From lawson@argus.cem.msu.edu Tue Oct 22 08:16:26 1996 Received: from argus.cem.msu.edu for lawson@argus.cem.msu.edu by www.ccl.net (8.8.0/950822.1) id HAA05296; Tue, 22 Oct 1996 07:32:15 -0400 (EDT) Received: by argus.cem.msu.edu (951211.SGI.8.6.12.PATCH1042/951211.SGI) for CHEMISTRY@www.ccl.net id HAA29762; Tue, 22 Oct 1996 07:33:21 -0400 Date: Tue, 22 Oct 1996 07:33:21 -0400 From: lawson@argus.cem.msu.edu (Dan Lawson) Message-Id: <199610221133.HAA29762@argus.cem.msu.edu> To: CHEMISTRY@www.ccl.net Subject: Summary of curve fitting CCLer's, Thanks to all the people who responded to my question. Although I had a more specific answer (subroutine) in mind, the dozen or more responses will prove useful to me for other applications. ORIGINAL POST: > > Hello, > I am looking for a program (fortran or C) that will fit > a function (Morse like or n-order polynomial) to data (potential > curve). Does anyone know of any free programs available. I > checked the net and could not readily locate anything. I will > summarize results. > SUMMARY: People fit there equations to curves in two ways, canned code or subroutine(FORTRAN). -These are the basic "subroutine/code" responses referenced either by location or name. subroutines located in http://veng-server.pharmacy.uiowa.edu/CD_1/netlib/dierckx/00_index.htm 1mdif and nl2sol http://www.netlib.com/ then search for "curve fit" or "nl2sol" ... There are also fitting programs and subroutines in "Numerical Recipes" fortran and C versions. DLPOLY2 from a Molecular Dynamics program http://gserv1.dl.ac.uk/CCP/CCP5/dl_poly.html -These are the basic software packages available FREE: fit_any_function using simplex method ftp www.ccl.net /pub/chemistry/software/SOURCES/FORTRAN/fit_any_function survibtm for polyatoms ftp.tcg.anl.gov /pub/survibtm/ gnuplot also/and fudgit or gnufit http://sunsite.unc.edu xmgr ftp://ftp.teleport.com/pub/users/pturner/acegr/xmgr-3.01pl6.tar.gz MacCurveFit - its in the info-mac archives cvxpt124.zip - Windows( 3.1, 95, NT) ShareWare ftp://garbo.uwasa.fi/windows/science/cvxpt124.zip NOT FREE: (can do some kind of fitting) SigmaPlot Origin (linear fitting only) Mathematica MCAD Again, thanks to all those who responded. Sorry if I missed anyones response. Dan Lawson lawson@argus.cem.msu.edu Michigan State University From cbonner@vger.nsu.edu Tue Oct 22 11:16:42 1996 Received: from vger.nsu.edu for cbonner@vger.nsu.edu by www.ccl.net (8.8.0/950822.1) id KAA06178; Tue, 22 Oct 1996 10:41:00 -0400 (EDT) Received: from cbonner.nsu.edu by vger.nsu.edu with SMTP ; Tue, 22 Oct 96 10:40:38 EST Message-ID: <326CDC4C.6277@vger.nsu.edu> Date: Tue, 22 Oct 1996 10:38:04 -0400 From: "Carl E. Bonner" Organization: Norfolk State University X-Mailer: Mozilla 2.02Gold (Win95; I) MIME-Version: 1.0 To: chemistry@www.ccl.net CC: cbonner@vigyan.nsu.edu Subject: X-ray structures for gemstone crystals e.g. YAG, YLF, etc. X-URL: http://www.ccl.net/ccl/welcome.html#3 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Netters, I am trying to perform calculations on the energy levels of an rare earth dopant in a gemstone crystal such as YAG or YLF. In particular I am looking for the crystal structure in some electronic data format. I have checked both Brookhaven and the Cambridge structures archive. They both contain organic or biorganic molecule structures. Is there an equivalent database for these inorganic structures. I will summarize the responses Thanks in advance Carl -- Carl E. Bonner, Jr. Ph.D | Departmen of Chemistry and Center for Materials Research, | You either do or you don't, there is no try. Norfolk State University, 2401 Corprew Ave., Norfolk, Va 23504 | -- Yoda -- Email: cbonner@vger.nsu.edu (757) 683-2381/2296/9054 (o/l/f) | From chpajt@bath.ac.uk Tue Oct 22 11:28:06 1996 Received: from goggins.bath.ac.uk for chpajt@bath.ac.uk by www.ccl.net (8.8.0/950822.1) id KAA06035; Tue, 22 Oct 1996 10:22:16 -0400 (EDT) Received: from bath.ac.uk (actually host midge.bath.ac.uk) by goggins.bath.ac.uk with SMTP (PP); Tue, 22 Oct 1996 14:55:06 +0100 Date: Tue, 22 Oct 1996 14:55:00 +0100 (BST) From: A J Turner To: chemistry@www.ccl.net Subject: function only fitting methods Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi! Does anyone know of a really good (public domain) algorithum for minimisation without analytical gradients where my number of degrees of freedom are many less than my error function? Ie I want to reduce the error function to as close to zero as posible. I have had a look at a flavour of Bartel's method - but I would appreciate any other ideas - or even a general pd implementation of Bartel's method. Thanks for any help Alex ------------------------------------------------------------------- |Alexander J Turner |A.J.Turner@bath.ac.uk | |Post Graduate |http://www.bath.ac.uk/~chpajt/home.html| |School of Chemistry |+144 1225 8262826 ext 5137 | |University of Bath | | |Bath, Avon, U.K. |Field: QM/MM modeling | ------------------------------------------------------------------- From ap16390@ggr.co.uk Tue Oct 22 12:16:42 1996 Received: from gate.ggr.co.uk for ap16390@ggr.co.uk by www.ccl.net (8.8.0/950822.1) id MAA07382; Tue, 22 Oct 1996 12:16:05 -0400 (EDT) From: Received: from mailhub.ggr.co.uk (uk0x07.ggr.co.uk [147.184.146.69]) by gate.ggr.co.uk; Tue, 22 Oct 1996 17:14:06 +0100 (BST) Received: from itsg02.italy.glaxo (itsg02.italy.glaxo [161.147.83.59]) by mailhub.ggr.co.uk; Tue, 22 Oct 1996 17:04:52 +0100 (BST) Received: by itsg02.italy.glaxo (8.7.5/imd160294) id RAA15569; Tue, 22 Oct 1996 17:14:16 GMT Date: Tue, 22 Oct 1996 17:14:16 GMT Message-Id: <199610221714.RAA15569@itsg02.italy.glaxo> To: CHEMISTRY@www.ccl.net Subject: Roto-matrix Dear Netters, I would like to ask for an expertise about liner transformations performed via rotational matrixes. Given the 3D coordinates of three points P1(xyz) P2(xyz) and P3(xyz) in their initial (T0) and final (T1) position. Which is the best way for calculating the rotational matrix and translation capable of such transformation ? (distances between the three points are constants so we can consider it "rigid" between each others) Any help and or information is very welcome and I will summarize your contributions. Yours sincerely -Alfonso Pozzan >>>>>>>>>>>>Alfonso Pozzan Ph.D, GlaxoWellcome e-mail: ap16390@ggr.co.uk, fax: +39-45-9218196 via Fleming 2, 37100 Verona ITALY <<<<<<<<<<<< From M.Biggs@surrey.ac.uk Tue Oct 22 12:22:37 1996 Received: from mailc.surrey.ac.uk for M.Biggs@surrey.ac.uk by www.ccl.net (8.8.0/950822.1) id MAA07348; Tue, 22 Oct 1996 12:11:42 -0400 (EDT) Message-Id: <199610221611.MAA07348@www.ccl.net> Received: from surrey.ac.uk by mailc.surrey.ac.uk id <23613-0@mailc.surrey.ac.uk>; Tue, 22 Oct 1996 17:10:26 +0100 Subject: CCL:Database of polycyclic and hetrocyclic compounds To: chemistry@www.ccl.net Date: Tue, 22 Oct 1996 17:10:25 +0100 (BST) X-Mailer: ELM [version 2.4 PL25] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit From: Dr Mark J Biggs Sender: M.Biggs@surrey.ac.uk I recently asked the following question: > I am trying to find a database that lists > atleast all the possible polycyclic/hetrocyclic > compounds upto about 12 rings and hetroatoms of > oxygen, sulphur and nitrogen. Of these hetroatoms, > the most important is oxygen as I guess the > number of permutations will become large with > sulphur included. > > I have looked in our library and am a little > daunted by the 50+ volumes of possible compounds > with no apparent global index or heirachy - I am > hoping a computer database exists or a good > hardcopy index with some sort of listing that > starts at 1 ring and no heteroatoms and goes down > from there (i.e. something that has done the sorting > for a non-organic chemist). I recieved several replies: 2 asking for the results >from this query, 3 with words of advice. It appears as if computer databases do exist but they cost #$. We have the RING INDEX in our library and this was useful. In summary: (a) RING INDEX (books with "nice" index). (b) Beilstein database - part of STN International information network. (c) Chapman and Hall, Derwent, Index Chemicus, Current Drugs etc 3D databases available in UNITY format (look at http://www.tripos.com for more info). (d) CAST-3D subsets tailored to your own specification from Chemical Abstracts. If you want any more details on these, please do not hesitate to contact me. Many thanks for all those who responded. Mark M.Biggs@surrey.ac.uk From chemtw@showme.missouri.edu Tue Oct 22 18:16:30 1996 Received: from mail.missouri.edu for chemtw@showme.missouri.edu by www.ccl.net (8.8.0/950822.1) id SAA10179; Tue, 22 Oct 1996 18:08:49 -0400 (EDT) Received: from black.missouri.edu (black.missouri.edu [128.206.2.222]) by mail.missouri.edu (8.7.3/8.7.3) with ESMTP id RAA91764 for ; Tue, 22 Oct 1996 17:08:37 -0500 Received: from localhost (chemtw@localhost) by black.missouri.edu (8.7.3/8.7.3) with SMTP id RAA40872 for ; Tue, 22 Oct 1996 17:08:47 -0500 X-Authentication-Warning: black.missouri.edu: chemtw owned process doing -bs Date: Tue, 22 Oct 1996 17:08:46 -0500 (CDT) From: Troy Wymore X-Sender: chemtw@black.missouri.edu To: chemistry@www.ccl.net Subject: Running CHARMM in Parallel on Power Challenge Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, I am having some problem getting CHARMM to run in parallel on a SGI Power Challenge L. Is there anyone who has compiled and ran a job on the SGI Power Challenge? If so maybe you could tell me what you did and I could see if our procedure was different. Of course we followed the directions in the install.doc but I am getting this error message when I run my job. libpvm [pid17348] : mksocs() connect: Connection refused libpvm [pid17348] : pvm_mytid() : Can't contact local daemon So it looks as though something is incompatible with PVM. Any help would be much appreciated. ********************************************************************* Troy Wymore e-mail: chemtw@showme.missouri.edu * Department of Chemistry http://www.showme.missouri.edu/ * University of Missouri-Columbia /~chemtw/troy.html * Columbia, MO 65211 * * * ********************************************************************* From echamot@xnet.com Tue Oct 22 19:16:32 1996 Received: from mail.xnet.com for echamot@xnet.com by www.ccl.net (8.8.0/950822.1) id SAA10393; Tue, 22 Oct 1996 18:39:59 -0400 (EDT) Received: from echamot.xnet.com by mail.xnet.com (8.7.5/XNet-2.1R) with SMTP id RAA21773; Tue, 22 Oct 1996 17:41:27 -0500 (CDT) Message-ID: Date: Tue, 22 Oct 96 17:36:48 EDT From: "Ernest Chamot" Subject: Re: CCL:X-ray structures for gemstone crystals e.g. YAG, YLF, etc. To: "Carl E. Bonner" , chemistry@www.ccl.net Cc: cbonner@vigyan.nsu.edu X-Mailer: VersaTerm Link v1.1.6 Hi Carl, You asked: > I am trying to perform calculations on the energy levels of an rare >earth dopant in a gemstone crystal such as YAG or YLF. . . Is there an >equivalent database for these inorganic structures. A web page has recently become available to point you to all sorts of sources of electronic structural information on the Internet. The URL is: http://www.unige.ch/crystal/w3vlc/data.index.html The Brookhaven and Cambridge Crystal Structure databases that you mentioned are included, but for you particular question, the data is probably in the Inorganic Crystal Structure Database, ICSD, if it is available anywhere. One of the leads to the ICSD from the web page is: http://www.fiz-karlsruhe.de/icsd_.html Happy hunting. EC --- Chamot Laboratories, Inc. 530 E. Hillside Rd. Naperville, Illinois 60540 Phone/Fax: (630) 637-1559 echamot@xnet.com http://www.xnet.com/~chamotlb From mac@elara.tripos.com Tue Oct 22 20:16:33 1996 Received: from gatekeeper.tripos.com for mac@elara.tripos.com by www.ccl.net (8.8.0/950822.1) id TAA10709; Tue, 22 Oct 1996 19:38:16 -0400 (EDT) Received: (from news@localhost) by gatekeeper.tripos.com (8.6.12/8.6.12) id SAA18320 for <@gatekeeper.tripos.com:chemistry@www.ccl.net>; Tue, 22 Oct 1996 18:39:00 -0500 Received: from elara.tripos.com(192.160.145.60) by gatekeeper.tripos.com via smap (V1.3) id sma018318; Tue Oct 22 18:38:55 1996 Received: from neptune by elara via ESMTP (951211.SGI.8.6.12.PATCH1042/951211.SGI.AUTO) for id SAA26446; Tue, 22 Oct 1996 18:38:14 -0500 From: mac@elara.tripos.com (Malcolm Cline) Received: by neptune (951211.SGI.8.6.12.PATCH1042) id XAA08245; Tue, 22 Oct 1996 23:38:12 GMT Date: Tue, 22 Oct 1996 23:38:12 GMT Message-Id: <199610222338.XAA08245@neptune> To: chemistry@www.ccl.net Subject: Chemistry on the WWW Intranet solutions for chemical discovery can play a critical role in your research. Check out the applets and servers available in the Discovery.Net club, available from Tripos, Inc. These servers and applets have been developed while creating our own web applications, so they are tools with proven usefulness-- the kind you will need in your drug discovery solutions. Find our more about the Discovery.Net Club by going to the Tripos home page at URL http://www.tripos.com/. mac Malcolm A. Cline WebMaster Tripos, Inc.