From chemistry-request@server.ccl.net Sun Jul 9 07:12:33 2000 Received: from md.huji.ac.il (md.huji.ac.il [132.64.169.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA26247 for ; Sun, 9 Jul 2000 07:12:31 -0400 Received: from localhost (talp@localhost) by md.huji.ac.il (8.9.3/8.9.3) with ESMTP id OAA137377 for ; Sun, 9 Jul 2000 14:12:03 +0300 (IDT) Date: Sun, 9 Jul 2000 14:12:03 +0300 From: Tal Peleg-Shulman To: CHEMISTRY@ccl.net Subject: surface potential calculations Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I would like to perform calculations of the surface potential of various proteins (pdb files available). I know that such things were previously carried out using Delphi. How can I do these calculations if Delphi is not available to me? Thank you for your assistance, Tal Peleg-Shulman. ******************************************************************************* Tal Peleg-Shulman talp@md2.huji.ac.il Dept. of Pharmaceutical Chemistry phone: 972-2-6757543 School of Pharmacy, P.O.B. 12065 fax: 972-2-6410740 The Hebrew University of Jerusalem Jerusalem 91120 ISRAEL. From chemistry-request@server.ccl.net Sun Jul 9 02:31:44 2000 Received: from mta1.263.net ([202.96.44.43]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id CAA24273 for ; Sun, 9 Jul 2000 02:31:43 -0400 Received: by mta1.263.net (Postfix, from userid 60001) id 2B16C1C999AC0; Sun, 9 Jul 2000 14:36:13 +0800 (CST) MIME-Version: 1.0 Message-Id: <39681D5D.04487@mta1> Date: Sun, 9 Jul 2000 14:36:13 +0800 (CST) From: "ีลตุ" To: chemistry@ccl.net Subject: help on PM3 in g98 optimization Dear cclers: when I use PM3 to do optimization using g98(use internal coordinate), there is often an incomplete coordinate error,how I avoid this. _____________________________________________ http://www.263.net http://fsurvey.cnnic.net.cn/survey/index.html From chemistry-request@server.ccl.net Sun Jul 9 12:23:55 2000 Received: from sunu450.rz.ruhr-uni-bochum.de (sunu450.rz.ruhr-uni-bochum.de [134.147.64.5]) by server.ccl.net (8.8.7/8.8.7) with SMTP id MAA27508 for ; Sun, 9 Jul 2000 12:23:54 -0400 From: Christoph.van.Wuellen@ruhr-uni-bochum.de Received: (qmail 11105 invoked from network); 9 Jul 2000 16:23:24 -0000 Received: from sgi249.rz.ruhr-uni-bochum.de (134.147.64.2) by mailhost.rz.ruhr-uni-bochum.de with SMTP; 9 Jul 2000 16:23:24 -0000 Received: (qmail 20826 invoked by uid 10283); 9 Jul 2000 16:23:10 -0000 Message-ID: <20000709162310.20825.qmail@sgi249.rz.ruhr-uni-bochum.de> Subject: Re: CCL:Are atoms spherical? To: amasunov@shiva.hunter.cuny.edu (AM) Date: Sun, 9 Jul 100 18:23:09 +0200 (MSZ) Cc: chemistry@ccl.net In-Reply-To: from "AM" at Jul 7, 0 04:03:16 pm X-Mailer: ELM [version 2.4 PL24] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Are atoms spherical? For an isolated atom, since the external potential is spherical, the "density" has to be spherical as well. For degenerate states, the "density" thus is the ensemble density. For an atom in an environment, there is no such argument. E.g. the density of a hydrogen atom will be deformed by the nearby presence of another hydrogen atom -- they form a bond. So, if atoms in VanDerWaals situations are nonspherical, this does not mean the "atom itself" is non-spherical. Nonspherical atoms as the result of a quantum-chemical calculations are a different topic, they mostly aris through symmetry breaking, that mostly is a defect of the chosen method. If, e.g. a fluorine atom is treated at the single-configuration level and if pz is chosen to be singly occupied, then the radial wave function of pz will be different from px and py --- no spherical density can be obtained even for an ensemble. This will change if one goes to a state-averaged calculation. Christoph van Wuellen