the "Theory Center Docking Workshop." Please make your reservation before April 1, 1997 if possible. Sheraton Inn (>3mi) One Sheraton Drive, Ithaca 607/257-2000 FAX: 607/257-3998 Statler Hotel (1 block away) Cornell University Campus 607/257-2500 FAX: 607/257-6432 Collegetown Motor Lodge (10 minutes walking) 312 College Avenue, Ithaca 607/273-3542 800/745-3542 FAX: 607/272-3542 Best Western University Inn (about 1 mile) East Hill Plaza, Rt. 393 and Judd Falls Road, Ithaca 607/272-6100 FAX: 607/272-1518 To Apply Due to restricted space, registration for this workshop is limited. The completed application form, along with payment, must be received by Thursday March 27, 1997. Applications will be accepted after this date if openings still remain. Local researchers may charge the registration fee to the appropriate Cornell University account number. Applications that do not include payment cannot be accepted. Payment checks will be returned promptly to applicants not accepted due to overenrollment. Payment scale, payable to Cornell University: Academic participants: $70 Corporate Partnership Program members: $250 Other corporate participants: $350 Notification will made upon receipt of your application with payment. ------------------------------------------------------------------------- REGISTRATION FORM Flexible Ligand Docking Name __________________________________ Institution ______________________________ Address ________________________________ Phone _____________ Fax _________________ Preferred e-mail address ___________________ Do you have a current Theory Center account: __no __yes; my userid is:__ __ (e.g., RS/6000 Cluster, etc.) Do you have a pending allocation request: __no __yes Social Security Number: ___________________ (required to set up new supercomputer accounts) List special needs: ________________________ (e.g., mobility impaired) Account number to charge: _________________ (Cornell applicants only) Academic discipline _______________________ (e.g., mathematical sciences, geosciences, chemical engineering) Status (check all that apply): __ Academic __ Undergraduate Student __ Graduate Student __ Postdoctoral __ Faculty __ Smart Node Consultant __ Smart Node Advisor __ Other (explain): ________________________ __ Corporate/Commercial __ Research staff __ Other (explain): ________________________ __ Name of Firm: _________________________ Indicate which of the following best describes you (optional): __ African American __ Caucasian __ Asian American __ Hispanic American __ Native American or Alaskan Native __ Other (please specify) ____________________ This application form and payment must be received by March 27, 1997 Send to: Kathy Shippos Workshop Assistant Cornell Theory Center 424 Rhodes Hall Ithaca, NY 14853-3801 (607) 254-8640 kshippos@tc.cornell.edu All trade names referenced are trademarks or registered trademarks of their respective companies. --------------623163DE6956-- From neuber@exp.bessy.de Mon Mar 10 10:28:23 1997 Received: from metaxa.exp.bessy.de for neuber@exp.bessy.de by www.ccl.net (8.8.3/950822.1) id KAA15208; Mon, 10 Mar 1997 10:19:45 -0500 (EST) Message-Id: <199703101519.KAA15208@www.ccl.net> Received: from metaxa.bessy.de (bes706.exp.bessy.de) by metaxa.exp.bessy.de (MX V4.1 VAX) with SMTP; Mon, 10 Mar 1997 14:11:26 MET From: "Michael Neuber" To: "ccl-liste" Subject: Bulb-it? Date: Mon, 10 Mar 1997 14:05:38 +0100 X-MSMail-Priority: Normal X-Priority: 3 X-Mailer: Microsoft Internet Mail 4.70.1155 MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Dear Netters, excuse me for an off-topic question: can anyone put me on the right track how to deal with *.cgi files, maybe with a programm or helper application called bulbit ? Where can I possibly get this bulbit ? (I am surfing with Netscape..) Never heard these names before, but it looks like I need to know now.... Thanks in advance! Michael @ Berlin --------------------------------------------------------------------------- Dr. Michael Neuber Universitaet Heidelberg Lentzeallee 100 D-14195 Berlin Phone (+49/0)-30-82004-237/-176 FAX ..