From chemistry-request@server.ccl.net Fri Aug 31 06:32:15 2001 Received: from anchor-post-31.mail.demon.net ([194.217.242.89]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7VAWCM17349 for ; Fri, 31 Aug 2001 06:32:12 -0400 Received: from chmqst.demon.co.uk ([158.152.83.101] helo=daisy) by anchor-post-31.mail.demon.net with esmtp (Exim 2.12 #1) id 15claq-000BUp-0V for chemistry@ccl.net; Fri, 31 Aug 2001 11:32:08 +0100 From: "David Livingstone" Organization: ChemQuest To: chemistry@ccl.net Date: Fri, 31 Aug 2001 11:31:54 +0100 MIME-Version: 1.0 Content-type: text/enriched; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: Re: CCL:Bootstrap Reply-to: davel@chmqst.demon.co.uk Message-ID: <3B8F75AA.11611.5116CC@localhost> Priority: normal X-mailer: Pegasus Mail for Win32 (v3.12c) 0100,0100,0100Hi, Prashant Desai wrote: FF00,0000,0000> I am looking out for information about theory and application of > Bootstrap algorithm as applied for vaidation of QSAR equations. > Any relevant refrences and reprints are welcome. You might be better off posting this message to theTimes New Roman ArialQSAR and Modelling Society mailing list. In fact I often see questions on the CCL which might be better answered by a posting on the QSAR list. The address of the list is: qsar_society@msi.com Regards, Dave. ------------------------------------------------------------------ D.J. Livingstone ChemQuest Delamere House, 1 Royal Crescent, Sandown. Isle of Wight UK PO36 8LZ Phone & Fax: +44 (0)1983 401793 e-mail davel@chmqst.demon.co.uk http://www.chmqst.demon.co.uk ------------------------------------------------------------------ From chemistry-request@server.ccl.net Thu Aug 30 20:08:54 2001 Received: from epimetheus.hosting4u.net ([209.15.2.70]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f7V08sM19674 for ; Thu, 30 Aug 2001 20:08:54 -0400 Received: (qmail 22562 invoked from network); 31 Aug 2001 00:08:54 -0000 Received: from zeus.hosting4u.net (HELO proinformatix.com) (209.15.2.56) by mail-gate.hosting4u.net with SMTP; 31 Aug 2001 00:08:54 -0000 Received: from yersina ([202.138.17.62]) by proinformatix.com ; Thu, 30 Aug 2001 19:08:52 -0500 Reply-To: From: "Sergio Manzetti" To: "Chemistry Discussion G" Subject: Simulated Annealing in GROMACS Date: Fri, 31 Aug 2001 10:07:21 -0700 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) X-MIMEOLE: Produced By Microsoft MimeOLE V5.00.2919.6700 Importance: Normal Hello, I am working on simulated annealing with a protein, but the simulation doesn't even start..and I can't find what is wrongwith the *mdp file. Does anyone have a fresh sa.mdp file that I could obtain a copy of? How long should the simulation go for in order to try to find a global minimum? And how would you know if you found a global minimum? Best Regards Sergio ____________________________________________________________________________ ___________________________ Sergio Manzetti Research Scholar Centre of Molecular Biotechnology/ Supercomputer Facility Queensland University of Technology 2 George St. BRISBANE 4000 QLD AUSTRALIA email: s.manzetti@student.qut.edu.au Tlf: +61 7 3864 1434 www: http://www.life.sci.qut.edu.au/html/research/cmgenetics.html www2: http://www.its.qut.edu.au/hpc/ From chemistry-request@server.ccl.net Thu Aug 30 22:02:07 2001 Received: from femail31.sdc1.sfba.home.com ([24.254.60.21]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7V227M22841 for ; Thu, 30 Aug 2001 22:02:07 -0400 Received: from C1353359A ([65.4.172.51]) by femail31.sdc1.sfba.home.com (InterMail vM.4.01.03.20 201-229-121-120-20010223) with SMTP id <20010831020202.CJDT14944.femail31.sdc1.sfba.home.com@C1353359A>; Thu, 30 Aug 2001 19:02:02 -0700 Message-ID: <000c01c131c0$e1c7bcd0$33ac0441@sttln1.wa.home.com> Reply-To: "Mark A. Thompson" From: "Mark A. Thompson" To: , References: <200108301828.XAA25076@qasid.cc.iitk.ac.in> Subject: Re: CCL:any free software for ETH calculations Date: Thu, 30 Aug 2001 19:01:43 -0700 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.3018.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.3018.1300 Yes, ArgusLab http://www.planaria-software.com ------------------------------------------------------------------------- home page: http://members.home.net/markt158/ ----- Original Message ----- From: To: Sent: Thursday, August 30, 2001 11:17 AM Subject: CCL:any free software for ETH calculations > Dear CClers, > Could any one tell me if there are free softwares available for doing > Extended huckel calculations. > > >. > Chinmoy > > > > -= 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 > > > > > > From chemistry-request@server.ccl.net Thu Aug 30 19:53:36 2001 Received: from epimetheus.hosting4u.net ([209.15.2.70]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f7UNraM19138 for ; Thu, 30 Aug 2001 19:53:36 -0400 Received: (qmail 18422 invoked from network); 30 Aug 2001 23:53:35 -0000 Received: from zeus.hosting4u.net (HELO proinformatix.com) (209.15.2.56) by mail-gate.hosting4u.net with SMTP; 30 Aug 2001 23:53:35 -0000 Received: from yersina ([202.138.17.62]) by proinformatix.com ; Thu, 30 Aug 2001 18:53:33 -0500 Reply-To: From: "Sergio Manzetti" To: "Chemistry Discussion G" Subject: Gibbs Free Energy in GROMACS Date: Fri, 31 Aug 2001 09:52:02 -0700 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) X-MIMEOLE: Produced By Microsoft MimeOLE V5.00.2919.6700 Importance: Normal Hi every1. This might be a very stupid question , but I JUST can't find how to view average andoverall free energy results for a 100ps simulation in GROMACS. I use the following parameters: ; Free energy control stuff = free-energy = yes init-lambda = 0 delta-lambda = 10 sc-alpha = 0 sc-sigma = 0.3 Is something done wrong here? Cheers Sergio ____________________________________________________________________________ ___________________________ Sergio Manzetti Research Scholar Centre of Molecular Biotechnology/ Supercomputer Facility Queensland University of Technology 2 George St. BRISBANE 4000 QLD AUSTRALIA email: s.manzetti@student.qut.edu.au Tlf: +61 7 3864 1434 www: http://www.life.sci.qut.edu.au/html/research/cmgenetics.html www2: http://www.its.qut.edu.au/hpc/ From chemistry-request@server.ccl.net Fri Aug 31 03:23:38 2001 Received: from hamiltonian.chem.cornell.edu (IDENT:root@[128.253.229.83]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7V7NcM32473 for ; Fri, 31 Aug 2001 03:23:38 -0400 Received: from localhost (marketa@localhost) by hamiltonian.chem.cornell.edu (8.11.2/8.11.2) with ESMTP id f7V7Pn020028; Fri, 31 Aug 2001 03:25:50 -0400 Date: Fri, 31 Aug 2001 03:25:49 -0400 (EDT) From: To: cc: Subject: Re: CCL:any free software for ETH calculations In-Reply-To: <200108301828.XAA25076@qasid.cc.iitk.ac.in> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Chinmoy, > Could any one tell me if there are free softwares available for doing > Extended huckel calculations. You can try the following EH calculation & visualisation packages: Cacao98, http://www.chembio.uoguelph.ca/oakley/310/cacao/cacao.htm - applicable to molecular systems or YAeHMOP, http://yaehmop.sourceforge.net -applicable to both molecular and extended structures. Marketa From chemistry-request@server.ccl.net Fri Aug 31 10:03:40 2001 Received: from MAIL.AD.Berry.edu ([66.20.28.66]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7VE3eM00498 for ; Fri, 31 Aug 2001 10:03:40 -0400 Received: from [10.16.232.24] ([10.16.232.24]) by MAIL.AD.Berry.edu with Microsoft SMTPSVC(5.0.2195.2966); Fri, 31 Aug 2001 10:12:49 -0400 User-Agent: Microsoft-Outlook-Express-Macintosh-Edition/5.02.2022 Date: Fri, 31 Aug 2001 10:03:37 -0400 Subject: NICS chemical shifts From: Gary Breton To: Message-ID: Mime-version: 1.0 Content-type: text/plain; charset="US-ASCII" Content-transfer-encoding: 7bit X-OriginalArrivalTime: 31 Aug 2001 14:12:49.0431 (UTC) FILETIME=[03F0CA70:01C13227] Hello all, A straightforward and practical question: I am interested in computing Nucleus Independent Chemical Shifts (NICS) on some potentially aromatic ring systems via the exquisite method described by Schleyer in several articles (a recent example: Organic Letters 2001, 2465). Am I able to do this utilizing Gaussian98W via the GaussView GUI (both of which I intend to buy soon)? Furthermore, is this method described in a "practical manner" in the manuals or somewhere else? (i.e., can I figure it out after becoming better acquainted with Gaussian, or will I look forward to becoming hopelessly lost?? I currently use Spartan and Hyperchem for computational work and have no previous experience with Gaussian). Thanks for suggestions! Gary W. Breton Department of Chemistry Berry College PO Box 495016 Mount Berry, GA 30149 "There's a light at the end of the tunnel, but it may be an oncoming train" From chemistry-request@server.ccl.net Fri Aug 31 11:50:08 2001 Received: from csww75 ([207.243.182.130]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f7VFo7M05163 for ; Fri, 31 Aug 2001 11:50:08 -0400 Subject: How would results from MD simulation (in water) compare with NMR results (in dmso) for same peptide? To: CHEMISTRY@ccl.net X-Mailer: Lotus Notes Release 5.0.5 September 22, 2000 Message-ID: From: dmaxwell@tbc.com Date: Fri, 31 Aug 2001 11:01:40 -0500 X-MIMETrack: Serialize by Router on tbcnotes/TBC(Release 5.0.8 |June 18, 2001) at 08/31/2001 11:01:40 AM MIME-Version: 1.0 Content-type: text/plain; charset=us-ascii I am trying to compare my MD simulation results (in water) with data from a paper describing NMR results (in dmso) for the same peptide. Could someone please comment on the effects of solvent on the conformation in NMR? I would expect some difference due to the H-bonding differences, but I was told that actual structures are rather similar. I am most interested in the differences for peptides. Any relevant papers would also be appreciated. Thanks very much, Dave --- David Maxwell, Ph.D. Principal Scientist Texas Biotechnology Corp. 7000 Fannin, Suite 1920 Houston, TX 77030 Phone: (713) 796-8822 x102 Fax : (713) 796-8232 E-mail: dmaxwell@tbc.com From chemistry-request@server.ccl.net Fri Aug 31 13:40:44 2001 Received: from hermes.bmc.uu.se ([130.238.39.159]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7VHeiM08463 for ; Fri, 31 Aug 2001 13:40:44 -0400 Received: from XRAY.bmc.uu.se ([130.238.37.10]) by hermes.bmc.uu.se (Post.Office MTA v3.5.3 release 223 ID# 0-62649U1500L1000S0V35) with ESMTP id se; Fri, 31 Aug 2001 19:42:09 +0200 Received: from zorn.bmc.uu.se (IDENT:spoel@zorn.bmc.uu.se [130.238.37.95]) by XRAY.bmc.uu.se (8.9.3/8.8.7) with ESMTP id TAA28061; Fri, 31 Aug 2001 19:41:57 +0200 Date: Fri, 31 Aug 2001 17:44:17 +0200 (CEST) From: David van der Spoel X-Sender: spoel@zorn.bmc.uu.se To: dmaxwell@tbc.com cc: CHEMISTRY@ccl.net Subject: Re: CCL:How would results from MD simulation (in water) compare with NMR results (in dmso) for same peptide? In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Fri, 31 Aug 2001 dmaxwell@tbc.com wrote: >I am trying to compare my MD simulation results (in water) with data from a >paper describing NMR results (in dmso) for the same peptide. Could someone >please comment on the effects of solvent on the conformation in NMR? I >would expect some difference due to the H-bonding differences, but I was >told that actual structures are rather similar. I am most interested in >the differences for peptides. Any relevant papers would also be >appreciated. @Article{Mierke91, author = "D. F. Mierke and H. Kessler", title = "Molecular Dynamics with Dimethyl Sulfoxide as a Solvent. Conformation of a Cyclic Hexapeptide.", journal = {J. Am. Chem. Soc.}, year = "1991", volume = "113", pages = "9446", } @Article{Spoel97a, author = {D. van der Spoel and H. J. C. Berendsen}, title = {Molecular Dynamics Simulations of {Leu}-Enkephalin in water and {DMSO}}, year = 1997, journal = {Biophys. J.}, volume = 72, pages = {2032-2041} } Groeten, David. ________________________________________________________________________ Dr. David van der Spoel, Biomedical center, Dept. of Biochemistry Husargatan 3, Box 576, 75123 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel@xray.bmc.uu.se spoel@gromacs.org http://zorn.bmc.uu.se/~spoel ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From chemistry-request@server.ccl.net Fri Aug 31 13:29:48 2001 Received: from sas.asc.hpc.mil ([129.48.244.126]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7VHTmM08319 for ; Fri, 31 Aug 2001 13:29:48 -0400 Received: from asc.hpc.mil (wk32.asc.hpc.mil [129.48.245.32]) by sas.asc.hpc.mil (8.11.6/8.11.6) with ESMTP id f7VHTmp245782 for ; Fri, 31 Aug 2001 13:29:48 -0400 (EDT) Sender: duanx@asc.hpc.mil Message-ID: <3B8FC96C.5FD7D541@asc.hpc.mil> Date: Fri, 31 Aug 2001 13:29:16 -0400 From: XIAOFENG FRANK DUAN Organization: CSC X-Mailer: Mozilla 4.76 [en] (X11; U; IRIX 6.5 IP22) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Compiling Crystal98 on Compaq machines Content-Type: multipart/alternative; boundary="------------BCF3832D5A2F5C89E82AF308" --------------BCF3832D5A2F5C89E82AF308 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, all! I was wondering if someone here has successfully done so. We are particularly interested in compiling it on ES40 or GS320 clusters? Thanks in advance! -- Xiaofeng Frank Duan, Ph.D | Phone: 937-904-8307 ASC MSRC | Email: duanx@asc.hpc.mil 2435 5th St., ASC/HP Bldg. 676 | URL: http://www.asc.hpc.mil Wright-Patterson AFB, OH 45433 | --------------BCF3832D5A2F5C89E82AF308 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, all!

I was wondering if someone here has successfully done so. We are particularly interested in compiling it on ES40 or GS320 clusters?

Thanks in advance!
  

-- 
 Xiaofeng Frank Duan, Ph.D         |  Phone: 937-904-8307
 ASC MSRC                          |  Email: duanx@asc.hpc.mil   
 2435 5th St., ASC/HP Bldg. 676    |  URL:   http://www.asc.hpc.mil
 Wright-Patterson AFB, OH 45433    |
  --------------BCF3832D5A2F5C89E82AF308--