From chemistry-request@ccl.net Tue Jun 24 13:17:05 2003 Received: from mailserver.unimi.it (mailserver.unimi.it [159.149.10.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5OHH45u000656 for ; Tue, 24 Jun 2003 13:17:05 -0400 Received: from smtp.unimi.it (smtp.unimi.it [159.149.10.3]) by mailserver.unimi.it (iPlanet Messaging Server 5.2 Patch 1 (built Aug 19 2002)) with ESMTP id <0HGZ00AK9XCI33^at^mailserver.unimi.it> for chemistry^at^ccl.net; Tue, 24 Jun 2003 19:17:06 +0200 (MEST) Received: from heisenberg.chimica.unimi.it (heisenberg.chimica.unimi.it [159.149.240.30]) by smtp.unimi.it (iPlanet Messaging Server 5.1 (built May 7 2001)) with ESMTP id <0HGZ00LSSXCF9C^at^smtp.unimi.it> for chemistry^at^ccl.net; Tue, 24 Jun 2003 19:17:03 +0200 (MEST) Date: Tue, 24 Jun 2003 19:22:39 +0200 From: Alessandro Contini Subject: Re: CCL:local search in AutoDock In-reply-to: <3EF8BB49@webmail1> To: Robert Flight Cc: CCL Message-id: <200306241922.39557.alessandro.contini^at^unimi.it> Organization: Istituto di Chimica Organica "Alessandro Marchesini" MIME-version: 1.0 Content-type: text/plain; charset=iso-8859-1 Content-disposition: inline User-Agent: KMail/1.5.1 References: <3EF8BB49@webmail1> Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h5OHH55u000661 Hi Robert, wat you are experiencing is probaly a bug in ADT. I don't know wich version you are using, but try to download the last one. I had the same problem a few month ago and I solved it by choosing a random start, because it seemed that ADT didn't recognize properly the ligand starting coordinates relative to the receptor file; the docking run was correct but there was some sort of offset between the ligand conformations and the receptor. By choosing a random start, If everything works fine, you should be able to properly reproduce your docking and to correctly visualize results. Hope this help Alessandro Contini Alle 15:07, martedl 24 giugno 2003, Robert Flight ha scritto: > Hi, > > I'm trying to use a local search (pseudo-sw) to minimize a docked pose of a > ligand into a receptor. When I look at the ligand and the receptor in ADT, > the ligand is in the correct starting position. The Grid box is large > enough to contain the search space. I'm using a non-random start, > non-random relative dihedral offset, and initial relative dihedrals, which > should all start the local search from the specified initial coordinates. > > The output ligand poses end up completely outside the docking box, and > outside the receptor as well, with an RMSD of 85 Angstroms!!! Can anyone > tell me what is happening, as I see no reason why the ligand should end up > outside the docking box! > > Thank you for your help, > > -Robert > > ******************************** > Robert Flight > Masters Student > Department of Chemistry > University of New Brunswick > Fredericton, NB Canada E3B 6E2 > e-mail: robert.flight^at^unb.ca > > ******************************** > > "People think it must be fun to be a super genius, but they don't realize > how hard it is to put up with all the idiots in the world." -Calvin from > Calvin & Hobbes > > > -= This is automatically added to each message by mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: > line and send your message to: CHEMISTRY^at^ccl.net > > Send your subscription/unsubscription requests to: > CHEMISTRY-REQUEST^at^ccl.net HOME Page: http://www.ccl.net | Jobs Page: > http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jkl^at^ccl.net (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ -- Alessandro Contini, Ph.D. Istituto di Chimica Organica "Alessandro Marchesini" Facolt` di Farmacia Universit` degli Studi di Milano Via Venezian, 21 20133 Milano Tel. +390250314480 Fax +390250314476 http://users.unimi.it/istchimorg/pagconthtm.htm ------------------------------------------------------------------- ------------------------------------------------------------------- This e-mail and any attachments is confidential and may contain attorney privileged information intended for the addressee(s) only. Reading, copying, disclosure or use by anybody else is unauthorised. If you are not the intended recipient, please delete this message and any attachments and advise the sender by return e-mail. ------------------------------------------------------------------- Il contenuto di questo messaggio elettronico e' riservato e tutelato dal segreto professionale ed e' rivolto eslusivamente al/ai destinatario/i identificato/i. Pertanto e' proibito leggerlo, copiarlo, divulgarlo o utilizzarlo da parte di chiunque salvo il/i destinatario/i. Se non siete il destinatario, vi invitiamo a cancellare il messaggio ed eventuali allegati dandocene immediatamente comunicazione scritta a mezzo posta elettronica.