From Jeffrey.Gosper@brunel.ac.uk Wed Jul 2 03:49:18 1997 Received: from eros.brunel.ac.uk for Jeffrey.Gosper@brunel.ac.uk by www.ccl.net (8.8.3/950822.1) id DAA05847; Wed, 2 Jul 1997 03:13:15 -0400 (EDT) Received: from castjjg.brunel.ac.uk (actually chem-pc-03.brunel.ac.uk) by eros.brunel.ac.uk with SMTP-BRUNEL (PP); Wed, 2 Jul 1997 08:13:08 +0100 Date: Wed, 2 Jul 1997 08:09:48 PDT From: Jeffrey Gosper Subject: Re: CCL:XYZ --> POV To: "s.hogg" cc: chemistry@www.ccl.net Message-ID: Priority: Normal MIME-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII On Tue, 1 Jul 1997 19:00:52 +0100 (BST) s.hogg wrote: > From: s.hogg > Date: Tue, 1 Jul 1997 19:00:52 +0100 (BST) > Subject: CCL:XYZ --> POV > To: chemistry@www.ccl.net > > Is there a way to produce POVRAY .pov files from an XYZ input file? I > actually have a concatenated series of xyz data points from an MD simulation > and would like them, so that when read, they would make a 'movie'. > > I would like to put them into POVRAY in sequence, and render them as a > movie, but what is the best way of doing that? > > I don't really want to have to de-concatenate them, use babel, then PDB2POV > and then render them. I *think* I have seen someone do this, but can't > remember who it was, but if anyone can give me a kick in the right > direction, I would be very grateful. > > (p.s. Is XMol available for Linux?) > Re_View will do exactly this and the original version is still free for individual user! Re_View automates the POV interface and will automatically create AAWin animations. Its also extremely easy to generate Mpegs. If you want to depict multiple/partial bonds as well and automatic Mpgeg production then Re_View2 is what you need. /\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\ Dr. Jeff Gosper, Dept. of Chemistry, BRUNEL University Uxbridge Middx UB8 3PH, UK voice: 01895 274000 x2187, facsim: 01895 256844 internet/email/work: Jeffrey.Gosper@brunel.ac.uk internet/WWW: http://www.brunel.ac.uk/~castjjg Re_View's home page (molecular animations or Chem-4D): http://www.brunel.ac.uk/depts/chem/ch241s/re_view/re_view.htm \/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/ From jim.henshaw@aeat.co.uk Wed Jul 2 07:49:26 1997 Received: from aeat.co.uk for jim.henshaw@aeat.co.uk by www.ccl.net (8.8.3/950822.1) id HAA06439; Wed, 2 Jul 1997 07:34:29 -0400 (EDT) Received: from ccgate.aeat.co.uk by aeat.co.uk with SMTP (8.8.5/AEAT-GW-1.6) id MAA18626; Wed, 2 Jul 1997 12:34:23 +0100 (BST) sender jim.henshaw for Received: from ccMail by ccgate.aeat.co.uk (IMA Internet Exchange 2.02 Enterprise) id 3BA3CA90; Wed, 2 Jul 97 12:34:01 +0100 Mime-Version: 1.0 Date: Wed, 2 Jul 1997 12:28:17 +0100 Message-ID: <3BA3CA90.1268@ccgate.aeat.co.uk> From: jim.henshaw@aeat.co.uk (Jim Henshaw) Subject: MOPAC93 - Questions To: chemistry@www.ccl.net Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Description: cc:Mail note part Dear All, I posted a question recently about some problems I was having using MOPAC6 and 7. The main answer that came back was, "buy the commercial version of the code". I am therefor taking this advice. I am thinking of buying CHEM3D Draw, which includes MOPAC93 and runs under Windows NT. I have a couple of questions which current users might be able to answer: 1. How many large atoms can this version deal with ? 2. Has anyone used this package to do thermodynamic calc's on large molecules > 50 large atoms ? Regards Jim Henshaw e-mail jim.henshaw@aeat.co.uk From msj@fskru5.hre.hydro.com Wed Jul 2 08:49:20 1997 Received: from fskru5.hre.hydro.com for msj@fskru5.hre.hydro.com by www.ccl.net (8.8.3/950822.1) id IAA06545; Wed, 2 Jul 1997 08:00:19 -0400 (EDT) Received: by fskru5.hre.hydro.com (950413.SGI.8.6.12/930416.SGI.AUTO) for chemistry@www.ccl.net id OAA02611; Wed, 2 Jul 1997 14:00:22 +0200 From: "Merethe Sjovoll" Message-Id: <9707021400.ZM2609@fskru5.hre.hydro.com> Date: Wed, 2 Jul 1997 14:00:22 -0600 Reply-To: Merethe.Sjovoll@hre.hydro.com X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: chemistry@www.ccl.net Subject: Forcefields for organic/inorganic interfaces Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hello everyone, I would appreciate very much any reference to publications on molecular mechanics simulations of organic/inorganic interfaces, particularly in the field of scale and corrosion inhibition. I know of the article by Catlow et al. on barium sulfate. Does anybody know of any other references? Best wishes Merethe Sjovoll -- ******************************************************** Merethe Sjovoll, Ph.D. * * Research Scientist * * Norsk Hydro a.s Research Center * * * * P.O.Box 2560 * HYDRO * N-3901 Porsgrunn, * RESEARCH * Norway * * * ((( * email: Merethe.Sjovoll@hre.hydro.com * (=====) * Phone:+47 35 56 48 97 * * Fax :+47 35 56 36 86 * * ******************************************************** From vkitzing@sunny.mpimf-heidelberg.mpg.de Wed Jul 2 09:49:20 1997 Received: from otto.mpimf-heidelberg.mpg.de for vkitzing@sunny.mpimf-heidelberg.mpg.de by www.ccl.net (8.8.3/950822.1) id JAA06969; Wed, 2 Jul 1997 09:25:56 -0400 (EDT) Received: from sunny.mpimf-Heidelberg.mpg.de by otto.mpimf-heidelberg.mpg.de (4.1/SMI-4.1) id AA25781; Wed, 2 Jul 97 15:25:38 +0200 Received: from [149.217.50.47] (mac20) by sunny.mpimf-Heidelberg.mpg.de (4.1/SMI-4.1) id AA06278; Wed, 2 Jul 97 15:21:28 +0200 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Wed, 2 Jul 1997 15:21:13 +0200 To: , chemistry@www.ccl.net From: vkitzing@sunny.mpimf-heidelberg.mpg.de (Eberhard von Kitzing) Subject: Re: CCL:MD in various solvents. The unfortunate summary At 11:34 Uhr 30.06.1997, wrote: >> I would like to receive informations on comparisons of MD simulations >> in vacuo with simulations done by using explicit solvents. >> In particular, how compare in vacuo simulations with those performed >> in CHCl3 ? >> >> Any reference is appreciated. > > >Well, I received several requests for a summary, it means that some >peoples around the world are interested to the subject, but... > > !!! NO INFORMATIONS AT ALL !!! > >Like nobody has never done such comparisons. Unbelivable. Because CHCl3 as a solvent was particularly stressed, water examples may have been considered to be of lesser value to you. For water you can also look at: Andrea Amadei, Antonius B.M. Linssen and Herman J.C. Berendsen (1993). "Essential dynamics of proteins." Proteins-Structure Function and Genetics 17(4) 412-425. ====================================================================== Eberhard von Kitzing Max-Planck-Institut fuer Medizinische Forschung Jahnstr. 29 D 69115 Heidelberg Germanny email: vkitzing@sunny.mpimf-heidelberg.mpg.de WWW: http://sunny.mpimf-heidelberg.mpg.de/people/vkitzing/Eberhard.html From tvd@msi.com Wed Jul 2 13:49:28 1997 Received: from bioc1.msi.com for tvd@msi.com by www.ccl.net (8.8.3/950822.1) id NAA08987; Wed, 2 Jul 1997 13:09:33 -0400 (EDT) Received: by bioc1.msi.com (5.64/0.0) id AA25900; Wed, 2 Jul 97 10:09:01 -0700 Received: from iris69.msi.com(146.202.3.69) by bioc1.msi.com via smap (V2.0) id xma025887; Wed, 2 Jul 97 10:08:51 -0700 Received: by iris69.msi.com (950413.SGI.8.6.12/930416.SGI) for CHEMISTRY@www.ccl.net id KAA22076; Wed, 2 Jul 1997 10:08:50 -0700 Date: Wed, 2 Jul 1997 10:08:50 -0700 From: tvd@msi.com (Ton van Daelen) Message-Id: <199707021708.KAA22076@iris69.msi.com> To: CHEMISTRY@www.ccl.net Subject: Re: 3D visualisation software Dear Luca - MSI's software developer's kit does exactly what you want. It includes an API set to visualize iso-surfaces, molecular structure, trajectories, normal modes, plots/graphs, etc. It also allows you in a few steps to put an interface together to any computational chemistry code. For general information about this toolkit visit: http://www.msi.com/support/sdk/ for specific information on plotting iso-surfaces visit: http://www.msi.com/support/sdk/users/examples/iso/README.html Regards - Ton ------ Ton van Daelen tvd@msi.com Molecular Simulations, Inc. San Diego > Dear CCLers, although I'm pretty sure this question has been already > posed (and I beg your pardon for posing it again), I have to ask about a > 3D visualisation tool. I worked with SciAn, which is pretty good indeed, > but the only existing version needs Z buffer and DGL. Looking on the net > I found a software called vis5d, pretty good the same but tuned for > metereological data and I found too time-expensive to adapt it to > visualize orbitals, electronic density and so on. I'm using molden but I > would like to find out soemthing more general (I'm trying to use ELF > also, and this feature is not implemented in molden). > The software I'm looking for should manage x,y,z,function_value in order > to give isosurfaces of the function I'm trying to plot. Something not > strictly platform-dependant would be very fine. > Thank you for all the information you will provide. > Luca > > Dr. Luca Pedocchi > Laboratorio di Chimica Fisica delle Interfasi > via Cavour, 82 - 50129 Firenze - ITALY