From chemistry-request@server.ccl.net Mon Mar 18 13:59:37 2002 Received: from linman.isisph.com ([204.255.125.131]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2IIxbp06837 for ; Mon, 18 Mar 2002 13:59:37 -0500 Received: from domino2.isisph.com (mail.isisph.com [10.1.1.5]) by linman.isisph.com (8.9.1/8.9.1) with ESMTP id KAA21615 for ; Mon, 18 Mar 2002 10:59:30 -0800 Subject: Conformational analysis of nucleosides To: chemistry@ccl.net X-Mailer: Lotus Notes Release 5.0.8 June 18, 2001 Message-ID: From: PDande@isisph.com Date: Mon, 18 Mar 2002 10:58:01 -0800 X-MIMETrack: Serialize by Router on Domino2/ISIS(Release 5.0.9a |January 7, 2002) at 03/18/2002 10:57:12 AM MIME-Version: 1.0 Content-type: text/plain; charset=us-ascii Hi All! My question to you fellow CClers is as follows: I need to analyze (computationally) the conformations of various nucleosides, and ribonucleosides having modifications in the furanose and the heterocyclic base regions. Are you aware of any commercial and/ or shareware package that can achieve this. I will need to calculate atomic charges, assign proper atom properties and then perform molecular mechanics and dynamics simulations to assign determine the likely conformation of the molecules under study. A program that has the requisite force fields ( any suggestions for the proper force field to use would be appreciated), and should have reasonable cost and hardware requirements ( PC compatibility would be best). I look forward to the usual helpful responses and thank all respondents in advance. Sincerely, Prasad Dande ************************************************************************************************************************************************************** Prasad Dande, Ph. D. Senior Scientist Research Chemistry ISIS Pharmaceuticals 2292 Faraday Avenue Carlsbad, CA 92008 Tel: 760 603 4671 Fax: 760 603 4654 Prasad_Dande@isisph.com