From chemistry-request@server.ccl.net Wed May 16 04:54:22 2001 Received: from smtp.csc.fi ([193.166.0.99]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4G8sJI06230 for ; Wed, 16 May 2001 04:54:20 -0400 Received: from sampo.csc.fi (sampo.csc.fi [193.166.1.154]) by smtp.csc.fi (8.9.3/8.9.3/CSC) with ESMTP id LAA25609 for ; Wed, 16 May 2001 11:54:19 +0300 Date: Wed, 16 May 2001 11:54:19 +0300 (EEST) From: Maija Lahtela To: Subject: Gaussian 98 in PCcluster Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear All, We are going to build up a PC cluster wiht Red Hat linux in order to run Gaussian 98 A.9. Our propose is to start with 16 PCs and then enlarge it 100 PCs. We have have tested by running Gaussian with one PC but the results has not been very couraging while the code is slow. We have do not have Kinda yet. However, I have found articles about running Gaussian with mpi which sounds interesting for us. We would appreciate if you could give us hint where we could find gaussian mpi version or how you have build up your custer to run Gaussian jobs. Thanks in advance! I will summarize. Yours Sincerely, Maija Lahtela-Kakkonen ***************************************************** Maija Lahtela-Kakkonen, Application Scientist / Chemistry CSC-Scientific Computing Tekniikantie 15 a D, P.O.Box 405 FIN-02101 ESPOO FINLAND TEL 358-9-4572079 /050-3819506, FAX 358-9-4572302 E-MAIL mlahtela@csc.fi, Internet:www.csc.fi **************************************************** From chemistry-request@server.ccl.net Wed May 16 13:27:54 2001 Received: from mailer.psc.edu ([128.182.58.100]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4GHRsI01863 for ; Wed, 16 May 2001 13:27:54 -0400 Received: from pscuxc.psc.edu (unix.psc.edu [128.182.66.177]) by mailer.psc.edu (8.11.2/8.11.2/psc) with ESMTP id f4GHRpa24241; Wed, 16 May 2001 13:27:51 -0400 (EDT) Received: from localhost (wymore@localhost) by pscuxc.psc.edu (8.9.3/8.9.3/psc) with ESMTP id NAA28454; Wed, 16 May 2001 13:27:50 -0400 (EDT) Date: Wed, 16 May 2001 13:27:50 -0400 (EDT) From: Troy Wymore To: cc: , Subject: PSC BIOMEDICAL WORKSHOPS 2001 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII The following PITTSBURGH SUPERCOMPUTING CENTER BIOMEDICAL WORKSHOPS for the summer of 2001 are being offered: More information can be obtained at: http://www.psc.edu/biomed/training/workshops/2001/index.html ****************************************** NUCLEIC ACID AND PROTEIN SEQUENCE ANALYSIS July 8 - 13, 2001 Registration deadline is May 25, 2001 This intense five and one-half day workshop will teach the basics of sequence analysis, including: remote supercomputing; inferring structures and functions using internet resources; database searching and pairwise sequence alignment; multiple sequence alignments; pattern identification; inverse structure prediction and homology modeling; and visualization of macromolecular structures. Special emphasis will be placed on parameter selection, and the mathematical and statistical foundations of the algorithms and methods presented as well as the biological correlates of those foundations. Information will also be provided on the latest pattern identification techniques including hidden Markov models, advanced position-specific weight matrix techniques, and bayesian estimation. ****************************************** METHODS AND APPLICATIONS OF MOLECULAR DYNAMICS TO BIOPOLYMERS August 15 - 18, 2001- Registration dealine is July 6, 2001 PSC will host "Methods and Applications of Molecular Dynamics to Biopolymers." The workshop will familiarize biomedical researchers with computational methods and provide practice in applying supercomputing