From chemistry-request:~at~:ccl.net Fri Jun 17 13:52:43 2005 Received: from mail.ic.sunysb.edu (mail.ic.sunysb.edu [129.49.1.4]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5HHqcfI019593 for ; Fri, 17 Jun 2005 13:52:38 -0400 Received: from postal.ic.sunysb.edu (mail [129.49.1.4]) by mail.ic.sunysb.edu (8.13.1/8.13.1) with SMTP id j5HH8N50029494 for ; Fri, 17 Jun 2005 13:08:26 -0400 (EDT) Received: from smtp.ic.sunysb.edu ([129.49.1.24]) by postal.ic.sunysb.edu (SMSSMTP 4.1.5.31) with SMTP id M2005061713082602919 for ; Fri, 17 Jun 2005 13:08:26 -0400 Received: from sparky.ic.sunysb.edu (daemon.-at-.sparky.ic.sunysb.edu [129.49.1.3]) by smtp.ic.sunysb.edu (8.13.1/8.13.1) with ESMTP id j5HH8QEf029511 for ; Fri, 17 Jun 2005 13:08:26 -0400 (EDT) Received: from localhost (yonyang {*at*} localhost) by sparky.ic.sunysb.edu (8.12.10/8.12.9) with ESMTP id j5HH8L4X009231 for ; Fri, 17 Jun 2005 13:08:25 -0400 (EDT) Date: Fri, 17 Jun 2005 13:08:21 -0400 (EDT) From: Yong Liang Yang To: chemistry.-at-.ccl.net Subject: Re: CCL:autodock3 dies upon launch with multiple errors In-Reply-To: <20050617151356.79959.qmail.-at-.web41210.mail.yahoo.com> Message-ID: References: <20050617151356.79959.qmail.-at-.web41210.mail.yahoo.com> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Dear Robyn: In a command window in IRIX, try, # mkdpf3 .pdbq .pdbqs this will produce a ..dpf file, then try # autodock3 -p ..dpf -l ..dlg& This might work if ADT could not launch the job. Cheers Yong On Fri, 17 Jun 2005, Robyn Ayscue wrote: > All, > > Sorry for the cross-post. > > I'm running AutoDockTools using autodock/autogrid > version 3.05 on an SGI machine with IRIX 6.5.24. I'm > trying to dock an effector molecule in the active site > of an enzyme (p450 2c9) with a substrate molecule also > present. Autogrid finishes out with no problems, but > autogrid dies immediately upon launch with the > following errors: > > > Can't find ".dpf" in the dock-parameter filename. > > AutoDock needs the extension of the grid parameter > file to be ".gpf" > and that of the docking parameter file to be ".dpf". > > /disk02/usr/local/autodock/dist305/bin/sgi4D.IRIX64_6.5_R10000/autodock3: > Wrong number of x grid-points in grid-map file > "2c9q_HEMq_FLPq.A.map". > /disk02/usr/local/autodock/dist305/bin/sgi4D.IRIX64_6.5_R10000/autodock3: > Use either 32 or 1129013060 throughout! > /disk02/usr/local/autodock/dist305/bin/sgi4D.IRIX64_6.5_R10000/autodock3: > ERROR: Using wrong grid-map file. > > /disk02/usr/local/autodock/dist305/bin/sgi4D.IRIX64_6.5_R10000/autodock3: > Aborting... > > /disk02/usr/local/autodock/dist305/bin/sgi4D.IRIX64_6.5_R10000/autodock3: > Unsuccessful Completion. > > > First it complains about not being able to find a > docking parameter file with .dpf as the suffix, but > the file DOES have a .dpf suffix and it is listed as > having one in the command that is typed in the command > line used to launch autodock. The .dpf file looks fine > as far as I can tell, compared to other .dpf files > I've used for other docking runs that have completed > successfully. > > The next thing it complains about is the differing > number of grid points. It keeps referring to the > number "1129013060" but I can't find that number in > any of the grid-map files. The number of x- grid > points in all grid-map files is the same. > > Autodock comes to the conclusion that I'm using the > wrong grid-map files, but the files I'm using ARE the > correct files (I checked and double-checked). > > If anyone has had experience with this kind of error > message and knows how to resolve it, I'd appreciate > any input. Thanks much! > > Robyn Ayscue > rayscue.-at-.hsc.wvu.edu > kajsicat.-at-.yahoo.com > > > > > > > ____________________________________________________ > Yahoo! Sports > Rekindle the Rivalries. Sign up for Fantasy Football > http://football.fantasysports.yahoo.com > > > -= This is automatically added to each message by the 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 is mail bouncing from ccl.net domain due to spam filters, please > use the Web based form from CCL Home Page > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > >