From owner-chemistry@ccl.net Mon May 8 10:51:01 2006 From: "Nuno R. L. Ferreira nunolf]|[ci.uc.pt" To: CCL Subject: CCL: Energy minimization protocol for protein structures? Message-Id: <-31706-060508104208-27040-Iy2XdyyYuzVn9VL/n29VOg**server.ccl.net> X-Original-From: "Nuno R. L. Ferreira" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-8859-1" Date: Mon, 8 May 2006 15:40:35 +0100 MIME-Version: 1.0 Sent to CCL by: "Nuno R. L. Ferreira" [nunolf(_)ci.uc.pt] Hi Gromacs and NAMD are two free software packs you can use to perform molecular dynamics simulations, but there are others. In both these packs you must write a script with the parameters to perform your task. But, there's always tutorials with self-explanatory examples. There's also SwissPDB Viewer, which has a GUI. To start with, this could be a good choice. The choice would rely on your background about the subject and the final goal. Best regards, Nuno ----- Original Message ----- > From: "Gerard Pujadas gerard.pujadas-.-urv.cat" To: "Ferreira, Nuno R. L. " Sent: Monday, May 08, 2006 2:09 PM Subject: CCL: Energy minimization protocol for protein structures? > Sent to CCL by: "Gerard Pujadas" [gerard.pujadas,,urv.cat] > > Dear CCL list subscribers, > > I wonder if there is any standard protocol to follow when doing an energy minimization of a protein structure. > > I would like to know also if there is a free (or low cost for non commercial or academic) and easy-to-use software that can do this kind of energy minimization > > With many thanks in advances. > > Yours sincerely, > > Gerard> > > > > > --- > avast! Antivirus: Inbound message clean. > Virus Database (VPS): 0619-0, 08-05-2006 > Tested on: 08-05-2006 14:18:57 > avast! - copyright (c) 1988-2006 ALWIL Software. > http://www.avast.com > > > --- avast! Antivirus: Outbound message clean. Virus Database (VPS): 0619-0, 08-05-2006 Tested on: 08-05-2006 15:40:37 avast! - copyright (c) 1988-2006 ALWIL Software. http://www.avast.com