-149 e-mail neuber@exp.bessy.de --------------------------------------------------------------------------- From huang@nissan.wavefun.com Mon Mar 10 14:39:23 1997 Received: from volvo.wavefun.com for huang@nissan.wavefun.com by www.ccl.net (8.8.3/950822.1) id OAA16611; Mon, 10 Mar 1997 14:07:08 -0500 (EST) Received: by volvo.wavefun.com (931110.SGI/930416.SGI) for CHEMISTRY@www.ccl.net id AA24329; Mon, 10 Mar 97 11:08:54 -0800 Received: from nissan.wavefun.com(198.147.95.2) by volvo.wavefun.com via smap (V1.3) id sma024325; Mon Mar 10 11:07:25 1997 Received: by nissan.wavefun.com (931110.SGI/940406.SGI.AUTO) for @volvo.wavefun.com:CHEMISTRY@www.ccl.net id AA12888; Mon, 10 Mar 97 11:03:51 -0800 From: "Wayne Huang" Message-Id: <9703101103.ZM12886@nissan.wavefun.com> Date: Mon, 10 Mar 1997 11:03:41 -0800 In-Reply-To: Suleyman Bahceci "CCL:Spartan's Minimizer failure" (Mar 8, 4:43pm) References: Reply-To: huang@wavefun.com X-Mailer: Z-Mail (3.2.2 10apr95 MediaMail) To: Suleyman Bahceci , CHEMISTRY@www.ccl.net Subject: Re: CCL:Spartan's Minimizer failure Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii On Mar 8, 4:43pm, Suleyman Bahceci wrote: > Subject: CCL:Spartan's Minimizer failure > > Hi, > > I have got some problem in Spartan Builder. If you push the Minimize > botton in the fragment panel, you get the message like "Minimizer failure: > Unable to create client semaphore". Can onyone help me to solve this > problem? > > Thanks very much > > Suleyman This problem is probably due to too many shared memory being used. With SGI machine, try "ipcs -m" to list and "ipcrm -m ID" to remove them. Try to remove all ID with non-root owner. The easier way is to reboot the machine. All shared memory should be cleared then. One other remote possibility is running out of RAM due to e.g. molecular size too big etc. In this case, it might not exit so gracefully. It might also be out of processors (check with the top command). Hope this helps! --Wayne -- +---------------------------------------------------------------+ | Wayne Huang, Ph.D. | 18401 Von Karman, Suite 370 | | Computational Chemist | Irvine, California 92612 | | Wavefunction, Inc. | 714-955-2120 <> 955-2118(fax)| | huang@wavefun.com | Web: http://www.wavefun.com | +---------------------------------------------------------------+ From ccl@www.ccl.net Mon Mar 10 21:36:26 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id VAA18811; Mon, 10 Mar 1997 21:20:41 -0500 (EST) Received: from entropy.ucsc.edu for richmc@entropy.ucsc.edu by bedrock.ccl.net (8.8.3/950822.1) id VAA22928; Mon, 10 Mar 1997 21:20:40 -0500 (EST) Received: (qmail 24633 invoked by uid 500); 11 Mar 1997 02:20:41 -0000 From: "Rich McClellan" Message-Id: <9703101820.ZM24631@entropy.ucsc.edu> Date: Mon, 10 Mar 1997 18:20:40 -0800 X-Mailer: Z-Mail (3.2.1 24feb96 Caldera) To: chemistry@ccl.net Subject: Re: CCL: G94 on LINUX Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii > Dear Members of CCL: > Last week I posed a question about problems compiling G94.D4 on > RedHat Linux 4.0. I have had a number of interesting replies which > I plan to summarize. But I still have a problem. > Gaussian, Inc. wrote me to suggest a hardware problem. It turns > out this this is quite likely the actual problem. But how to fix? > It seems that I have a faulty memory chip. My computer, a Gateway > P6 has 64 Mbytes of new memory. The machine says all is ok on boot- > up. But I have random problems with the C-compiler quitting. > So maybe there is a memory problem. Gaussian suggested removing > or switching memory. Now it appear I can compile the program > with only 2x16 Mbytes of memory. > So the question is, how does one test memory? OK, the computer > thinks the memory is ok. But all the boot-up test is doing is > writing 1, 0 into memory and then seeing if it is still there > in a few microseconds. But it would seem that to compile and run > a big FORTRAN program, one would be interested in having this > same test performed 10 seconds later. How then does one test the > long-term refresh function of big memory blocks? > Regards, Dave Close. There are two ways of testing your memory without rebooting your Linux box to another OS. The first is to use memtest available from a mirror near you (or entropy.ucsc.edu/pub/linux/memtest86-1.1.tar.gz). The second is a series of kernel makes. You can read more about the second at http://www.bitwizard.nl/sig11/ good luck, Rich