From chemistry-request@server.ccl.net Sun Jun 6 06:00:24 1999 Received: from oc30.uni-paderborn.de (oc30.uni-paderborn.de [131.234.240.90]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA23001 for ; Sun, 6 Jun 1999 06:00:23 -0400 Received: from localhost (cpilger@localhost) by oc30.uni-paderborn.de (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id LAA52228; Sun, 6 Jun 1999 11:58:10 +0200 (CEST) Date: Sun, 6 Jun 1999 11:58:10 +0200 From: Christian Pilger To: maoxiang cc: chemistry@ccl.net Subject: Re: CCL:question about autodock In-Reply-To: <37588DC9.167E@iris.sipp.ac.cn> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Sat, 5 Jun 1999, maoxiang wrote: > Hi, everyone: > I am an new man in the CCL. > Here is a question I wish you can help me. I am using AUTODOCK(ver > 2.4) to dock my ligand, but I find almost all of the result of the > position of ligand have bumps with the receptor. Does someone have met > the problem in the work, maybe there are some mistakes in my setup. Hope > to hear from you soon. > > > With best regards, > Mao Xiang > Dear Mao Xiang, we obtained similar results with AutoDock. I think one cause may be the grid-spacing you enter into AutoGrid (by default: 0.375 A). If you decreased the distance between the grid points I would expect you to get better energies and less bumbs. However to overcome this problem and at the same time the problem of receptor rigidity we used a different force field (i.e. TRIPOS) to achive some "fine-tuning" of the ligand-enzyme- alignments suggested by AutoDock. The applied force field distinguished more atom types than AutoDock does and additionally allowed us to keep those amino acid residues flexible, that were flanking our proposed binding site ("induced fit"). Regards, Christian ----------------------------------------------------------------- Dipl.-Chem. Christian Pilger Uni-GH Paderborn FB 13 - Organische Chemie Warburger Str. 100 D-33098 Paderborn/Germany Tel.: 05251-60279/-602183 Fax : 05251-603245 email: cpilger@oc30.uni-paderborn.de Word Wide Web: http://oc30.uni-paderborn.de/~cpilger -----------------------------------------------------------------