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Request our free E-mail information by replying to: mailto:qwen76@yahoo.com?subject=INFO_PLEASE **************************************************** Remove at mailto:veng91@netscape.net?subject=remove **************************************************** From owner-molec-model@net.bio.net Mon Oct 04 05:12:00 1999 Path: biosci!pvrr.ru!pay30 From: pay30@pvrr.ru (h75659i3) Newsgroups: bionet.molec-model Subject: Make 10K A Month, Famous Private-Eye Tells All Date: 3 Oct 1999 23:12:45 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 107 Sender: daemon@net.bio.net Distribution: world Message-ID: <199910043670TAA54612@3984him78434.office.de> NNTP-Posting-Host: net.bio.net Oprah, Nightline, Maria Shriver, 48 Hours, 20/20 and more have all interviewed this famous Private Investigator. Now, you too can make substantial income using Schweitzers highly sought- after SECRETS. Thank you for your interest in our training Course! 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Please call us at 1-888-309-5852 (Toll Free) and speak with Al Schweitzer directly (between the hours of 9:00am - 5:00pm, Mountain Time) Thank you for your time and interest. wsb44@yahoo.com ///// S 5 From owner-molec-model@net.bio.net Mon Oct 04 14:51:00 1999 Path: biosci!newshost.lanl.gov!logbridge.uoregon.edu!hammer.uoregon.edu!vixen.cso.uiuc.edu!not-for-mail From: John Stone Newsgroups: bionet.molec-model Subject: Announce: VMD 1.4 beta 1 Date: Mon, 04 Oct 1999 10:44:55 -0500 Organization: Theoretical Biophysics, Beckman Institute, UIUC Lines: 29 Message-ID: <37F8CB77.4B90A745@ks.uiuc.edu> NNTP-Posting-Host: geneseo.ks.uiuc.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.7 [en] (X11; I; SunOS 5.7 sun4u) X-Accept-Language: en VMD "Visual Molecular Dynamics" 1.4 beta 1 Announcement ------------------------------------------------------- The Theoretical Biophysics group at the Beckman Institute For Advanced Science and Technology, the University of Illinois (U-C), is proud to announce the release of VMD 1.4 beta 1. 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New site: http://www.fortunecity.com/skyscraper/byte/517/ From owner-molec-model@net.bio.net Fri Oct 08 15:02:00 1999 Path: biosci!TOR.STG.SE!OM4xfxXPV From: OM4xfxXPV@TOR.STG.SE Newsgroups: bionet.molec-model Subject: Hurricane Warning!! Date: 8 Oct 1999 09:02:38 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 37 Sender: daemon@net.bio.net Distribution: world Message-ID: <9910099393.AA939397574@salmat.com.au> NNTP-Posting-Host: net.bio.net ============================================================== This message was composed using Extractor Pro Bulk E- Mail Software. If you wish to be removed from this advertiser's future mailings, please CLICK HERE--------- mailto:listkeeper@eastmail.com?subject=REMOVE and this software will automatically block you from their future mailings. ============================================================== HURRICANE WARNING!! 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To discuss rates or services (NOT FOR REMOVES) , please contact: Inet Mailing Group, S.A. 37 Rua Antigua Playa del Ingl?s, Gran Canaria Tel: (928) 77 63 54 To be removed from our mailing list, please follow directions above. ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From owner-molec-model@net.bio.net Fri Oct 08 21:14:00 1999 Path: biosci!newsfeed.stanford.edu!arclight.uoregon.edu!hammer.uoregon.edu!vixen.cso.uiuc.edu!not-for-mail From: Jim Phillips Newsgroups: bionet.molec-model Subject: ANNOUNCE: NAMD 2.1b2 Date: Fri, 08 Oct 1999 17:07:10 -0500 Organization: University of Illinois Lines: 34 Message-ID: <37FE6B0E.CCCFF5FC@ks.uiuc.edu> NNTP-Posting-Host: verdun.ks.uiuc.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.7 [en] (X11; I; SunOS 5.7 sun4u) X-Accept-Language: en +--------------------------------------------------------------------+ | | | NAMD 2.1b2 Release Announcement | | | +--------------------------------------------------------------------+ October 8, 1999 The Theoretical Biophysics Group at the University of Illinois is proud to announce the public release of a new version of NAMD, a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD is distributed free of charge and includes source code. NAMD development is supported by the NIH National Center for Research Resources. NAMD 2.1b2 is more stable than NAMD 2.0 and adds several new features: - Mollified impulse multiple timestepping method. - Faster particle mesh Ewald implementation. - Periodic boundaries for non-orthogonal cells. - New interactive molecular dynamics interface to VMD. NAMD is available from http://www.ks.uiuc.edu/Research/namd/. The Theoretical Biophysics group encourages NAMD users to be closely involved in the development process through reporting