From owner-chemistry@ccl.net Mon Oct 15 05:28:00 2007 From: "Konrad Hinsen hinsen_._cnrs-orleans.fr" To: CCL Subject: CCL: AminoAcid Rotamer Analysis Message-Id: <-35382-071015030855-8191-CM+jN/Zc8FaWSvYSsaUUrg..server.ccl.net> X-Original-From: "Konrad Hinsen" Date: Mon, 15 Oct 2007 03:08:50 -0400 Sent to CCL by: "Konrad Hinsen" [hinsen^^cnrs-orleans.fr] On 13.10.2007, at 01:57, Cesar Millan pachequin:-:gmail.com wrote: > Hi everyone! I have a couple of protein dynamics made by CHARMM (dcd format) > and I want to do a dihedral analysis of the aminoacids on my protein. I knew a > program called Dials and Windows that could this kind of analysis, but it only > runs on SGI machines. > Does anyone knows any free software that could realize this kind of > analysis on linux machines? The Molecular Modelling Toolkit, available freely at http://dirac.cnrs-orleans.fr/MMTK/ lets you write this kind of analysis programs in a few lines of Python code. What it does for you is reading the trajectory file and calculating the dihedral angles. What you have to do yourself is plug these two actions together and decide about the formatting of the output. Once you have some experience with MMTK, it will take you less time to write your analysis program than to search for an existing one. -- --------------------------------------------------------------------- Konrad Hinsen Centre de Biophysique Molculaire, CNRS Orlans Synchrotron Soleil - Division Expriences Saint Aubin - BP 48 91192 Gif sur Yvette Cedex, France Tel. +33-1 69 35 97 15 E-Mail: hinsen,+,cnrs-orleans.fr ---------------------------------------------------------------------