resources to problems of concern in molecular dynamics. There will be lectures, extensive hands-on sessions, and discussion of general aspects of molecular dynamics software. NAMD will be discussed in detail. Participants are encouraged to work on the examples provided or on their own experimental data. No prior supercomputing experience is necessary. A list of topics and other information is available at: http://www.psc.edu/biomed/training/workshops/2001/mamd/index.html ****************************************** From chemistry-request@server.ccl.net Wed May 16 03:04:38 2001 Received: from mx2.mr.netbig.com ([211.99.207.170]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f4G74aI21039 for ; Wed, 16 May 2001 03:04:37 -0400 Received: (qmail 31703 invoked by uid 99); 16 May 2001 07:04:29 -0000 Message-ID: <20010516070429.31702.qmail@mx2.mr.netbig.com> From: =?gb2312?B?Qm9va3dvcm0=?= To: chemistry@ccl.net Cc: amber@heimdal.compchem.ucsf.edu Subject: =?gb2312?B?VGhlcm1hbC0gYW5kIGNoZW1pY2FsLWluZHVjZWQgZGVuYXR1cmF0aW9u?= Date: Wed, 16 May 2001 15:04:29 +0800 MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=gb2312 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from BASE64 to 8bit by server.ccl.net id f4G74cI21040 Hello, everyone Would someone be so kind to suggest me some references about the comparison of mechanism of thermal- and chemical-induced denaturation? Another question is, are there any methods to measure the ordering of solvent or cosolvent molecules within the solvation shell of the protein? Thank you in advance. Regards Jien ----------------------------------------------------- 系我应得的----熊猫贤才（http://www.pp11.com) From chemistry-request@server.ccl.net Wed May 16 07:43:25 2001 Received: from mail1.uniroma1.it ([151.100.4.5]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4GBhOI32189 for ; Wed, 16 May 2001 07:43:24 -0400 Received: from rcmdpc450w ([151.100.64.10]) by mail1.uniroma1.it (Lotus Domino Release 5.0.7) with SMTP id 2001051613495952:70605 ; Wed, 16 May 2001 13:49:59 +0200 From: "Rino Ragno" To: Cc: Subject: Date: Wed, 16 May 2001 13:47:15 +0200 Message-ID: MIME-Version: 1.0 X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 X-MIMETrack: Itemize by SMTP Server on mail1/Uniroma1/it(Release 5.0.7 |March 21, 2001) at 16/05/2001 13.49.59, Serialize by Router on mail1/Uniroma1/it(Release 5.0.7 |March 21, 2001) at 16/05/2001 13.50.01, Serialize complete at 16/05/2001 13.50.01 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-8859-1" Hello, everyone I'm new at AMBER and I try to learning it. Since I have always used TRIPOS I have lots of stuff in mol2 format I'd like to use in amber. Till here there is no problem at all, but at the time I convert the mol2 molecules into PDB files all the problems come out. When I try to use the new PDB file, leap (or xleap) turned out that the molecule have no atom type. I checked and this is true, but I work with ligand-receptor complexes and unfortunately the ligands are not protein based molecules and are thus converted in a UNK residue. Going around the AMBER distribution I founf a tripos_util command, but it is not working or I do not how to use it. Is there any utilities to convert a TRIPOS mol2 file into a AMBER one or in a PDB file with the right atom types. Anyone out there can help me? Thank you in advance, I will summarize the answers i got. Rino ++-------------------------------------------------------++ || Dr. Rino Ragno || || Dip. Studi Chimica Tecnonologia Sostanze || || Biologicamente Attive || || Facolta' di Farmacia - Universita' "La Sapienza" || || P.le Aldo Moro, 5 - 00185 - Roma/Italia || || || || E-mail: rino.ragno@uniroma1.it (work) || ++-------------------------------------------------------++ From chemistry-request@server.ccl.net Wed May 16 15:16:51 2001 Received: from gip.u-picardie.fr ([193.49.184.17]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4GJGpI03083 for ; Wed, 16 May 2001 15:16:51 -0400 Received: from labo5 (labo5.sa.u-picardie.fr [195.83.150.83]) by gip.u-picardie.fr (8.9.3/8.9.3) with SMTP id VAA22532 for ; Wed, 16 May 2001 21:16:50 +0200 Date: Wed, 16 May 2001 21:16:50 +0200 Message-Id: <200105161916.VAA22532@gip.u-picardie.fr> X-Sender: fyd-phar@mailx.u-picardie.fr X-Mailer: Windows Eudora Light Version 1.5.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@ccl.net From: Francois Dupradeau Subject: regression software under IRIX 6.5 Dear all, I look for regression software (non-linear regression; works under SGI IRIX 6.5) I found a lot of Web sites presenting regression software that works under Windows and sometimes Linux but not on IRIX 6.5 (not 5.2...) I know "gnuplot" can make some regressions and I already use it but I would like to find some other ones. Moreover, if it is free for academic labs, it is better ;-) Thanks, Best regards, Francois -- F.-Y. Dupradeau http://www.u-picardie.fr/UPIC/UPJV/recherche/labos/bpd/fyd.htm From chemistry-request@server.ccl.net Wed May 16 16:26:14 2001 Received: from amchismtp01.bp.com ([65.196.235.158]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4GKQEI03487 for ; Wed, 16 May 2001 16:26:14 -0400 Received: from virlmx04.amoco.com (inetgate5.bp.com [207.24.72.12]) by amchismtp01.bp.com (Switch-2.1.0/Switch-2.1.0) with ESMTP id f4GKQK213601 for ; Wed, 16 May 2001 15:26:21 -0500 (CDT) Received: from virlmx04.amoco.com by virlmx04.amoco.com (8.11.3/SMI-SVR4) id f4GKQ2H14291; Wed, 16 May 2001 15:26:02 -0500 (CDT) Received: from amhoux4.bp.com by virlmx04.amoco.com (8.11.3/SMI-SVR4) id f4GKPYT13835; Wed, 16 May 2001 15:25:36 -0500 (CDT) Received: by AMHOUX4 with Internet Mail Service (5.5.2653.19) id ; Wed, 16 May 2001 15:23:04 -0500 Message-ID: From: "Golab, Joseph T" To: "Ccl (E-mail)" Subject: Group Contribution Methods Date: Wed, 16 May 2001 15:23:02 -0500 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" Hello: In updating a software catalogue, are there any other programs (in addition to NIST database 25 and CHETAH) that can calculate heats of formation, entropy, heats of reaction, etc. based on Benson's (or Benson-like) Group Contribution Methods. Thanks in advance. Joe ________________________________________________________________ Joseph T. Golab Phone: +1 (630) 961-7878 BP Naperville Complex, C-7 Fax: +1 (630) 420-4382 150 W. Warrenville Rd e-mail: GolabJT@BP.com Naperville, IL 60563 SOCON: 231 From chemistry-request@server.ccl.net Wed May 16 17:56:18 2001 Received: from mailrelay2.lrz-muenchen.de ([129.187.254.102]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4GLuHI03814 for ; Wed, 16 May 2001 17:56:17 -0400 Received: from [129.187.26.73] by mailout.lrz-muenchen.de with ESMTP; Wed, 16 May 2001 23:56:16 +0200 Sender: Eugene.Leitl@lrz.uni-muenchen.de Message-Id: <3B0312F5.71E6001D@lrz.uni-muenchen.de> Date: Thu, 17 May 2001 01:53:25 +0200 From: Eugene.Leitl@lrz.uni-muenchen.de X-Mailer: Mozilla 4.75 [en] (X11; U; Linux 2.2.17-21mdksecure i586) X-Accept-Language: en, de-DE, ru MIME-Version: 1.0 To: chemistry@ccl.net Subject: [Fwd: Re: CCL:Gaussian 98 in PCcluster (fwd)] Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit -------- Original Message -------- From: Art Edwards Subject: Re: CCL:Gaussian 98 in PCcluster (fwd) To: Eugene Leitl For what it's worth, we are running GAMESS-US on a Scyld cluster in MPI mode. It required minimal alteration and seems to run well (we are actually in the second day of testing). As you know GAMESS is free and for most things, it works well. Art Edwards On Wed, May 16, 2001 at 03:26:21PM +0200, Eugene Leitl wrote: > > > ______________________________________________________________ > ICBMTO : N48 10'07'' E011 33'53'' http://www.lrz.de/~ui22204 > 57F9CFD3: ED90 0433 EB74 E4A9 537F CFF5 86E7 629B 57F9 CFD3 > > ---------- Forwarded message ---------- > Date: Wed, 16 May 2001 11:54:19 +0300 (EEST) > From: Maija Lahtela > To: chemistry@ccl.net > Subject: CCL:Gaussian 98 in PCcluster > > Dear All, > > We are going to build up a PC cluster wiht Red Hat linux in order to run > Gaussian 98 A.9. Our propose is to start with 16 PCs and then enlarge it > 100 PCs. > > We have have tested by running Gaussian with one PC but the results has > not been very couraging while the code is slow. We have do not have Kinda > yet. However, I have found articles about running Gaussian with mpi which > sounds interesting for us. > > We would appreciate if you could give us hint where we could find gaussian > mpi version or how you have build up your custer to run Gaussian jobs. > > Thanks in advance! I will summarize. > > Yours Sincerely, > Maija Lahtela-Kakkonen > > ***************************************************** > Maija Lahtela-Kakkonen, > Application Scientist / Chemistry > CSC-Scientific Computing > Tekniikantie 15 a D, P.O.Box 405 > FIN-02101 ESPOO FINLAND > TEL 358-9-4572079 /050-3819506, FAX 358-9-4572302 > E-MAIL mlahtela@csc.fi, Internet:www.csc.fi > **************************************************** > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > > > _______________________________________________ > Beowulf mailing list, Beowulf@beowulf.org > To change your subscription (digest mode or unsubscribe) visit http://www.beowulf.org/mailman/listinfo/beowulf -- Arthur H. Edwards 712 Valencia Dr. NE Abq. NM 87108 (505) 256-0834 From chemistry-request@server.ccl.net Wed May 16 18:56:52 2001 Received: from web13206.mail.yahoo.com ([216.136.174.191]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f4GMuqI04067 for ; Wed, 16 May 2001 18:56:52 -0400 Message-ID: <20010516225652.94948.qmail@web13206.mail.yahoo.com> Received: from [129.105.55.29] by web13206.mail.yahoo.com; Wed, 16 May 2001 15:56:52 PDT Date: Wed, 16 May 2001 15:56:52 -0700 (PDT) From: mike smith Subject: Confusion on ensemble average for biomolecule To: CHEMISTRY@ccl.net In-Reply-To: MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hello, I am confused with the ensemble average(const T) of biomolecule. As far as I know, for the long time MD of biomolecules, there are usually very finite number of trajectories, and at some times results were from only one trajectory. However, for such a simulation, how the ensemble average for constant T(temperature) is fulfilled? Are the results from very finite number of trajs reliable? The initial velocities are normally sampling from the Boltzman distribution (Gaussian random variables), with a mean value 0, a standard deviation of sqrt(kT/m). To have the IDEAL T, velocity scaling is used frecuently during the simulation, or use some kind of heat bath. THEORETICALLY, should we do sampling of initial velocities for a large number of trajectories to let the STATISTICAL MECHANICS make sense? However, in reality, it's impratical to do that. Is there any better way to overcome this technical problem, or maybe I am wrong in understanding this issue? Please help me with this confusion. Thanks a lot in advance. Mike __________________________________________________ Do You Yahoo!? Yahoo! Auctions - buy the things you want at great prices http://auctions.yahoo.com/