bugs, contributing fixes, periodical surveys and via other means. Any questions or comments may be directed to namd@ks.uiuc.edu. We are eager to hear from you, and thank you for using our software! From owner-molec-model@net.bio.net Sat Oct 09 03:14:00 1999 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!news.maxwell.syr.edu!newsfeeds.belnet.be!news.belnet.be!colt.net!Pollux.Teleglobe.net!server-b.cs.interbusiness.it!TESORO.GREEN.MinisterodelTesoro-CentroComunicativo.com NNTP-Posting-Host: 12.79.19.39 Newsgroups: bionet.molec-model Date: Fri, 8 Oct 1999 17:48:20 +0200 Message-ID: <04B596965534D31196710000F81EA08901E6E044@news.tesoro.it> From: cfjxyz@rec.uk Subject: Feel much better NOW 3049 [2/2] Lines: 2 From owner-molec-model@net.bio.net Sun Oct 10 19:27:00 1999 Path: biosci!rutgers!gatech!purdue!yuma!usenet From: "Ryan D. Alexander" Newsgroups: comp.lang.fortran,bionet.molec-model,comp.programming,sci.math,sci.stat.math,bionet.biophysics Subject: Monte Carlo Minimization Routine ??? Date: Sun, 10 Oct 1999 14:09:29 -0600 Organization: CSU-LBNL NSCORT Lines: 26 Message-ID: <3800F279.AD543BD3@lamar.colostate.edu> NNTP-Posting-Host: mc5126.cvmbs.colostate.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.7 [en] (Win95; U) X-Accept-Language: en Xref: biosci bionet.molec-model:2749 bionet.biophysics:5264 In attempting to model chromosomes packed within a nucleus, I've decided that I need a type of Monte Carlo Minimization routine. Scouring the Web has turned up little in the way progress, so I've turned to you all in NG-Land... Essentially I'm looking for an algorithm (in Fortran 77/90, preferably) where I may enter a set of initial cartesian coordinates, the associated radii for each "chromosome," and an objective function (i.e. Lennard-Jones potential function). Let the program calculate the value of my objective function, Monte Carlo (smartly) to re-position the chromosomes, recalculate the potential, etc., etc. until the function value is minimized. Anyone's help (books, articles, URL's) would be greatly appreciated!! If anyone in the realm of molecular dynamics, or packing theory (of non-uniform shapes) have any ideas, I'd obviously welcome them as well. Thanks in advance... (oh & as this is probably not of general interest to these ng's please just e-mail me directly if you'd like) -- Ryan D. Alexander ========================================================= Ryan D. Alexander, CSU-LBNL NSCORT Ph.D. Trainee Colorado State Univ., Dept. of Radiological Health Sciences E-mail: ryanalex@lamar.colostate.edu Office Ph: 970-491-0520, Dept. Fax: 970-491-0623 ========================================================= From owner-molec-model@net.bio.net Mon Oct 11 01:31:00 1999 Path: biosci!newsfeed.stanford.edu!nntp1!nntp.primenet.com!nntp.gctr.net!nuq-peer.news.verio.net!news.verio.net!easynews!news.good.net!news.goodnet.com!not-for-mail Reply-To: "Hilton Evans" From: "Hilton Evans" Newsgroups: bionet.molec-model Subject: Molecular Mechanics Lines: 8 Organization: ChemPen Software MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Newsreader: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Message-ID: Date: Mon, 11 Oct 1999 02:27:27 GMT NNTP-Posting-Host: 207.180.40.116 X-Complaints-To: abuse@winstar.net X-Trace: news.goodnet.com 939608847 207.180.40.116 (Sun, 10 Oct 1999 19:27:27 MST) NNTP-Posting-Date: Sun, 10 Oct 1999 19:27:27 MST ChemPen3D Molecular Mechanics for Win95/NT -- http://home.ici.net/~hfevans/chempen3d.htm -- Hilton Evans NMRPen--C-13 NMR Shifts -- http://home.ici.net/~hfevans/nmrpen.htm Organic Reactions -- http://home.ici.net/~hfevans/reactions.htm Chempen Chemical Structure Drawing -- http://home.ici.net/~hfevans/chempen.htm From owner-molec-model@net.bio.net Mon Oct 11 08:32:00 1999 Path: biosci!newshost.lanl.gov!logbridge.uoregon.edu!dispose.news.demon.net!demon!news-lond.gip.net!news-raspail.gip.net!news.gsl.net!gip.net!grolier!MGN!jussieu.fr!univ-lyon1.fr!not-for-mail From: Boudeville Yves Newsgroups: comp.lang.fortran,bionet.molec-model,comp.programming,sci.math,sci.stat.math,bionet.biophysics Subject: Re: Monte Carlo Minimization Routine ??? Date: Mon, 11 Oct 1999 11:24:19 -0700 Organization: CNRS Message-ID: <38022B53.6418@catalyse.univ-lyon1.fr> References: <3800F279.AD543BD3@lamar.colostate.edu> Reply-To: Yves.Boudeville@ens-lyon.fr NNTP-Posting-Host: armagedo.univ-lyon1.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (Win95; I; 16bit) Lines: 46 Xref: biosci bionet.molec-model:2751 bionet.biophysics:5268 Ryan D. Alexander wrote: > Monte-Carlo methods and simulated annealing are good for monomodal mathematical functions. But is it really the case in MM ? Two ways : One random based "the genetic algoritms", David E; Goldberg, Addison Wesley can be benefit because you have not only the "minimum minimorum" but also the "local minima" of a multimodal function. The most robust way, a little less expensive, can be the flexible simplex methods (from G.E.P. Box ? if my memory is right). Friendly. Yves. > In attempting to model chromosomes packed within a nucleus, I've decided that I > need a type of Monte Carlo Minimization routine. Scouring the Web has turned up > little in the way progress, so I've turned to you all in NG-Land... > > Essentially I'm looking for an algorithm (in Fortran 77/90, preferably) where I > may enter a set of initial cartesian coordinates, the associated radii for each > "chromosome," and an objective function (i.e. Lennard-Jones potential > function). Let the program calculate the value of my objective function, Monte > Carlo (smartly) to re-position the chromosomes, recalculate the potential, etc., > etc. until the function value is minimized. > > Anyone's help (books, articles, URL's) would be greatly appreciated!! If anyone > in the realm of molecular dynamics, or packing theory (of non-uniform shapes) > have any ideas, I'd obviously welcome them as well. > > Thanks in advance... (oh & as this is probably not of general interest to these > ng's please just e-mail me directly if you'd like) > -- Ryan D. Alexander > ========================================================= > Ryan D. Alexander, CSU-LBNL NSCORT Ph.D. Trainee > Colorado State Univ., Dept. of Radiological Health Sciences > E-mail: ryanalex@lamar.colostate.edu > Office Ph: 970-491-0520, Dept. Fax: 970-491-0623 > ========================================================= -- ------------------------------------------------- I Dr. Yves Boudeville; Theory Group / ENS-Lyon, I I Institut de Recherches sur la Catalyse, CNRS I I 2, Avenue Albert EINSTEIN ; I I F69626 VILLEURBANNE Cedex ; FRANCE . I I Ph: (+33.4.72...or) 04.72.44.53.49 (in France)I I Fax:(+33.4.72...or) 04.72.44.53.99 (in France)I I E-mail: boudevil@catalyse.univ-lyon1.fr I I http://www.ens-lyon.fr/~boudevil/ I ------------------------------------------------- From owner-molec-model@net.bio.net Mon Oct 11 12:34:00 1999 From: "David Jones" Newsgroups: comp.lang.fortran,bionet.molec-model,comp.programming,sci.math,sci.stat.math,bionet.biophysics References: <3800F279.AD543BD3@lamar.colostate.edu> Subject: Re: Monte Carlo Minimization Routine ??? Date: Mon, 11 Oct 1999 12:29:41 +0100 X-Priority: 3 X-MSMail-Priority: Normal X-Newsreader: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 NNTP-Posting-Host: 192.171.178.132 Message-ID: <3801ca27.0@news.nwl.ac.uk> X-Trace: 11 Oct 1999 12:29:43 GMT, 192.171.178.132 Path: biosci!pravda.ucr.edu!awabi.library.ucla.edu!128.32.206.55!newsfeed.berkeley.edu!dispose.news.demon.net!demon!newsfeed.icl.net!newspeer.clara.net!news.clara.net!news-lond.gip.net!news.gsl.net!gip.net!tank.news.pipex.net!pipex!server1.netnews.ja.net!server2.netnews.ja.net!news.nwl.ac.uk!192.171.178.132 Lines: 26 Xref: biosci bionet.molec-model:2752 bionet.biophysics:5270 Ryan D. Alexander wrote in message news:3800F279.AD543BD3@lamar.colostate.edu... > In attempting to model chromosomes packed within a nucleus, I've decided that I > need a type of Monte Carlo Minimization routine. Scouring the Web has turned up > little in the way progress, so I've turned to you all in NG-Land... > An interesting alternative to the suggestions already made is the approach of the algorithm by A.Zilinskas (published as "Optimization of one-dimensional multimodal functions", Applied Statistics 1978, v27, p367-375 (Algorithm AS133)). This gives Fortran code, which should also be available from statlib under directory apstat. This approach seems only suited to 1-D problems because of the number of function evaluations. It has the effect of balancing doing extra function evauations in regions where the function is "roughest", with evaluations in the neighbourhoods of possibly competing local optima. The locations where the function is evaluated are decided so as to supply the best improvement of information about the location of the overall optimum in a statistical sense. However, the "genetic" algorithms already mentioned seem well suited to the problem. From owner-molec-model@net.bio.net Mon Oct 11 17:03:00 1999 Path: biosci!newsfeed.stanford.edu!newsfeed.berkeley.edu!ctu-gate!news.nctu.edu.tw!news.sinica!not-for-mail From: "vecko" Newsgroups: bionet.molec-model Subject: How to do affinity of Hg2+ to tetrapeptide Date: Tue, 12 Oct 1999 02:02:49 +0800 Organization: Computing Center, Academia Sinica Lines: 7 Message-ID: <7tt8bs$pch$1@news1.sinica.edu.tw> NNTP-Posting-Host: 140.109.64.201 X-Trace: news1.sinica.edu.tw 939664572 26001 140.109.64.201 (11 Oct 1999 17:56:12 GMT) X-Complaints-To: usenet@news.sinica.edu.tw NNTP-Posting-Date: 11 Oct 1999 17:56:12 GMT X-Priority: 3 X-MSMail-Priority: Normal X-Newsreader: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Hi, I would like to do Hg^2+ ion binding to a tetrapeptide (4 Amino acids). Can someone show me how to do this job? Thanks I thought to use Affinity_docking/insightII but dont know how to start with. From owner-molec-model@net.bio.net Fri Oct 15 01:54:00 1999 Path: biosci!newshost.lanl.gov!arclight.uoregon.edu!newsfeed.mathworks.com!news.maxwell.syr.edu!ameritech.net!nntp0.detroit.mi.ameritech.net.POSTED!not-for-mail From: "Jim Kress" Newsgroups: comp.lang.fortran,bionet.molec-model,comp.programming,sci.math,sci.stat.math,bionet.biophysics References: <3800F279.AD543BD3@lamar.colostate.edu> Subject: Re: Monte Carlo Minimization Routine ??? Lines: 48 X-Priority: 3 X-MSMail-Priority: Normal X-Newsreader: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Message-ID: Date: Thu, 14 Oct 1999 22:47:08 -0400 NNTP-Posting-Host: 199.179.189.44 X-Trace: nntp0.detroit.mi.ameritech.net 939956000 199.179.189.44 (Thu, 14 Oct 1999 22:53:20 EDT) NNTP-Posting-Date: Thu, 14 Oct 1999 22:53:20 EDT Organization: Ameritech.Net www.ameritech.net Complaints: abuse@ameritech.net Xref: biosci bionet.molec-model:2757 bionet.biophysics:5275 http://dasher.wustl.edu/tinker/ -- Jim Check out my web site http://www.kressworks.com/ It'll blow your mind (politically), stimulate your senses (artistically) and provide scientific insights that boggle the mind! Ryan D. Alexander wrote in message news:3800F279.AD543BD3@lamar.colostate.edu... > In attempting to model chromosomes packed within a nucleus, I've decided that I > need a type of Monte Carlo Minimization routine. Scouring the Web has turned up > little in the way progress, so I've turned to you all in NG-Land... > > Essentially I'm looking for an algorithm (in Fortran 77/90, preferably) where I > may enter a set of initial cartesian coordinates, the associated radii for each > "chromosome," and an objective function (i.e. Lennard-Jones potential > function). Let the program calculate the value of my objective function, Monte > Carlo (smartly) to re-position the chromosomes, recalculate the potential, etc., > etc. until the function value is minimized. > > Anyone's help (books, articles, URL's) would be greatly appreciated!! If anyone > in the realm of molecular dynamics, or packing theory (of non-uniform shapes) > have any ideas, I'd obviously welcome them as well. > > Thanks in advance... (oh & as this is probably not of general interest to these > ng's please just e-mail me directly if you'd like) > -- Ryan D. Alexander > ========================================================= > Ryan D. Alexander, CSU-LBNL NSCORT Ph.D. Trainee > Colorado State Univ., Dept. of Radiological Health Sciences > E-mail: ryanalex@lamar.colostate.edu > Office Ph: 970-491-0520, Dept. Fax: 970-491-0623 > ========================================================= > > From owner-molec-model@net.bio.net Fri Oct 15 08:27:00 1999 Path: biosci!newshost.lanl.gov!arclight.uoregon.edu!hammer.uoregon.edu!newsfeed.direct.ca!su-news-hub1.bbnplanet.com!news.gtei.net!pln-w!spln!extra.newsguy.com!newsp.newsguy.com!not-for-mail From: vjp2@smtp.dorsai.org (Vasos Panagiotopoulos +1-917-287-8087 Bioengineer-Financier) Newsgroups: comp.lang.fortran,bionet.molec-model,comp.programming,sci.math,sci.stat.math,bionet.biophysics Subject: Re: Monte Carlo Minimization Routine ??? Followup-To: comp.lang.fortran,bionet.molec-model,comp.programming,sci.math,sci.stat.math,bionet.biophysics Date: 15 Oct 1999 08:24:28 GMT Organization: Samani Marions Panyaught NYC-11357-3436-287-USA Lines: 18 Distribution: world Message-ID: <7u6obs$u86@enews4.newsguy.com> References: <3800F279.AD543BD3@lamar.colostate.edu> NNTP-Posting-Host: amanda.dorsai.org Mail-Copies-To: vjp2@dorsai.org,vjp2@compuserve.com,vjp2@mcimail.com,vjp2@csi.com X-Sys-Config: The configuration of my system is described in my web page. X-Disclaim: Nothing herein constitutes advice; everything fully disclaimed. X-Quiet: My silence is not reluctant acquiescence rather confident deprecation. X-URL: http://www.dorsai.org/~vjp2 X-Newsreader: TIN [UNIX 1.3 950824BETA PL0] Xref: biosci bionet.molec-model:2758 bionet.biophysics:5276 There was one in SCS "Simulation" like about 1986, but there was a big debate if the Mt Carlo made a difference. If you bug me a few days from now, I might dig up a PL/I test program I wrote with the article refs embedded in it. Perhaps it can be understood by looking at a related area: In chosing PDE solution points, Mt Carlo is said to be more effective because beyond two dimensions, rectangularisation is inefficient. IBM's million-dollar Simulation Blaster works along those lines by providing a file of non-random best sampling points so you don't have to use Mt Carlo. - = - Vasos-Peter John Panagiotopoulos II, Columbia'81+, Bioengineer-Financier, NYC BachMozart ReaganQuayle EvrytanoKastorian http://WWW.Dorsai.Org/~vjp2 vjp2@{MCIMail.Com|CompuServe.Com|Dorsai.Org} ---{Nothing herein constitutes advice. Everything fully disclaimed.}--- [DQ2K: Make the Murky Clown Frown!] From owner-molec-model@net.bio.net Sun Oct 17 20:26:00 1999 Path: biosci!newsfeed.stanford.edu!newsfeed.berkeley.edu!nntp.primenet.com!nntp.gctr.net!nuq-peer.news.verio.net!news.verio.net!easynews!news.good.net!news.goodnet.com!not-for-mail Reply-To: "Hilton Evans" From: "Hilton Evans" Newsgroups: bionet.molec-model Subject: C-13 NMR Shift Software Lines: 7 Organization: ChemPen Software MIME-Version: 1.0 Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Newsreader: Microsoft Outlook Express 5.00.2615.200 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 Message-ID: Date: Sun, 17 Oct 1999 21:21:55 GMT NNTP-Posting-Host: 207.180.12.122 X-Complaints-To: abuse@winstar.net X-Trace: news.goodnet.com 940195315 207.180.12.122 (Sun, 17 Oct 1999 14:21:55 MST) NNTP-Posting-Date: Sun, 17 Oct 1999 14:21:55 MST NMRPen C-13 NMR Shift -- http://home.ici.net/~hfevans/nmrpen.htm Molecular Mechanics for Win95/NT -- http://home.ici.net/~hfevans/chempen3d.htm Chemical Structure Drawing -- http://home.ici.net/~hfevans/chempen.htm Organic Reactions -- http://home.ici.net/~hfevans/reactions.htm From owner-molec-model@net.bio.net Mon Oct 18 14:01:00 1999 Path: biosci!YES.ZZN.COM!uolips From: uolips@YES.ZZN.COM Newsgroups: bionet.molec-model Subject: SAVE MONEY MAKE$1400/wk Date: 18 Oct 1999 08:01:41 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 45 Sender: daemon@net.bio.net Distribution: world Message-ID: <199910181443.WAA15750@pigeon.szptt.net.cn> NNTP-Posting-Host: net.bio.net After accessing your info I thought you might be interested in the following. 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Go To: http://209.1.224.17/MadisonAvenue/Suite/6875/index.html From owner-molec-model@net.bio.net Fri Oct 22 13:35:00 1999 Path: biosci!newsfeed.stanford.edu!skynet.be!newsfeed.icl.net!newsfeed.icl.net!news-x.support.nl!knews.uk0.vbc.net!vbcnet-gb!news.uk0.vbc.net!not-for-mail From: "SelectScience" Newsgroups: bionet.molec-model Subject: Free resources for chemists & life scientists Date: Fri, 22 Oct 1999 13:45:10 -0000 Organization: SelectScience Lines: 19 Message-ID: <940602466.781886@news.uk1.vbc.net> NNTP-Posting-Host: news.uk1.vbc.net X-Newsreader: Microsoft Outlook Express 4.72.3110.1 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Cache-Post-Path: news.uk1.vbc.net!unknown@194.207.229.158 X-Cache: nntpcache 2.3.3 (see http://www.nntpcache.org/) `At www.selectscience.net we have details on hundreds of free sites for chemists and life scientists, from tutorials and glossaries to societies and free software resources. If you want to find out about other internet resources in your discipline, come to www.selectscience.net If you have a page which you think should be included in our specialist database, please drop me a line (andrew@selectscience.net). I'm looking forward to hearing from you, Andrew Smith (andrew@selectscience.net) Editor, www.selectscience.net From owner-molec-model@net.bio.net Fri Oct 22 15:55:00 1999 Path: biosci!seu.edu.cn!hwang From: hwang@seu.edu.cn (Wang Hong) Newsgroups: bionet.molec-model Subject: subscribe Date: 22 Oct 1999 09:55:31 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 3 Sender: daemon@net.bio.net Distribution: world Message-ID: <199910221640.AAA05328@seu.edu.cn> NNTP-Posting-Host: net.bio.net -- [ From: Wang Hong * EMC.Ver #2.5.02 ] -- subscribe From owner-molec-model@net.bio.net Sat Oct 23 05:36:00 1999 Path: biosci!seu.edu.cn!hwang From: hwang@seu.edu.cn (Wang Hong) Newsgroups: bionet.molec-model Subject: Genchip Hybridization simulation Date: 22 Oct 1999 23:36:34 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 10 Sender: daemon@net.bio.net Distribution: world Message-ID: <199910230621.OAA11144@seu.edu.cn> NNTP-Posting-Host: net.bio.net -- [ From: Wang Hong * EMC.Ver #2.5.02 ] -- Can any one give me some advice on DNA hybridization simulation on the solid surface of DNA chip? 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Go To: http://209.1.224.17/Hollywood/Derby/4936/index.html From owner-molec-model@net.bio.net Mon Oct 25 08:42:00 1999 Path: biosci!newsfeed.stanford.edu!newsfeed.berkeley.edu!newsfeed.tli.de!news3-muc.ecrc.net!news-mue1.dfn.de!news-stu1.dfn.de!news-koe1.dfn.de!RRZ.Uni-Koeln.DE!news.rz.uni-duesseldorf.de!usenet From: Stefanie Bendels Newsgroups: bionet.molec-model Subject: Rotamer Date: Mon, 25 Oct 1999 11:26:13 +0200 Organization: Heinrich Heine Universitaet Duesseldorf Lines: 44 Message-ID: <38142235.8FB4F2ED@pharm.uni-duesseldorf.de> NNTP-Posting-Host: alberich05.pharm.uni-duesseldorf.de Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="------------BBED7BEF8BF70CDA8EEFBF2B" X-Mailer: Mozilla 4.05C-SGI [en] (X11; I; IRIX 6.5 IP32) --------------BBED7BEF8BF70CDA8EEFBF2B Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I need some help! Does anybody know a freely available program for rotameric analysis? Thanks!! -- Stefanie Bendels Institut fuer Pharmazeutische Chemie Heinrich-Heine-Universitaet Universitaetsstr. 1 40 225 Duesseldorf phone +49 211 811 3662 fax +49 211 811 3847 --------------BBED7BEF8BF70CDA8EEFBF2B Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit I need some help!

Does anybody know a freely available program for rotameric analysis?

Thanks!! 

-- 
Stefanie Bendels
Institut fuer Pharmazeutische Chemie
Heinrich-Heine-Universitaet
Universitaetsstr. 1
40 225 Duesseldorf
phone +49 211 811 3662
fax   +49 211 811 3847
  --------------BBED7BEF8BF70CDA8EEFBF2B-- From owner-molec-model@net.bio.net Mon Oct 25 17:14:00 1999 Path: biosci!newsfeed.stanford.edu!newsfeed.berkeley.edu!news.he.net!easynews!news.good.net!news.goodnet.com!not-for-mail Reply-To: "Hilton Evans" From: "Hilton Evans" Newsgroups: bionet.molec-model Subject: Reaction Energetics Lines: 7 Organization: ChemPen Software MIME-Version: 1.0 Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Newsreader: Microsoft Outlook Express 5.00.2615.200 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 Message-ID: Date: Mon, 25 Oct 1999 18:10:21 GMT NNTP-Posting-Host: 207.180.12.42 X-Complaints-To: abuse@winstar.net X-Trace: news.goodnet.com 940875021 207.180.12.42 (Mon, 25 Oct 1999 11:10:21 MST) NNTP-Posting-Date: Mon, 25 Oct 1999 11:10:21 MST Molecular Mechanics for Win95/NT -- http://home.ici.net/~hfevans/chempen3d.htm NMRPen C-13 NMR Shift -- http://home.ici.net/~hfevans/nmrpen.htm Chemical Structure Drawing -- http://home.ici.net/~hfevans/chempen.htm Organic Reactions -- http://home.ici.net/~hfevans/reactions.htm From owner-molec-model@net.bio.net Mon Oct 25 21:44:00 1999 Path: biosci!newsfeed.stanford.edu!newsfeed.berkeley.edu!howland.erols.net!vixen.cso.uiuc.edu!not-for-mail From: Jim Phillips Newsgroups: bionet.molec-model Subject: ANNOUNCE: NAMD 2.1b3 Date: Mon, 25 Oct 1999 17:37:07 -0500 Organization: University of Illinois Lines: 35 Message-ID: <3814DB93.93C2C0B7@ks.uiuc.edu> NNTP-Posting-Host: verdun.ks.uiuc.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.7 [en] (X11; I; SunOS 5.7 sun4u) X-Accept-Language: en +--------------------------------------------------------------------+ | | | NAMD 2.1b3 Release Announcement | | | +--------------------------------------------------------------------+ October 25, 1999 The Theoretical Biophysics Group at the University of Illinois is proud to announce the public release of a new version of NAMD, a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD is distributed free of charge and includes source code. NAMD development is supported by the NIH National Center for Research Resources. NAMD 2.1b3 is more stable than NAMD 2.0 and adds several new features: - Tcl scripting language interface and config file parsing. - Mollified impulse multiple timestepping method. - Faster particle mesh Ewald implementation. - Periodic boundaries for non-orthogonal cells. - New interactive molecular dynamics interface to VMD. NAMD is available from http://www.ks.uiuc.edu/Research/namd/. The Theoretical Biophysics group encourages NAMD users to be closely involved in the development process through reporting bugs, contributing fixes, periodical surveys and via other means. Questions or comments may be directed to namd@ks.uiuc.edu. We are eager to hear from you, and thank you for using our software! From owner-molec-model@net.bio.net Wed Oct 27 08:00:00 1999 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.molec-model Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 27 Oct 1999 02:00:09 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 239 Sender: daemon@net.bio.net Distribution: world Message-ID: <199910270900.CAA07784@net.bio.net> NNTP-Posting-Host: net.bio.net (LAST REVISION: 14-AUG-99) This BIOSCI "miniFAQ" is designed to answer the questions that come up the *most frequently*. The main BIOSCI FAQ (Frequently Asked Questions) is accessible on the World Wide Web at URL http://www.bio.net/. If you can not find an answer to your question in this or other documentation, the BIOSCI technical support staff answers e-mail queries sent to biosci-help@net.bio.net We can only answer questions about the use of the newsgroups and mailing lists. We unfortunately do not have the staff to do Internet information searches or answer scientific questions. Please post those to the appropriate BIOSCI/bionet newsgroups. Contents: -------- 0) BIOSCI NEEDS YOUR SUPPORT!! 1) Using the WWW to access the BIOSCI/bionet newsgroups. 