From mdoyle@msi.com Thu May 21 20:21:44 1998 Received: from bioc1.msi.com (bioc1.msi.com [146.202.0.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id UAA07650 Thu, 21 May 1998 20:21:43 -0400 (EDT) Received: by bioc1.msi.com (931110.SGI/930416.SGI) for chemistry@www.ccl.net id AA28501; Thu, 21 May 98 17:18:52 -0700 Received: from mdoyle-pc.msi.com(146.202.24.32) by bioc1.msi.com via smap (V2.0) id xmag28472; Thu, 21 May 98 17:18:25 -0700 Message-Id: <3.0.32.19980521170618.006d78b8@146.202.6.217> X-Sender: mdoyle@146.202.6.217 X-Mailer: Windows Eudora Pro Version 3.0 (32) Date: Thu, 21 May 1998 17:18:51 -0700 From: Michael Doyle Subject: Re: CCL:Question about CERIUS 2 To: "'CCL'" Mime-Version: 1.0 Content-Type: text/enriched; charset="us-ascii" Dear CCLers, Derick and David, The free volume calculations is part of the specialist polymer analysis tools and does not form a direct part of the C2 QSAR and C2-Descriptor+ sets. It is however a set of information that using the C2SDk can be passed into the QSAR tables. MICHAEL -----------------------------------------------------------------------------------------\-- Free volume analysis using Voronoi tessellation The model is subdivided into space filling complex polyhedra surrounding each atom. Each polyhedron can be thought of as encompassing the volume "belonging" to that atom. The tesselation process can be more easily visualized in 2D. A line is drawn between each pair of atoms and a plane is placed normal to the line at its center (shown as a solid line). As the planes intersect they produce a polyhedra. The tesselation results give much more information than the simple measures of total, occupiable and unoccupiable free volume. The distribution of hole sizes and the shapes of the holes (the surface area/volume ratio = (S/4)/(3V/4) where S and V refer to the polyhedron surface area and volume, it has a minimum value of 1.0 for a sphere) are likely to correlate with properties involving molecular packing. By selecting the atoms used for the tesselation the free volume associated with different parts of the system can be studied. For example: free volume around chain ends verses chain center to look at molecular weight effects (ref), free volume around additives such as plasticizers, etc. References: Ferry, J. D. "Viscoelastic Properties of Polymers" John Wiley & sons, New York (1980) D. Rigby and R. J. Roe, "Molecular Dynamics Simulation of Polymer Liquid and Glass 4. Free Volume Distribution" Gusev, A. A.; Suter, U. W. "Dynamics of small molecules in dense polymers subject to thermal motion" J. Chem. Phys., 99, 2228 (1993). Gusev, A. A.; Arizzi, S.; Suter, U. W.; Moll, D. J. "Dynamics of light gases in rigid matrices of dense polymers" J. Chem. Phys., 99, 2221 (1993). Gusev, A. A.; Muller-Plathe, F.; van Gunsteren, W. F.; Suter, U. W. "Dynamics of small molecules in bulk polymers" in Atomistic Modeling of Physical Properties, Adv. Polym. Sci., 116, 207 (1994).
ffff,0000,0000 -=-=-=-=-=-=-=-=-=-=-=- 0000,0000,ffff-=-=-=-=-=-=-=-=-=-=-=- Michael Doyle @ MSI Materials Informatics and QSAR Product Manager WRK 619-546-5358 FAX 619-458-0136 HME 760-471-2910 (VOX&FAX) CAR 760-809-1225 WEB www.msi.com ffff,0000,0000-=-=-=-=-=-=-=-=-=-=-=- 0000,0000,ffff-=-=-=-=-=-=-=-=-=-=-=- ffff,0000,0000 ffff,0000,0000 Technology that was available to expert modelers for thousands of dollars a few years ago is now available to all research scientists for under five hundred dollars! Go get a copy for yourself before you are left behind! Check out 0000,0000,fefehttp://www.msi.com/weblab/viewer/info/index.shtml ffff,0000,0000The opinions expressed here are solely those of Michael J. Doyle and do not reflect those of MSI Inc.
From anina01@iona.cryst.bbk.ac.uk Sun May 24 10:18:19 1998 Received: from pandora.cryst.bbk.ac.uk (pandora.cryst.bbk.ac.uk [192.84.212.49]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA07439 Sun, 24 May 1998 10:18:18 -0400 (EDT) Received: from localhost (anina01@localhost) by pandora.cryst.bbk.ac.uk (8.8.7/8.8.7) with SMTP id PAA08855 for ; Sun, 24 May 1998 15:22:49 +0100 X-Authentication-Warning: pandora.cryst.bbk.ac.uk: anina01 owned process doing -bs Date: Sun, 24 May 1998 15:22:47 +0100 (BST) From: Henrick Alex Ninaber X-Sender: anina01@pandora.cryst.bbk.ac.uk To: chemistry@www.ccl.net Subject: Correlating data with two or more (Gaussian) distributions: possible? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL, The distribution of certain variables I calculate sometimes show more than one mean: in my case this means that the distribution is a sum of two or more separate distributions. Calculating the correlation with (for instance) a single Gaussian distribution does not make much sense. Is anyone familiar with this branch of statistics? I am looking for a theory dealing with this problem. I will summarize any responses to the list, Alex Ninaber From szilagyi@indy.mars.vein.hu Sun May 24 09:46:07 1998 Received: from indy.mars.vein.hu (indy.mars.vein.hu [193.6.36.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id JAA07380 Sun, 24 May 1998 09:46:05 -0400 (EDT) Received: from szilagyi.mars.vein.hu by indy.mars.vein.hu via SMTP (940816.SGI.8.6.9/940406.SGI.AUTO) id PAA25785; Sun, 24 May 1998 15:47:41 -0700 Message-ID: <35682425.6C00@mm2.vein.hu> Date: Sun, 24 May 1998 15:44:06 +0200 From: "Robert K. Szilagyi" Reply-To: szilagyi@indy.mars.vein.hu Organization: University of Veszprem X-Mailer: Mozilla 3.01Gold (Win95; I) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: G94 compilation Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Members, I am looking for contact with fellows, who are/were involved in installation process of the software G94 on a SUN Enterprise Ultra 2 workstation having Solaris 2.6 op.sys. Please do not reply to the CCL, but directly to me! Thanks in advance, -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Robert K. Szilagyi Mueller Laboratory ph.d. student Dept. Organic Chemistry University of Veszprem szilagyi@mm2.vein.hu Veszprem, H-8201 POB. 158; Egyetem u. 10. Phone: +36 88 422022 extn. 395 HUNGARY Mobile: +36 20 745915 Fax: +36 88 427492 http://mm1.vein.hu/ ====================================================================== ********** All opinions are my own, NOT my employer's ! ********** ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From giulio@indigo.farma.unimi.it Mon May 25 06:10:08 1998 Received: from indigo.farma.unimi.it (indigo.farma.unimi.it [159.149.11.213]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id GAA10992 Mon, 25 May 1998 06:10:06 -0400 (EDT) Received: (from giulio@localhost) by indigo.farma.unimi.it (950413.SGI.8.6.12/950213.SGI.AUTOCF) id LAA19249 for CHEMISTRY@www.ccl.net; Mon, 25 May 1998 11:58:13 -1500 From: "Giulio Vistoli" Message-Id: <9805251158.ZM19247@indigo.farma.unimi.it> Date: Mon, 25 May 1998 11:58:13 +0000 X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: CHEMISTRY@www.ccl.net Subject: Zn with CHARMM Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear CCLers, we have some problems with the simulation of a zn-protein with Quanta/CHARMM package. We think that the problems arise by bad Zn parametrization. Can anybody give us informations about possible solutions at this problem?? Best regards Dott. Giulio Vistoli From jaouad@csc.fi Mon May 25 09:24:25 1998 Received: from pobox.csc.fi (pobox.csc.fi [128.214.46.62]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id JAA11795 Mon, 25 May 1998 09:24:24 -0400 (EDT) Received: from cypress.csc.fi (cypress-e.csc.fi [128.214.46.7]) by pobox.csc.fi (8.9.0.Beta5/8.9.0.Beta5/CSC/Rtrs-1.22) with SMTP id QAA08552 for ; Mon, 25 May 1998 16:24:24 +0300 (EET DST) Date: Mon, 25 May 1998 16:24:24 +0300 (EET DST) From: Jaouad El-Bahraoui To: chemistry@www.ccl.net Subject: G94 problem..... In-Reply-To: <31452944DD@wchuwr.chem.uni.wroc.pl> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Does any one know how to solve this kind of problem in g94, I use the version E.2 Density matrix breaks symmetry, PCut= 1.00D-04 Density matrix has no symmetry -- integrals replicated. Density matrix breaks symmetry, PCut= 1.00D-04 Density matrix has no symmetry -- integrals replicated. thanks Jaouad \^ ^/ )@ @( +-----------------------oOO--(_)----------------------------------+ | Jaouad El-Bahraoui , Ph.D | +-----------------------------------------------------------------+ | Inorganic Chemistry Laboratory | Tel: +358-9-19140199 | | department of Chemistry, P.O. BOX 55 | Fax: +358-9-19140198 | | University of Helsinki,FIN-00040 | jaouad@ccsc.fi | | Helsinki, Finland |http://w3.ugr.es/~jaouad/| +----------------------Oooo--oOO----------------------------------+ oooO ( ) ( ) ) / \ ( (_/ \_) -------------------------------------------------------------------- I know you believe you understand what you think I said, but I am not sure you realize that what you heard is not what I meant. --------------------------------------------------------------------