From chemistry-request@server.ccl.net Mon May 13 16:29:39 2002 Received: from gull.prod.itd.earthlink.net ([207.217.120.84]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4DKTZJ08110 for ; Mon, 13 May 2002 16:29:38 -0400 Received: from user-2ivftha.dialup.mindspring.com ([165.247.246.42] helo=uci.edu) by gull.prod.itd.earthlink.net with esmtp (Exim 3.33 #2) id 177MRq-00045G-00 for chemistry@ccl.net; Mon, 13 May 2002 13:29:34 -0700 Sender: heffron@ccl.net Message-ID: <3CE0214E.DC99FA72@uci.edu> Date: Mon, 13 May 2002 13:25:50 -0700 From: Susan Heffron Organization: University of California, Irvine X-Mailer: Mozilla 4.76C-SGI [en] (X11; I; IRIX64 6.5 IP30) X-Accept-Language: en MIME-Version: 1.0 To: Computational Chemistry List Subject: rotatable bonds question, using autodock Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi. Forgive my basic chemistry questions... I am planning to dock various small molecules to a protein using Autodock. Some of my small molecules have structures such that I am not sure how to assign certain bonds... rotatable or not (e.g., partial double-bond character or not). Specifically, my questions are: 1. In a structure with -N-C-N- would there be partial double-bond " O character to both C-N bonds, or only one (like a peptide bond)? 2. In a structure with -N-C-N- would there be a partial double-bond " S character to the N-C and C=S bonds, or not? Thanks in advance for your help. Susan -- ------------------------------------------------------------------ Susan Heffron Dept. of Physiology and Biophysics University of California, Irvine Irvine, CA 92697-4560 U.S.A. phone: (949) 824-4625 FAX: (949) 824-8540 ------------------------------------------------------------------