From chemistry-request@ccl.net Sun Jan 2 19:04:38 2005 Received: from student.gsu.edu (student.gsu.edu [131.96.2.25]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0304bTf001377 for ; Sun, 2 Jan 2005 19:04:38 -0500 Received: from pathri1 [131.96.145.92] by student.gsu.edu with NetMail ModWeb Module; Sun, 02 Jan 2005 19:21:27 -0500 Subject: 3D QSAR - Receptor independent alignment From: "Prashanth Athri" To: chemistry^at^ccl.net Date: Sun, 02 Jan 2005 19:21:27 -0500 X-Mailer: NetMail ModWeb Module X-Sender: pathri1 MIME-Version: 1.0 Message-ID: <1104711687.1ac758e0pathri1^at^student.gsu.edu> Content-Type: text/plain; charset="UTF-8" X-Spam-Status: No, hits=0.3 required=7.5 tests=FVGT_s_OBFU_Q1 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id j0304cTf001381 Hello all, I am using SYBYl and want to design a 3D QSAR CoMSIA model on a set of ~50 compounds. I do not have any X-ray Cryst, NMR constraints etc. since we do not know the receptor. Therefore, I do not have a template/ pharmacophore, just biological activities of structurally related(similar) molecules. Besides, using alignment-free options, 1. what are the 'typical' rules/ guidelines one follows when performing such an alignment 2. and what are the best options, in terms of tools/ modules that I can use? ( Maybe suggest your favourite to answer this ?) I would appreciate a response very much. Thanks in advance. Best wishes, Prashanth From chemistry-request@ccl.net Mon Jan 3 07:54:05 2005 Received: from smtp1.iitb.ac.in ([203.197.62.149]) by server.ccl.net (8.12.8/8.12.8) with SMTP id j03Cs1n5000449 for ; Mon, 3 Jan 2005 07:54:03 -0500 Received: (qmail 3942 invoked from network); 3 Jan 2005 14:40:50 +0530 Received: from unknown (HELO ldns2.iitb.ac.in) (10.209.12.2) by smtp1.iitb.ac.in with SMTP; 3 Jan 2005 14:40:50 +0530 Received: (qmail 553 invoked by uid 780); 3 Jan 2005 09:10:50 -0000 Received: from 10.103.1.1 by ldns2 (envelope-from , uid 502) with qmail-scanner-1.23 (spamassassin: 2.64. Clear:RC:1(10.103.1.1):. Processed in 0.017791 secs); 03 Jan 2005 09:10:50 -0000 Received: from unknown (HELO ether.chem.iitb.ac.in) (10.103.1.1) by ldns2.iitb.ac.in with SMTP; 3 Jan 2005 09:10:49 -0000 Date: Mon, 3 Jan 2005 14:28:23 +0530 (IST) From: "Geetha Navada K." To: chemistry)at(ccl.net Subject: modredundant and freezing dihedral angles Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=3.0 required=7.5 tests=NO_RDNS2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi, I am trying to use opt=modredundant to selectively optimise (hydrogen atoms only) in a molecule of 43 atoms. I have the coordinates (xyz) and I use the wildcard technique to freeze/activate the parameters. I am able to freeze the intended bond distances and angles, however, all the dihedral angles are taken as variables, inspite of my input '**** F'. I donot have access to the interactive interfaces such as Gaussview. Any help is greatly appreciated Thanks -geetha