2) What to do about "spams," i.e., junk mail, ads, etc. 3) Examples of subscribing and unsubscribing to the mailing lists. 4) The BIOSCI user address and research interest directory. 0) BIOSCI NEEDS YOUR SUPPORT!! ------------------------------ BIOSCI's government funding has been expended, and we are now operating solely from advertising revenue that we have raised from our Web site at http://www.bio.net/. We need just a few minutes of your time to help us serve you. You can do two important things which will take very little time for you individually and will immensely help us continue to help you. First, please use our WWW system at http://www.bio.net/ to access the archives. You can post or reply to messages via your Web browser as described in item #1 below. Your usage helps attract sponsors. If you contact any of our sponsors, please be sure to thank them for supporting BIOSCI. It is critical for them to get this feedback if they are to continue their sponsorship for the long term. Second, if you work for a company or organization that provides products or services of interest to the biology community, please pass this message on to your marketing or marketing communications department or other appropriate group. Please ask them to help support BIOSCI by sponsoring our Web site and explain the uses and benefits of the system to the biology community. If they are interested, they can then contact us for further information at our tech support address, biosci-help@net.bio.net. 1) Using the WWW to access the BIOSCI/bionet newsgroups. -------------------------------------------------------- All BIOSCI/bionet full newsgroups are accessible through the World Wide Web (WWW) at URL http://www.bio.net. One can read and reply publicly or privately to both recent postings and archived messages through one's Web browser if it is configured properly to send e-mail. Each newsgroup is equipped with its own WAIS index. The main BIOSCI home page also has access to the BIO-JOURNALS Table of Contents database WAIS index and the BIOSCI user address database described in another item further below. 2) What to do about "spams," i.e., junk mail, ads, etc. ------------------------------------------------------- BIOSCI is a set of parallel USENET newsgroups (the "bionet" groups), mailing lists, and a hypermail archive at URL http://www.bio.net/. The same postings are distributed on all media (except for a small number of mailing-list-only groups at net.bio.net). Unfortunately it is becoming a despicable practice on the Internet (by a few people out to make a fast buck) to do automated mass postings to thousands of newsgroups and mailing lists. These attempts to grab free advertising are refered to as "spams" in the usual, somewhat boneheaded, net terminology. USENET is more susceptible to this practice, and many spams originate on the USENET groups and then are passed on to the mailing lists. However, spammers also get lists of mailing addresses and hit these too, so neither medium is immune. What should you do personally if you get junk mail? --------------------------------------------------- Just delete it and move on without reading it further. Filing a protest is becoming increasingly useless because spammers are often disguising the addresses where the messages are sent from. Unless you really understand Internet mail systems, your attempt at protest by sending replies to the message will often end up being sent to the address of an innocent person that the spammer is victimizing. What can BIOSCI/bionet do to protect its newsgroups? ---------------------------------------------------- The only solution currently available is to moderate the newsgroup. If this newsgroup is already moderated, then you are in good shape. Moderation protects the USENET distribution from about 95% of the spams that are being sent to date and protects the mailing lists completely. Moderation means, however, that someone has to take the time to review each message before it goes out. We have set up software here that simply allows the moderator to forward to an address at net.bio.net messages that (s)he wishes to have distributed. This takes no more time than that needed to read the message and pass it on, say about 1 min. per message. Most newsgroups currently have a discussion leader who is responsible for their newsgroup. The discussions leaders and their e-mail addresses are listed in the BIOSCI Information Sheet which is available on the Web at http://www.bio.net/. If a newsgroup is being hit with too many junk postings, please contact the discussion leader for that group and see if there is interest in moderating the group. Please do not assume that by simply posting a complaint to the newsgroup itself, anyone on the BIOSCI staff will act on your complaint. With close to 100 newsgroups to run, the BIOSCI staff has to rely on the