From chemistry-request -AatT- ccl.net Wed Apr 28 11:50:53 2004 Received: from mailserv.unb.ca (mailserv.unb.ca [131.202.3.23]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i3SGoqkh003987 for ; Wed, 28 Apr 2004 11:50:52 -0500 Received: from gollum.unb.ca (gollum.unb.ca [131.202.3.51]) by mailserv.unb.ca (8.12.10/8.12.10) with ESMTP id i3SGiQ3v029680; Wed, 28 Apr 2004 13:44:26 -0300 Received: from gollum.unb.ca (localhost.localdomain [127.0.0.1]) by gollum.unb.ca (8.12.8/8.12.8) with ESMTP id i3SGqDAD032124; Wed, 28 Apr 2004 13:52:13 -0300 Received: (from apache &$at$& localhost) by gollum.unb.ca (8.12.8/8.12.8/Submit) id i3SGqC1U032118; Wed, 28 Apr 2004 13:52:12 -0300 Received: from raven.chem.unb.ca (raven.chem.unb.ca [131.202.164.46]) by webmail.unb.ca (IMP) with HTTP for ; Wed, 28 Apr 2004 13:52:12 -0300 Message-ID: <1083171132.408fe13c1adc2[at]webmail.unb.ca> Date: Wed, 28 Apr 2004 13:52:12 -0300 From: "Flight, Robert Maxwell" Reply-to: robert.flight[at]unb.ca To: Raju Vishwanathan , Computational Chemistry List Subject: Re: CCL:Query regarding AutoDock software. References: In-Reply-To: MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.2.2 X-Originating-IP: 131.202.164.46 X-UNB-MailScanner-Information: Please contact the ISP for more information X-UNB-VirusScanner: Found to be clean X-UNB-SpamDetails: X-MailScanner-From: l72k6[at]unb.ca X-Spam-Status: No, hits=2.6 required=7.5 tests=FROM_HAS_MIXED_NUMS, FVGT_m_MULTI_ODD2,IMPRONONCABLE_1 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 Raju, The PDB file from the docking log (get-dockings) command will have the ligands in the same orientation with respect to the macromolecule. You must load the original file (PDB, MOL2, etc) of the macromolecule that you used to create the PDBQS in order to view the interactions of the ligands with the receptor. -Robert *************************** Robert Flight Master Candidate Computational Chemistry Department of Chemistry University of New Brunswick Fredericton NB, Canada E3B 6E2 e-mail: robert.flight[at]unb.ca *************************** "A computer terminal is not some clunky old television with a typewriter in front of it. It is an interface where the mind and body can connect with the universe and move bits of it about." -- Hitch Hikers Guide to the Galaxy Quoting Raju Vishwanathan : > Problem with AutoDock 3.0.5. Installed AutoDock in Red Hat Linux 8.0. > > AutoDock FAQ point no 3 says "I used "get-dockings" to extract the docked > conformations. Where is the macromolecule?" > http://www.scripps.edu/pub/olson-web/doc/autodock/faq.html#WHERE_MACRO > > > $ get-dockings xk2A.1hvr.dlg { Its working, generates output file > xk2A.1hvr.dlg.pdb } > $ pdbqtopdb 1hvr.pdbqs >> xk2A.1hvr.dlg.pdb { Not working, shows the > following error} > > awk: /home/raju/src/autodock/dist305/share/pdbtopdb2.awk:49: fatal: Invalid > range end: /[0-9][+- ]/ > /home/raju/src/autodock/dist305/share/fixatomnames: line 8: 1839 Broken > pipe > sed -f $AUTODOCK_UTI/fixatomnames.sed $* > /home/raju/src/autodock/dist305/share/getpdbrecords: line 2: 1840 Broken > pipe > egrep "^ATOM|^HETATM|^REMARK|^USER|^END |^TER|^MODEL |^ENDMDL" $* > > I donot know how to solve this problem. Please let me know how to overcome > this problem. > > Thanking you, > Raju Vishwanathan > Sr. Consultant - Life Science Division > SysArris Software, Bangalore, India > > > > > > > > -= 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 mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jlabanow[at]nd.edu (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > >