From chemistry-request@server.ccl.net Sat Oct 9 03:16:52 1999 Received: from atom.cem.uct.ac.za (atom.cem.uct.ac.za [137.158.165.198]) by server.ccl.net (8.8.7/8.8.7) with SMTP id DAA13242 for ; Sat, 9 Oct 1999 03:16:49 -0400 Received: from hydrogen.cem.uct.ac.za (hydrogen.cem.uct.ac.za [137.158.164.149]) by atom.cem.uct.ac.za (950413.SGI.8.6.12/950213.SGI.AUTOCF) via SMTP id CAA06474 for ; Sat, 9 Oct 1999 02:07:56 -0500 From: "Robert B. Best" Reply-To: rbest@atom.cem.uct.ac.za To: chemistry@ccl.net Subject: Water structuring in truncated octahedron Date: Thu, 16 Sep 1999 07:22:27 +0200 X-Mailer: KMail [version 1.0.24] Content-Type: text/plain MIME-Version: 1.0 Message-Id: <99091607301500.05308@hydrogen.cem.uct.ac.za> Content-Transfer-Encoding: 8bit Hi all Does anybody know whether the use of a truncated octahedron as opposed to a cube as a periodic box is known to have an effect on the rdf of water models. We have run two water boxes at 300K, one a truncated octahedron of 846 molecules and the other a cube of 512 molecules, both with density exactly 1.00. The octahedron gives a markedly more structured rdf than the cube for gOO(r). We are using the SPC/E model implemented in CHARMM. Has anyone got any ideas? Or possibly references to water-only simulations done in an octahedron, since there are already plenty for orthogonal boxes. Thanks Robert -- ________________________________________ Robert Best 89 Sandown Road Rondebosch 7700 Cape Town South Africa email: rbest@atom.cem.uct.ac.za ________________________________________ From chemistry-request@server.ccl.net Sat Oct 9 15:16:42 1999 Received: from omega.omrf.ouhsc.edu (omega.omrf.ouhsc.edu [157.142.200.207]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA16580 for ; Sat, 9 Oct 1999 15:16:41 -0400 Received: from omega.omrf.ouhsc.edu (pcxt13.omrf.ouhsc.edu [157.142.200.245]) by omega.omrf.ouhsc.edu (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id OAA74623 for ; Sat, 9 Oct 1999 14:12:18 -0500 (CDT) Message-ID: <37FF9358.6B0743F4@omega.omrf.ouhsc.edu> Date: Sat, 09 Oct 1999 14:11:20 -0500 From: Elizabeth Yuriev Organization: OMRF X-Mailer: Mozilla 4.51 [en] (Win98; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Summary: sulfonamide force field parameters Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers, A couple of weeks ago I posted the following question: *** I am interested in force field parameters for sulfonamides, especially aryl derivatives. I know that this question has been asked, answered and summarized by David Chalmers in ca. '95 (can't check for sure since I have not been able to use CCL search recently for some reason). Therefore, I am after the papers or reviews on the subject appeared since then. I am thinking about using MM2 but pointers to other force fields are of interest as well. *** The only response I got was from Takanori Kanazawa who suggested the following references: 1. "Ab initio calculations and molecular mechanics(MM3) force field development for sulfonamide and its alkyl derivatives" G.Liang et al. J.Mol.Stuct.(Theochem) 401(1997)165-179 2. "A Molecular Mechanics Valence Force Field for Sulaonamides Derived by ab Initio Methods" J.B.Nicholas et al. JPC 95(1991)9803-9811 3. "Ab Initio Calculations on N-Methylmethanesulfonamimde and Methyl Methanesulfonamide for the Development of Force Field Torsional Parameters and Their Use in the Conformational Analysis of Some Novel Estrogens" R.D.Bindal et al. JACS 112(1990)7861-7868 4. "An Ab Initio Study of Amino-Sulfur Compounds" M.Sabio et al. J.Mol.Struct.(Theochem) 206(1990)335-357 5. "An Ab Initio Comparative Study of the Electronic Properties of Sulfonamide and Amides" J.Elguero et al. J.Mol.Struct.(Theochem) 184(1989)115-129 If more answers come, I will summarize again. cheers, Elizabeth -- Elizabeth Yuriev, Ph.D. Postdoctoral Fellow Oklahoma Medical Research Foundation Protein Crystallography 825 NE 13th Street Oklahoma City, OK 73104 Ph: 405 271 1672 Fax: 405 271 3980 Email: yurieve@omega.omrf.ouhsc.edu