From chemistry-request@ccl.net Sat Sep 13 21:27:28 2003 Received: from postoffice9.mail.cornell.edu (postoffice9.mail.cornell.edu [132.236.56.39]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8E1QvBS006194 for ; Sat, 13 Sep 2003 21:26:57 -0400 Received: from cornell.edu ([128.84.183.113]) by postoffice9.mail.cornell.edu (8.12.9/8.12.6) with ESMTP id h8E1Qo8x029870; Sat, 13 Sep 2003 21:26:54 -0400 (EDT) Date: Sat, 13 Sep 2003 21:26:50 -0400 Subject: Re: CCL:Autodock and Rigid Body Docking Content-Type: text/plain; delsp=yes; charset=US-ASCII; format=flowed Mime-Version: 1.0 (Apple Message framework v552) Cc: CHEMISTRY To: Chris Arthur From: Richard Gillilan In-Reply-To: <006d01c37a12$04f486c0$3b2ade89.-at-.chm.bris.ac.uk> Message-Id: <839C1E2C-E652-11D7-975E-000393D59F68.-at-.cornell.edu> Content-Transfer-Encoding: 7bit X-Mailer: Apple Mail (2.552) X-Spam-Status: No, hits=-2.0 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,QUOTED_EMAIL_TEXT, REPLY_WITH_QUOTES,USER_AGENT_APPLEMAIL version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) I think this question has come up before on the list. You might want to search the archives to see what was said before. In case you are not aware, there are free programs available specifically for rigid protein-protein docking. I've found ZDOCK to be very easy to use: http://zlab.bu.edu/~rong/dock/index.shtml. A special issue of Proteins, Structure Function and Genetics is devoted to the CAPRI blind docking test has lots of good stuff (Volume 52 Issue 1 - 1 July 2003 (1 - 122)) Another issue summarizing the latest meeting may be out before long. RDOCK (goes with ZDOCK) does some conformational refinement, but that's still the subject of considerable current research. I believe there is also an NMR structure refinement program that holds backbone fixed while allowing sidechain movement. Don't have the reference handy at the moment. Let me know if you want it and I'll dig it up. Richard Gillilan MacCHESS, Cornell On Saturday, September 13, 2003, at 12:13 PM, Chris Arthur wrote: > Hi > > I would like to try to dock a small protein (88aa) to a larger one > (300ish > aa) - now I know autodock is really designed for small molecules but i > was > wondering if there was any way to get it to essentially run a rigid > body > dock of these two together? and if so, how i would go about it? or if > thats > not possible to limit the flexibility of the small protein so that only > considers side chain rotation/flexibility and not the whole protein > > Thanks in advance > > Chris > > > -= 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, jkl.-at-.ccl.net (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+ > > > > > From chemistry-request@ccl.net Sun Sep 14 18:54:28 2003 Received: from lorica.ucc.usyd.edu.au (lorica.ucc.usyd.edu.au [129.78.64.15]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8EMrtBS023228 for ; Sun, 14 Sep 2003 18:53:56 -0400 Received: from pharm.usyd.edu.au (pc-012.pharm.usyd.edu.au [129.78.154.44]) by lorica.ucc.usyd.edu.au (8.12.9/8.12.9) with ESMTP id h8EMrlMQ019427 for ; Mon, 15 Sep 2003 08:53:51 +1000 (EST) Date: Mon, 15 Sep 2003 08:54:46 +1000 Mime-Version: 1.0 (Apple Message framework v546) Content-Type: text/plain; charset=US-ASCII; format=flowed Subject: Amber 7 on an SGI From: Michael Ivery To: chemistry|at|ccl.net Content-Transfer-Encoding: 7bit Message-Id: <6FDDC26D-E706-11D7-86D0-0003933DA89C|at|pharm.usyd.edu.au> X-Mailer: Apple Mail (2.546) X-RAVMilter-Version: 8.4.3(snapshot 20030401) (lorica) X-Spam-Status: No, hits=0.0 required=7.0 tests=USER_AGENT_APPLEMAIL version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear CClers I am trying to put amber 7 onto an SGI octane we recently aquired. I don't have the SGI C-compiler but have down loaded the freeware gcc compiler for SGI my question is what machine link file should I use ie linux or SGI or should I use either and modify settings. Any suggestions would be greatly appreciated. Best Wishes Michael Ivery