discussion leaders of each newsgroup to report problems directly to us at biosci-help@net.bio.net. We will moderate any of our newsgroups if the discussion leader tells us that the readership of the group wishes to do so and if a moderator is willing to do the work. For most BIOSCI/bionet groups, this entails only a few minutes of work each day. Moderating a newsgroup will resolve probably 95% of the junk postings on the USENET distribution. Unfortunately there are easy ways for determined spammers to override the moderation mechanism on USENET, but we can protect our e-mail subscribers from unwanted postings if the newsgroup is moderated. You can also access our newsgroups over the WWW at URL http://www.bio.net. While this Web interface will not stop spammers from trying to post to the groups, this will give you yet another way, besides using USENET news, to keep the junk out of your personal mail files. For those of you with local USENET news systems, the Web interface will also give you faster access to new newsgroups and recent postings. 3) Examples of subscribing and unsubscribing to the mailing lists. ------------------------------------------------------------------ PLEASE NOTE: The BIOSCI management does NOT act on subscription/unsubscription requests that are posted improperly to the newsgroups and mailing lists. People who do this only bother everyone on the lists to no avail. Please be sure to follow the proper procedures below. Gory details are in the BIOSCI Information sheets on the Web at http://www.bio.net. Below we give an example utilizing the METHODS-AND-REAGENTS list at both of our two BIOSCI sites: Users in the Americas and Pacific Rim countries who use the BIOSCI ------------------------------------------------------------------ node at computer net.bio.net: ---------------------------- A) Determine the "listname" which is the <=8 character mail address ^^^^^^^^^^^^^ for the group. These can be found in the BIOSCI Info. Sheet. For the METHODS-AND-REAGENTS group the mailing address is methods@net.bio.net. The listname is the portion of the address to the left of the @ sign, i.e., "methods". The listname is used with the "subscribe" and "unsubscribe" commands illustrated below. B) Mail all commands in the body of a mail message addressed to biosci-server@net.bio.net. Do NOT send commands to the newsgroup posting addresses! Leave the Subject: line blank, any text on it will be ignored. C) In the body of your message put one or more of the following commands with an "end" command on the last line, e.g., subscribe methods unsubscribe methods end Do NOT put your e-mail address or other text on these lines. The server only allows you to cancel your subscription if the address on your mail header matches the address on our mailing list. Please ask for help at biosci-help@net.bio.net if your address has changed, e.g., if you know you are on the list but the server tells you that you are not a member. Users in Europe, Africa, and Central Asia who use the BIOSCI node at -------------------------------------------------------------------- the UK-HGMP-Resource Centre (known as hgmp.mrc.ac.uk): ----------------------------------------------------- A) Determine the "listname" which is the <=8 character mail address ^^^^^^^^^^^^^ for the group. These can be found in the BIOSCI Info. Sheet. For the METHODS-AND-REAGENTS group the mailing address is methods@hgmp.mrc.ac.uk. The listname is the portion of the address to the left of the @ sign, i.e., "methods". The listname is used with the "subscribe" and "unsubscribe" commands illustrated below. B) Mail all commands in the body of a mail message addressed to majordomo@hgmp.mrc.ac.uk. Do NOT send commands to the newsgroup posting addresses! Leave the Subject: line blank, any text on it will be ignored. C) In the body of your message put one or more of the following commands with an "end" command on the last line, e.g., subscribe methods unsubscribe methods end Please ask for help at biosci@hgmp.mrc.ac.uk if your address has changed, e.g., if you know you are on the list but the server tells you that you are not a member. 4) The BIOSCI user address and research interest directory. ----------------------------------------------------------- Please take this opportunity to add your name, address, and research interest information to the BIOSCI User Address Database if you have not already done so. You can fill out the address form directly through our Web page at URL http://www.bio.net/adrform.html. The address database is reindexed nightly for WWW access (the URL is http://www.bio.net/). If you are not directly on the Internet but can reach it by e-mail, please use our waismail server to access the user directory. waismail use is described above. 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