From chemistry-request@ccl.net Mon Jun 27 11:55:41 2005 Received: from rly09e.srv.mailcontrol.com (cluster-e.mailcontrol.com [217.79.216.190]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5RFtb0D013352 for ; Mon, 27 Jun 2005 11:55:38 -0400 Received: from sandmail01.sd.accelrys.com (rrcs-67-52-158-62.west.biz.rr.com [67.52.158.62]) by rly09e.srv.mailcontrol.com (MailControl) with ESMTP id j5RFtZjx005805; Mon, 27 Jun 2005 16:55:36 +0100 In-Reply-To: <200506270702.j5R72ofm028270_at_server.ccl.net> To: chemistry_at_ccl.net Cc: sritin_at_ibab.ac.in Subject: Re: CCL:W:A liitle help with Insight MIME-Version: 1.0 X-Mailer: Lotus Notes Release 6.5.1 January 21, 2004 Message-ID: From: Jeff Nauss Date: Mon, 27 Jun 2005 08:55:20 -0700 X-MIMETrack: Serialize by Router on sandmail01/Server/Accelrys(Release 6.5.2|June 01, 2004) at 06/27/2005 08:55:22 AM, Serialize complete at 06/27/2005 08:55:22 AM Content-Type: text/plain; charset="US-ASCII" X-Scanned-By: MailControl A-05-01-01 (www.mailcontrol.com) X-Spam-Status: No, score=0.4 required=5.0 tests=DNS_FROM_RFC_ABUSE, FORGED_RCVD_HELO autolearn=no version=3.0.4 X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net "Computational Chemistry List" wrote on 06/27/2005 12:02:50 AM: > I have modelled a protein(receptor) using modeller. Now i want to do > some minimization on my receptor and ligand and later docking using > insight. But i have got stuck with fixing potentials and charges of > both my receptor and ligand. > I get various errors like "Partial charges not equal to formal > charges" , "open or undefined valencies", "cannot assign cvff > forcefeild". While running discover it complains of unfound > parameters in .out file and run is stopped. Ensure that you have add hydrogen atoms to your molecule. Modeler typically does not place all hydrogens in your structure. Thus as far as InsightII and Discover are concerned you do not have the correct chemistry. > My ligand is a nonapeptide and has a -S03H group attached to > tyrosine aswell as -NH2 attached to phenylalanine. I am using CVFF > forcefield. The ligand modified as you have will probably be problematic. I do not know if the CVFF force field has robust parameters for such modified amino acids. It might but you need to have the correct chemistry for the ligand. That includes hydrogens, correct bond orders, and explicit definition of formal charges. If you have the CFF force field, that might perform better with respect to atom typing. If not, you may need to develop your own parameters or search the literature. > If anyone has good tutorials on performing minimization, > interactive and automated docking using insight than please send me > the link or material. Look in the Pilot tutorials that come with InsightII. Look under Help | Pilot_Tutorials. Jeff -- Jeffrey L. Nauss, Ph.D. Lead Training Scientist Accelrys 10188 Telesis Court, Suite 100 San Diego, CA 92121-4779 Phone: +1-858-799-5555 Fax: +1-858-799-5100 http://www.accelrys.com/training *AccelrysWorld 2005, London, Nov 14-16. http://www.accelrysworld.com*